A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

ac_ref - Variable in class object.common.Foq
Corrective action reference
accession - Variable in class object.annotation.Oligo_adhoc
Accession of this Oligo_adhoc Object
accession - Variable in class object.annotation.Oligo_affy
Accession of probe for this Oligo_affy Object
accession - Variable in class object.annotation.Oligo_control
Accession number of Oligo_control Object
accession - Variable in class object.annotation.Spodo_hit
accession
accession - Variable in class object.common.SessionBlastObject
Accession number of an existing Gene Object
accession - Variable in class object.microarray.MageProtocol
accession of this MageProtocol Object
accession_number - Variable in class object.annotation.Gene
Accession number of the Gene Object - refernce to a Bio Database like Refseq
accession_number - Variable in class object.annotation.Genoligo_affy_rel
accession_number
accession_number - Variable in class object.annotation.Oligo_annotation
Accession number asociated to this relation
accession_number - Variable in class object.annotation.Probeset
Accession number of the Gene Object - refernce to a Bio Database like Refseq
accessionOne - Variable in class object.common.BlastTwoSeq
Accession number one
accessionTwo - Variable in class object.common.BlastTwoSeq
Accession number two
action - Variable in class object.common.Journal
Action performed by the User
action - Variable in class object.common.SessionObject
Action asking by the User
action_corrective - Variable in class object.common.Foq
Is there a corrective action launch whith this Foq Object
action_ok - Variable in class object.common.Foq
Efficacity of action
add(String) - Method in class JRclient.RFactor
add a new element (by name)
add(int, int, int) - Method in class object.annotation.Histology
 
add_fact - Variable in class object.common.User
Billing address of User object
add_livr - Variable in class object.common.User
Sending address of User object
addAffyExprConsole(Biostats) - Method in class object.microarray.Quantification_file
 
addAffyLMGUI(Biostats) - Method in class object.microarray.Quantification_file
 
addGeneViewNormalizedDatas(Biostats) - Method in class object.microarray.Quantification_file
 
addLimmaNormalizedDatas(Biostats) - Method in class object.microarray.Quantification_file
 
addMatch(String, int) - Method in class object.microrna.Mttdata
 
addMatch(Match) - Method in class object.microrna.Target
 
addNormalizedDatas(Biostats) - Method in class object.microarray.Quantification_file
 
addOneChannelGUINormalizedDatas(Biostats) - Method in class object.microarray.Quantification_file
 
addSNPNormalizedDatas(Biostats) - Method in class object.microarray.Quantification_file
 
addToCart(String) - Method in class object.common.GeneCart
This function add a symbol or IDs to the gene Cart from symbol attribute of DisplayParams Object
addToCart(String[]) - Method in class object.common.GeneCart
This function add all symbols / IDs to misting parameter from String[] symbol received
addToCart() - Method in class object.common.ImageManager
 
addToCart(int) - Method in class object.common.ImageManager
 
addViewer(int) - Method in class object.common.Project
This function allowed to add a new Viewer to the Project Object
AddViewer(int) - Method in class object.microarray.Project_order
This function allowed to add a new Viewer to the Project_order Object
adresse - Variable in class object.common.Plateforme
Address of Plateforme Object
adresse - Variable in class object.common.User
Address of User object
ae_if_cy3 - Variable in class object.microarray.Protocol_labeling
Reference of this Protocol_labeling object for Arrayexpress in cy3
ae_if_cy5 - Variable in class object.microarray.Protocol_labeling
Reference of this Protocol_labeling object for Arrayexpress in cy5
ae_ref - Variable in class object.microarray.Nucleic_acid_type
Reference of this Nucleic_acid_type object for ArrayExpress
ae_ref - Variable in class object.microarray.Protocol_hybridization
Reference of this Protocol_hybridization object for ArrayExpress
agilent_design - Variable in class object.microarray.Microarray_project_type
 
align - Variable in class object.microrna.MatchMCB
align
alignment - Variable in class object.common.RNAfold
alignment
alignment - Variable in class object.common.RNAhybrid
alignment
alignmentSize - Variable in class object.common.BlastHit
Alignment size
allOk - Variable in class object.common.Blast
This boolean is true if the Blast program was execute well
amount - Variable in class object.hts.Hts_minseqe
Amount input of this Hts_minseqe object
amount_hyb - Variable in class object.microarray.Hybridization
Amount of RNA concerning this Hybridization Object
amount_input - Variable in class object.microarray.Labeling
ARN Amount input of this Labeling object
amount_output - Variable in class object.microarray.Labeling
ARN Amount output of this Labeling object
ampli_amount - Variable in class object.microarray.Labeling
RNA available_amount after amplification
ampli_concentration - Variable in class object.microarray.Labeling
Concentration of ARN after amplification
annotation - Variable in class object.annotation.Oligo_control
Annotation of Oligo_control Object
appli - Variable in class object.common.ImageManager
External application reference for download file (directory : 'file')
approximateScale(BigDecimal, BigDecimal) - Static method in class object.common.HypDistanceCalculator
 
apv_cutoff - Variable in class object.microrna.MicroTopTable
adjusted p.value cutoff
array_1 - Variable in class object.common.ImageManager
Int concerning the first microarray for graph visualization (directory : 'graph')
array_2 - Variable in class object.common.ImageManager
Int concerning the second microarray for graph visualization (directory : 'graph')
array_labo_id - Variable in class object.microarray.ArrayLabo
ID of ArrayLabo Object
array_labo_name - Variable in class object.microarray.ArrayLabo
Name of ArrayLabo Object
arrayexpress - Variable in class object.common.Public_database
ArrayExpress reference of this Public_database Object
arrayexpress - Variable in class object.microarray.Labeling_type
arrayexpress reference of this Labeling_type object
arrayexpress - Variable in class object.microarray.Microarray_project_type
ArrayExpress accession number
ArrayLabo - Class in object.microarray
Description
External laboratories owner of Array Objects
Infos : KLB - IPMC - 08/2003
ArrayLabo() - Constructor for class object.microarray.ArrayLabo
Default constructor
ArrayLabo(int) - Constructor for class object.microarray.ArrayLabo
Constructs an ArrayLabo object from an ArrayLabo ID
arrayLabo - Variable in class object.microarray.Microarray_project_type
ArrayLabo Object owner of this Array object
arrayQuality - Variable in class object.microarray.Microarray
 
asBool() - Method in class JRclient.REXP
get content of the REXP as RBool (if it is one)
asDouble() - Method in class JRclient.REXP
get content of the REXP as double (if it is one)
asDoubleArray() - Method in class JRclient.REXP
get content of the REXP as an array of doubles.
asDoubleMatrix() - Method in class JRclient.REXP
returns the content of the REXP as a matrix of doubles (2D-array: m[rows][cols]).
asFactor() - Method in class JRclient.REXP
get content of the REXP as RFactor (if it is one)
asInt() - Method in class JRclient.REXP
get content of the REXP as int (if it is one)
asIntArray() - Method in class JRclient.REXP
get content of the REXP as an array of integers.
asList() - Method in class JRclient.REXP
get content of the REXP as RList (if it is one)
asMatrix() - Method in class JRclient.REXP
this is just an alias for REXP.asDoubleMatrix().
assign(String, String) - Method in class JRclient.Rconnection
assign a string value to a symbol in R.
assign(String, REXP) - Method in class JRclient.Rconnection
assign a content of a REXP to a symbol in R.
assign(String, double[]) - Method in class JRclient.Rconnection
assign values of an array of doubles to a symbol in R (creating as vector of numbers).
assign(String, int[]) - Method in class JRclient.Rconnection
assign values of an array of integers to a symbol in R (creating as vector of numbers).
asString() - Method in class JRclient.REXP
get content of the REXP as string (if it is one)
asVector() - Method in class JRclient.REXP
get content of the REXP as Vector (if it is one)
at(int) - Method in class JRclient.RFactor
returns name for a specific ID
at(String) - Method in class JRclient.RList
get xpression given a key
at(int) - Method in class JRclient.RList
get element at the specified position
AT_crypt - Static variable in class JRclient.Rconnection
authorization type: unix crypt
AT_plain - Static variable in class JRclient.Rconnection
authorization type: plain text
attach() - Method in class JRclient.RSession
attach/resume this session
attachPacket - Variable in class JRclient.RSession
 
attr - Variable in class JRclient.REXP
attribute xpression or null if none
Attribution - Class in object.common
Description
Attribution Object
Infos : KLB - IPMC - 02/2004
Attribution() - Constructor for class object.common.Attribution
Default constructor
author - Variable in class object.microrna.Mirna_reference
author
authors - Variable in class object.annotation.GenbankRef
Authors of this GenbankRef object
authReq - Variable in class JRclient.Rconnection
 
authType - Variable in class JRclient.Rconnection
 
auto_mature - Variable in class object.microrna.Mcbmatch
auto_mature
auto_mature - Variable in class object.microrna.MicroCible
micro_name searched
auto_mature - Variable in class object.microrna.Mirna_mature
ID if this this Mirna_mature Object
auto_mature - Variable in class object.microrna.Mirna_target
auto_mature
auto_mirna - Variable in class object.microrna.Mirna
ID if this this Mirna Object
aveExpr - Variable in class object.microrna.Mttdata
aveExpr
average - Variable in class object.microarray.Feature
Average of feature
avgexpr - Variable in class object.microrna.MicroTopTable
avgexpr

B

b - Variable in class JRclient.RList
usual assumption is that both head and body are xpressions containing vectors.
b_cutoff - Variable in class object.microrna.MicroTopTable
b_cutoff
background - Variable in class object.common.Biostats
Background normalization method of Biostats Object
background - Variable in class object.common.Rstat
Background normalization method of Biostats Object
batchNumber - Variable in class object.microarray.Microarray
batchNumber of the Microarray Object
bcr_file - Variable in class object.microarray.Spotting
.BCR File describing this Spotting Object
bead_id - Variable in class object.hts.MaMatch
 
begin - Static variable in class object.common.Link
Beginning of a Http Url link (biomaterial - Variable in class object.hts.Hts_minseqe
 
Biostats - Class in object.common
Description
Biostats Objects : results of a statistical analysis
Infos : KLB - IPMC - 08/2007
Biostats() - Constructor for class object.common.Biostats
Default constructor
Biostats(int) - Constructor for class object.common.Biostats
Constructs a Biostats object from a Biostats ID
biostats_file - Variable in class object.common.Biostats
Path of biostats file
biostats_id - Variable in class object.common.Biostats
ID of Biostats Object
biostats_ref - Variable in class object.common.Biostats
reference of Biostats Object
black - Static variable in class object.common.Spidey
Image black for Blast alignment
Blast - Class in object.common
Description
Methodes used for executing Blast program on the server
Infos : KLB - IPMC - 08/2003
Blast() - Constructor for class object.common.Blast
Default constructor
Blast(String, String, String) - Constructor for class object.common.Blast
Constructs a Blast object
Blast(String, String) - Constructor for class object.common.Blast
Constructs a Blast object for the Microsite web interface
blast - Variable in class object.common.BlastTwoSeq
Blast object in which we are going to store the Blast results
blast - Variable in class object.common.SessionBlastObject
Blast Object containing informations concerning the Blast process
blastbase - Variable in class object.annotation.Specificity
BlastBase Object concerning this Specificity Object
BlastBase - Class in object.common
Description
Describe Blast Base used to make Blast process in the application
Infos : KLB - IPMC - 08/2003
BlastBase() - Constructor for class object.common.BlastBase
Default constructor
BlastBase(int) - Constructor for class object.common.BlastBase
Constructs an BlastBase object from a BlastBase ID
BlastBase(int, String) - Constructor for class object.common.BlastBase
Constructs an BlastBase object from Organism ID and BlastBase type
blastbase - Variable in class object.common.SessionBlastObject
BlastBase Object concerning the Blast Base against which the Sequence will be compare
blastbase_id - Variable in class object.common.BlastBase
ID of BlastBase object
blastbase_name - Variable in class object.common.BlastBase
Name of BlastBase object
blastbase_type - Variable in class object.common.BlastBase
Type of BlastBase object
BlastHit - Class in object.common
Description
When a Blast program is launch, the results are parsed and stored as BlastHit objects in an Hashtable results, data member of a Blast object
Infos : KLB - IPMC - 08/2003
BlastHit() - Constructor for class object.common.BlastHit
Default constructor
BlastHit(String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class object.common.BlastHit
 
blastOligo - Variable in class object.common.Project
Blast Object, describing the match beetween Mediante oligos and the SequenceObject Objects of the Project
BlastTwoSeq - Class in object.common
Description
Object with which we can make Blast 2 sequences analysis, we can proceed to a Blast 2 sequences in several ways :
- With accession_number present in our database
- With position number on our IPMC MicroArray
- With sequence directly entered in the form
- With uploading file (not active for the moment)
Infos : KLB - IPMC - 08/2003
BlastTwoSeq() - Constructor for class object.common.BlastTwoSeq
Default constructor
BlastTwoSeq(List, int) - Constructor for class object.common.BlastTwoSeq
Constructs a BlastTwoSeq object a List object and a user_id
bloc - Variable in class object.common.DisplayParams
Bloc number asked for image display
bloc - Variable in class object.microarray.ElementMap
Bloc in which the oligo is located
bloc - Variable in class object.microarray.Feature
Bloc in which the oligo is located
blue - Static variable in class object.common.Spidey
Image blue
blue_One - Static variable in class object.common.Spidey
Image blue 1 for Blast alignment
blue_Two - Static variable in class object.common.Spidey
Image blue 2 for Blast alignment
blueSize - Variable in class object.common.Spidey
Size of graph with correction due to approximation calcul
Board - Class in object.common
Description
Board object represent the current Project_order opened in Java interface by the user user
Infos : KLB - IPMC - 04/2004
Board() - Constructor for class object.common.Board
Default constructor
Board(User, int, boolean) - Constructor for class object.common.Board
Constructs a Board object from User Object and a project_order_id owned by the user.
Board_user - Class in object.common
Description
Board_user object represent all the Project_order define for one user
Infos : KLB - IPMC - 06/2008
Board_user() - Constructor for class object.common.Board_user
Default constructor
Board_user(int) - Constructor for class object.common.Board_user
Constructs a Board object from User Object
Initialize the vector of Project_order Object.
body(int[], int, int) - Static method in class JRclient.jcrypt
 
body - Variable in class JRclient.RList
xpressions containing head and body.
bubbleSearch(String[]) - Method in class object.common.ImageManager
This function proceed to a bubble sort on a String[]
bundle - Variable in class common.beans.locale.LocaleBean
 
bundleName - Variable in class common.beans.locale.LocaleBean
 
bundleName - Variable in class common.tags.generic.UseLocaleBundleTag
 
Bvalue - Variable in class object.common.ImageManager
 
byteToUnsigned(byte) - Static method in class JRclient.jcrypt
 

C

cachedBinaryLength - Variable in class JRclient.REXP
cached binary length; valid only if positive
calculateHypDistance(int, int, int, int, boolean) - Static method in class object.common.HypDistanceCalculator
 
can_be_update() - Method in class object.microarray.Spotting
 
cdf - Variable in class object.microrna.Target
 
cdf_down - Variable in class object.microrna.Mttdata
cdf_down
cdf_up - Variable in class object.microrna.Mttdata
cdf_up
cell_type - Variable in class object.microarray.Labeling
cell_type corresponding to this Subject object
centro - Static variable in class object.common.Spidey
Image of centromere
ch1 - Variable in class object.microarray.Serie
ch1
ch2 - Variable in class object.microarray.Serie
ch2
charset - Variable in class common.beans.locale.LocaleBean
 
check() - Method in class object.common.Attribution
This function check if the last microarray slide_code scanned and stored in microarrayRef attribute is a good Microarray to be attributed to this Order :
- check if it exists in the database
- check if it has not been scanned before
- check if Microarray project type is ok whith this Order
check() - Method in class object.common.Dilution
This function loadParams from HTML form
checkAllMicroarray() - Method in class object.common.Rstat
 
checkAllPlate() - Method in class object.common.CreationPlate
This function execute several test in the way to valid the creation plate process :
- check if all Plate384 concerns the same Organism
- check if all Plate96 concerns the same Organism
- check if the Plate384 slide_codes is following themselves
- check if the Plate96 slide_codes is following themselves
checkAllSlideCode() - Method in class object.microarray.Spotting
 
checkExtensionFile(String, String) - Method in class object.common.Common
This function check if the received match the type file received
checkForNormData() - Method in class object.microarray.Project_order
Check for all microarrays contains in this project if Normalized data are rpesent in biostats objects
checkGalToQuantif() - Method in class object.microarray.Scan
This function check if quantif file from this Scan Object come from quantification with .gal from Spotting Object
checkHts_order(Hts_order) - Method in class object.hts.Hts_RManager
 
checkHts_sample(Hts_sample) - Method in class object.hts.Hts_RManager
 
checkIsNotInCart(String) - Method in class object.common.GeneCart
This function check if symbol or ID to add to gene cart is already in gene cart
checkIsValidObject(Hts_type) - Method in class object.hts.Hts_RManager
 
checkKeyword(int) - Method in class object.microarray.Project_order
Check if the Keyword ID received is already in the vectorKeyword of this Project_order Object
checkMessage() - Method in class object.common.SessionObject
This function check Messages containing in the different Object of this SessionObject and return the current message.
checkMicroarray(Microarray) - Method in class object.common.Rstat
 
checkPlateRef384(String) - Method in class object.common.CreationPlate
This function check if the plate_ref received for a Plate384 Object is well-formatted
checkPlateRef96(String) - Method in class object.common.CreationPlate
This function check if the plate_ref received for a Plate96 Object is coherent :
- if it exists in database
- if the volume of this Plate96 Object is superior to the volume for the Plate384 in creation
checkReplicates() - Method in class object.hts.Hts_RManager
 
checkSlideCode(String) - Method in class object.microarray.Spotting
 
checkSyntaxFastaOk(String) - Method in class object.common.Project
This function check that the file receive is in a standard FASTA format The sequence's check is '^[atgcATGCnNkKyYrRsSdDwWmMhHwWbBvV]+$', and the name uis limited to 63 char, cos' of using Sequence Object latter
checkSyntaxFastaOk(String) - Method in class object.common.SessionBlastObject
This function check if the file received is FASTA well-formated
checkUserIsOwner(int, int) - Method in class object.common.Common
This function returns a boolean according to correspondance between user_id received
and User owner of the microarray_id received
checkUserNotExist() - Method in class object.common.User
This function return a Boolean concerning the existence of the User in the Database while trying to create new User The login must be unique as same as the firstname-lastname key.
checkValidUser() - Method in class object.common.User
This function check if the User in creation is valid to be save in the Database as a new Mediante User
chr - Variable in class object.hts.MaMatch
 
chr_nb - Variable in class object.annotation.Organism
Number of chromosomes of the Organism Object
Chromosome - Class in object.annotation
Description
Chromosome Object
Infos : KLB - IPMC - 08/2003
Chromosome() - Constructor for class object.annotation.Chromosome
Default constructor
Chromosome(int) - Constructor for class object.annotation.Chromosome
Constructs a Chromosome object from a Chromosome ID
chromosome - Variable in class object.annotation.GenomicPosition
Chromosome string concerning this GenomicPosition Object
chromosome - Variable in class object.microrna.Mstdata
chromosome
chromosome_id - Variable in class object.annotation.Chromosome
ID of Chromosome object
chromosome_id - Variable in class object.annotation.Cytoband
Chromosome owner of this Cytoband
chromosome_id - Variable in class object.annotation.GenomicPosition
Chromosome ID concerning this GenomicPosition Object
chromosome_id - Variable in class object.common.Search
ID of a Chromosome Object in the case of a cytoband type search
chromosome_name - Variable in class object.annotation.Chromosome
Description of this Chromosome
client - Variable in class object.common.Enquete
User Object for this Enquete Object
client_id - Variable in class object.common.Contact_client
ID of User Object who is the client
close() - Method in class JRclient.Rconnection
closes current connection
close() - Method in class JRclient.RFileInputStream
close stream - is not related to the actual Rconnection, calling close does not close the Rconnection
close() - Method in class JRclient.RFileOutputStream
close stream - is not related to the actual Rconnection, calling close does not close the Rconnection.
close(int) - Method in class object.microarray.Project_order
Close the Microarray_order at the index 'index' of the vectorMicroarray_order of this Project_order Object
closeCon() - Method in class common.sql.PgsqlConnector
Close Conn Object
closed - Variable in class JRclient.RFileInputStream
set to true when RFileInputStream.close() was called.
closed - Variable in class JRclient.RFileOutputStream
set to true when RFileOutputStream.close() was called.
closeHTS(int) - Method in class object.microarray.Project_order
Close the Microarray_order at the index 'index' of the vectorMicroarray_order of this Project_order Object
cmd - Variable in class JRclient.Rpacket
 
CMD_assignSEXP - Static variable in class JRclient.Rtalk
 
CMD_attachSession - Static variable in class JRclient.Rtalk
 
CMD_closeFile - Static variable in class JRclient.Rtalk
 
CMD_createFile - Static variable in class JRclient.Rtalk
 
CMD_detachedVoidEval - Static variable in class JRclient.Rtalk
 
CMD_detachSession - Static variable in class JRclient.Rtalk
 
CMD_eval - Static variable in class JRclient.Rtalk
 
CMD_login - Static variable in class JRclient.Rtalk
 
CMD_openFile - Static variable in class JRclient.Rtalk
 
CMD_readFile - Static variable in class JRclient.Rtalk
 
CMD_removeFile - Static variable in class JRclient.Rtalk
 
CMD_setBufferSize - Static variable in class JRclient.Rtalk
 
CMD_setSEXP - Static variable in class JRclient.Rtalk
 
CMD_shutdown - Static variable in class JRclient.Rtalk
 
CMD_voidEval - Static variable in class JRclient.Rtalk
 
CMD_writeFile - Static variable in class JRclient.Rtalk
 
color - Variable in class object.common.Point
Color of this Point Object
color - Variable in class object.microarray.Labeling_type
Color of this Labeling_type object
color - Variable in class object.microarray.SpotType
color
column - Variable in class object.annotation.Oligo_rel
Column of the oligo in the Plate Object (i.e. 1)
column - Variable in class object.microarray.ElementMap
Column in Bloc in which the oligo is located
column - Variable in class object.microarray.Feature
Column in Bloc in which the oligo is located
column - Static variable in class object.microarray.Plate384
 
column - Static variable in class object.microarray.Plate96
 
combinations(int, int) - Static method in class object.common.HypDistanceCalculator
 
Commande - Class in object.common
Description
Commande object represent an order of Oligonucleotides.
Commande() - Constructor for class object.common.Commande
Default constructor
Commande(int) - Constructor for class object.common.Commande
Constructs a Commande object from Commande ID
commande - Variable in class object.common.ExecuteCmd
String[] containing the list of the commande to execute on the server
commande_id - Variable in class object.common.Commande
ID of Commande object
commande_ref - Variable in class object.common.Commande
Reference of Commande object
comment - Variable in class object.common.Enquete
Comment
comment - Variable in class object.common.Order
Comments of this Order send by production
comment - Variable in class object.microarray.Hybridization
Comments concerning this Hybridization Object
comment - Variable in class object.microarray.Spotting
Comment concerning this Spotting Object
comments - Variable in class object.common.Journal
Comments added by the User cocnerning the action performed
Common - Class in object.common
Description
Object with which we can perform request in the database in the way to get informations about several objects
Infos : KLB - IPMC - 08/2003
Common() - Constructor for class object.common.Common
Default constructor
common.beans.locale - package common.beans.locale
 
common.sql - package common.sql
 
common.tags.generic - package common.tags.generic
 
common_name - Variable in class object.annotation.Organism
Common name or Organism object
con - Variable in class common.sql.PgsqlConnector
Connection Object
con_salt - Static variable in class JRclient.jcrypt
 
concentration - Variable in class object.microarray.Plate
Oligo concentration of this Plate object
concentration_bank - Variable in class object.hts.Hts_minseqe
 
concentration_sample - Variable in class object.hts.Hts_minseqe
 
conn - Variable in exception JRclient.RSrvException
 
connected - Variable in class JRclient.Rconnection
 
connexClass - Static variable in class common.sql.PgsqlConnector
Connexion Class use to connect PostgreSQL server
connexURL - Static variable in class common.sql.PgsqlConnector
URL location of PostgreSQL server ( jdbc:... )
cont - Variable in class JRclient.REXP
content of the xpression - its object type is dependent of REXP.Xt
cont - Variable in class JRclient.Rpacket
 
Contact_client - Class in object.common
Description
Contact_client object
Infos : KLB - IPMC - 12/2005
Contact_client() - Constructor for class object.common.Contact_client
Default constructor
Contact_client(int) - Constructor for class object.common.Contact_client
Constructs a Contact_client object from Contact_client ID
contact_client_id - Variable in class object.common.Contact_client
ID of Contact_client Object
context - Variable in class object.annotation.Oligo_adhoc_match
Genomic context for this Oligo_adhoc_match Object
contig_end - Variable in class object.microrna.Mirna_chromosome
contig_end
contig_start - Variable in class object.microrna.Mirna_chromosome
contig_start
Control - Class in object.microarray
Description
Control Object
Infos : KLB - IPMC - 08/2005
Control() - Constructor for class object.microarray.Control
Default constructor
Control(int, int, int, Date) - Constructor for class object.microarray.Control
Constructs a Control Object from several parameters received
control_type - Variable in class object.microarray.Control
Control_type Object concerning this Control Object
Control_type - Class in object.microarray
Description
Type of Microarray Control allowed in database.
Control_type() - Constructor for class object.microarray.Control_type
Default constructor
Control_type(int) - Constructor for class object.microarray.Control_type
Constructs a Control_type object from an Control_type ID
control_type_id - Variable in class object.microarray.Control_type
ID of Control_type Object
control_type_ref - Variable in class object.microarray.Control_type
Reference of Control_type Object
controlColor - Variable in class object.microarray.Scan
 
Convert - Class in object.common
Description
Allow to convert annotations following the parameters received from the JSP page
Infos : KLB - IPMC - 02/2008
Convert(int) - Constructor for class object.common.Convert
Default constructor
convert(String, String, String, String) - Method in class object.microarray.Scan
This function Convert images files of this Scan Object
convertFromSnip(String) - Method in class object.microrna.SnipMir
 
convertToMediante(Microarray_project_type) - Method in class object.microarray.Pattern_file
 
coord - Variable in class object.annotation.Chromosome
Coord of this Chromosome on the HTML map displayed in the Chromosome visualisation application part
coord2 - Variable in class object.annotation.Chromosome
Coord of this Chromosome on the HTML map displayed in the Viewer manager chromosome application part
couleur - Variable in class object.common.DisplayParams
Color asked for image display
count - Variable in class object.microrna.Target
 
cov_2char - Static variable in class JRclient.jcrypt
 
createAnnotationFile() - Method in class object.microarray.Spotting
 
createApplicationFile(Hashtable) - Method in class object.common.ImageManager
This function proceed to the creation of the External Application files.
createDatasFile(Hashtable) - Method in class object.common.ImageManager
This function proceed to the creation of the Datas files.
createFile(String) - Method in class JRclient.Rconnection
create a file on the Rserve for writing
createGeneAnovaFile(Vector) - Method in class object.common.ImageManager
This function proceed to the creation of GeneAnova analysis.
createGEOFile(Vector) - Method in class object.common.ImageManager
This function proceed to the creation of GEO submission file.
createGEOMatrix(Vector) - Method in class object.common.ImageManager
This function proceed to the creation of GEO matrix submission file.
createHeatMap(int) - Method in class object.common.MapEST
 
createHeatMap2(int) - Method in class object.common.MapEST
 
createIngenuityFile(Toptable) - Method in class object.common.ImageManager
This function proceed to the creation of Ingenuity file.
createLimmaFile(Vector) - Method in class object.common.ImageManager
This function proceed to the creation of the Limma Application file.
createMageFile(Vector) - Method in class object.common.ImageManager
This function proceed to the creation of the ArrayExpress submission files.
createMEVFile(Vector) - Method in class object.common.ImageManager
This function proceed to the creation of .
CreationPlate - Class in object.common
Description
Object used in the creation plate 384 process from plate 96
Infos : KLB - IPMC - 01/2004
CreationPlate() - Constructor for class object.common.CreationPlate
Default constructor
crypt(String, String) - Static method in class JRclient.jcrypt
 
CSTE_BLAST_NAME - Variable in class object.common.Xhtml
Node to Blast parameters
CSTE_CONNECT_NAME - Variable in class object.common.Xhtml
Node to PostgreSQL parameters
CSTE_ENV_BLASTS - Variable in class object.common.Xhtml
Tag 'blasts' du docment XML : config parameters concerning Blast process
CSTE_ENV_EXTS - Variable in class object.common.Xhtml
Tag 'exts' du docment XML : config parameters concerning extension naming
CSTE_ENV_MAILS - Variable in class object.common.Xhtml
Tag 'mails' du docment XML : config parameters concerning mails
CSTE_ENV_OLIGOARRAYS - Variable in class object.common.Xhtml
Tag 'oligoarrays' du docment XML : config parameters concerning OligoArray process
CSTE_ENV_PARAMS - Variable in class object.common.Xhtml
Tag 'params' du docment XML : config parameters concerning PosrgreSQL connexion
CSTE_ENV_PATHS - Variable in class object.common.Xhtml
Tag 'configs' du docment XML : config parameters concerning global application
CSTE_ENV_SPIDEYS - Variable in class object.common.Xhtml
Tag 'spideys' du docment XML : config parameters concerning Spidey Object
CSTE_OLIGOARRAY_NAME - Variable in class object.common.Xhtml
Node to OligoArray parameters
CSTE_ROOT_TAG - Variable in class object.common.Xhtml
Tag Root du document XML
CSTE_SPIDEY_NAME - Variable in class object.common.Xhtml
Node to Spidey informations parameters
currentPage - Variable in class object.common.Project
Current page of the Project which is viewing by the User in the oligo selection part
currentReference - Variable in class object.common.Attribution
Referrence of microarray or hts_sample
cy3_bruit - Variable in class object.microarray.ElementMap
Cy3 Signal Background of the spot
cy3_bruit - Variable in class object.microarray.Feature
Cy3 Signal Background of the spot
cy3_median - Variable in class object.microarray.ElementMap
Cy3 Signal of the spot
cy3_median - Variable in class object.microarray.Feature
Cy3 Signal of the spot
cy5_bruit - Variable in class object.microarray.ElementMap
Cy5 Signal Background of the spot
cy5_bruit - Variable in class object.microarray.Feature
Cy5 Signal Background of the spot
cy5_median - Variable in class object.microarray.ElementMap
Cy5 Signal of the spot
cy5_median - Variable in class object.microarray.Feature
Cy5 Signal of the spot
cy_pmol - Variable in class object.microarray.Labeling
Cy pmol for this Extraction Object
Cytoband - Class in object.annotation
Description
Cytoband Object define cytological band on Chromosome Object
Infos : KLB - IPMC - 01/2004
Cytoband() - Constructor for class object.annotation.Cytoband
Default constructor
Cytoband(int) - Constructor for class object.annotation.Cytoband
Constructs a Cytoband object from Cytoband ID
cytoband_id - Variable in class object.annotation.Cytoband
ID of Cytoband object
cytoband_id - Variable in class object.common.Search
ID of Cytoband Object in the case of a cytoband type search
cytoband_ref - Variable in class object.annotation.Cytoband
Description of this Cytoband

D

D_ENCRYPT(int, int, int, int, int, int[]) - Static method in class JRclient.jcrypt
 
database - Variable in class object.common.Blast
Database name
date - Variable in class object.common.Contact_client
Date of contact client
date - Variable in class object.common.CreationPlate
Date of the creation Plate Object process
date - Variable in class object.common.Diary
date
date - Variable in class object.common.Foq
Date of Foq creation
date - Variable in class object.common.Journal
Date of this Journal Object
date - Variable in class object.common.Project
Creation date of this Project Object
date - Variable in class object.common.ProjectObject
Date of creation of this Project
date - Variable in class object.common.SessionObject
Current Date
date - Variable in class object.hts.Hts_minseqe
Creation date of this Hts_minseqe Object
date - Variable in class object.hts.Hts_result
Creation date of this hts_result object
date - Variable in class object.hts.Hts_run
Date of the hts_run Object
date_attribution - Variable in class object.common.Attribution
Attribution Date
date_attribution - Variable in class object.hts.Hts_sample
Attribution Date for this Hts_sample Object
date_attribution - Variable in class object.microarray.Microarray
Attribution Date for this Microarray Object
date_control - Variable in class object.microarray.Control
Date of this control
date_creation - Variable in class object.microarray.Plate
Creation date of this Plate object
date_delivery - Variable in class object.common.Order
Delivery date of this Order Hts_order
date_dilution - Variable in class object.microarray.Plate384
Date of the dilution process
date_enquete - Variable in class object.common.Enquete
Date of this Enquete Object
date_expiration - Variable in class object.microarray.Microarray
Expiration Date for this Microarray Object
date_extraction - Variable in class object.microarray.Labeling
Date of creation of this Extraction object
date_hyb - Variable in class object.microarray.Hybridization
Creation date of this Hybridization Object
date_labeling - Variable in class object.microarray.Labeling
Creation Date this Labeling object
date_order - Variable in class object.common.Order
Ordering date of this Order Object
date_prevision - Variable in class object.common.Order
Prevision date of this Order
date_project_order - Variable in class object.microarray.Project_order
Creation date of this Project_order object
date_sample - Variable in class object.microarray.Labeling
Creation date of this Sample object
date_scan - Variable in class object.microarray.Scan
Creation date of this Scan object
date_spotting - Variable in class object.microarray.Spotting
Date of the Spotting Object
date_subject - Variable in class object.microarray.Labeling
Creation date of this Subject object
date_wish - Variable in class object.common.Order
Wishing reception date of this Order
dateFormat - Variable in class common.beans.locale.LocaleBean
 
delete(int) - Method in class object.common.Biostats
This function delete a Biostats Object if project_order_id received is the project_order_id for this Biostats Object.
delete(int) - Method in class object.common.Toptable
This function delete a TopTable Object if project_order_id received is the project_order_id for this TopTable Object
delete() - Method in class object.hts.Hts_minseqe
This function delete this Hybridization Object from database
delete() - Method in class object.hts.Hts_result
This function delete this hts_result Object from the database
delete() - Method in class object.hts.Hts_run
 
delete() - Method in class object.microarray.Hybridization
This function delete this Hybridization Object from database
delete() - Method in class object.microarray.Labeling
This function delete this labeling Object from database
delete() - Method in class object.microarray.Scan
This function delete this Scan Object from the database
delete() - Method in class object.microarray.Spotting
 
delete(int) - Method in class object.microarray.Spotting
 
deleteFromCart(String) - Method in class object.common.GeneCart
This function delete a symbol or IDs of the String[] listing
deleteMicroarrayAtIndex(int) - Method in class object.microarray.Spotting
 
deleteProject_orderView(int) - Method in class object.common.User
This function delete a project_order in Visualization Mode
deleteSequence(int) - Method in class object.common.Project
This function delete a sequenceObject from the vectorSequenceObject attribute of this Project Object
deleteSequence(String) - Method in class object.common.Project
This function delete a sequenceObject from the vectorSequenceObject attribute of this Project Object
demande - Variable in class object.common.Contact_client
Client question or problem
depackRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_common
 
depackRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_hts
 
depackRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_mediante
 
depackRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_medlab
 
depackRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_microrna
 
depackRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_rserve
 
des_set_key(byte[]) - Static method in class JRclient.jcrypt
 
description - Variable in class object.annotation.Gene
Description of the Gene object in the bio-litterature
description - Variable in class object.annotation.Oligo_adhoc
Description concerning this Oligo_adhoc Object
description - Variable in class object.annotation.Oligo_adhoc_match
Description concerning this Oligo_adhoc_match Object
description - Variable in class object.annotation.Probeset
description
description - Variable in class object.annotation.Spodo_hit
description
description - Variable in class object.common.BlastBase
Description of BlastBase object
description - Variable in class object.common.GeneCart
Description reference for this GeneCart Object
description - Variable in class object.common.IdDescriptionObject
Description reference of the ID for the IdDescriptionObject Object
description - Variable in class object.common.Project
Description of this Project Object
description - Variable in class object.common.ProjectObject
Description of this Project
description - Variable in class object.common.Public_database
Description of Public_database Object
description - Variable in class object.hts.Hts_analysis
Description of this Hts_analysis object
description - Variable in class object.hts.Hts_analysis_parameter
description
description - Variable in class object.hts.Hts_pipeline_outfile
description
description - Variable in class object.hts.Hts_pipeline_parameter
description
description - Variable in class object.hts.Hts_type
Description of this Hts_type object
description - Variable in class object.microarray.Microarray_project_type
Description of this Microarray_project_type object
description - Variable in class object.microarray.Project_order
Description of this Project_order object
description - Variable in class object.microrna.Mirna
Description concerning this Mirna Object
detach() - Method in class JRclient.Rconnection
detaches the session and closes the connection (requires Rserve 0.4+).
Diary - Class in object.common
Description
Diary event from developpement for Medlab and Mediante interface
Infos : KLB - IPMC - 03/2008
Diary(Date, String) - Constructor for class object.common.Diary
Default constructor
diluant - Variable in class object.common.Dilution
Type of liquid used for the dilution
diluant - Variable in class object.microarray.Plate384
Diluant use for the dilution of the oligos in this Plate384
Dilution - Class in object.common
Description
Dilution object
Infos : KLB - IPMC - 01/2004
Dilution() - Constructor for class object.common.Dilution
Default constructor
directory - Variable in class object.common.ImageManager
Type of datas to display at screen, could be :
- 'select' : selection of microarrays
- 'imag' : visualization of image of microarray quantification
- 'cart' : download of gene datas according to the gene cart
- 'file' : download of pre-formatted files for external applications
- 'chro' : visuallization of genes cart on a chromosome map
- 'graphe' : visualization of graphs concerning microarrays selected
- 'image' : modification of quantification image light and contrast
disease - Variable in class object.microarray.Labeling
Disease of this Subject object
display() - Method in class object.common.OnMouseOver
Display the OnMouseOver at the screen
display() - Method in class object.microarray.Plate384
This function return a string representing the Plate according to the Plate object composition give by the this.hashOligoPosition attribute.
display() - Method in class object.microarray.Plate96
This function return a string representing the Plate according to the Plate object composition give by the this.hashOligoPosition attribute.
display - Variable in class object.microrna.Mcbdata
display
display(int) - Method in class object.microrna.Mcbdata
 
displayBloc(String, String) - Method in class object.microarray.Spotting
 
displayJournal() - Method in class object.common.Order
This function return a HTML string concerning life-cylce steps for this order.
displayOligos() - Method in class object.annotation.Gene
The graph return by this function concern details of the Gene Object received : - 1st line concern exon structure - 2nd line concern Mediante Oligos Objects - 3rd Line concern Pcr Object relation - Nexts concern External Oligos
DisplayParams - Class in object.common
Description
Used to stock all parameters needed by ImageManager Object to make images of microarray
Infos : KLB - IPMC - 07/2004
DisplayParams() - Constructor for class object.common.DisplayParams
Default constructor
DisplayParams(String, String, String) - Constructor for class object.common.DisplayParams
Constructs a DisplayParams object from parameters
displayParams - Variable in class object.common.ImageManager
DisplayParams Object contains informations about displaying images (directory : 'file')
displaySpecificity() - Method in class object.annotation.Sonde
 
doAbundHisto() - Method in class object.hts.Hts_RManager
 
doAuthenticate(HttpServletRequest, HttpServletResponse, String) - Method in class servlets.Proxy
 
docXml - Variable in class servlets.Proxy
 
docXml - Variable in class servlets.Proxy_microrna
 
doEndTag() - Method in class common.tags.generic.GetLocalTextTag
Uses the LocaleBean, available in a scope as a variable specified by the "name" property, to retrieve the text resource specified by the "key" property.
doEndTag() - Method in class common.tags.generic.UseLocaleBundleTag
Creates and initializes a LocaleBean and saves it in the session scope using the name specified by the "id" property.
doHeatMap() - Method in class object.hts.Hts_RManager
 
doLimma() - Method in class object.hts.Hts_RManager
 
doMatchingPeak() - Method in class object.hts.Hts_RManager
 
doMergeCount() - Method in class object.hts.Hts_RManager
 
doNcrnaHisto() - Method in class object.hts.Hts_RManager
 
doParseBlastProgram(String) - Method in class object.common.Blast
Parse the results file of the Blast program and fill the Hashtable hashtableBlastHit of this Blast object
doParseMegaBlastProgram(String) - Method in class object.common.Blast
Parse the results file of the MegaBlast program and fill the Hashtable hashtableBlastHit of this MegaBlast object
doPdfRepport() - Method in class object.hts.Hts_RManager
 
doRNAfold() - Method in class object.microrna.MicroSite
 
doRNAhybrid() - Method in class object.microrna.Mcbmatch
 
doRNAhybrid() - Method in class object.microrna.MicroCible
 
doSageFiles() - Method in class object.hts.Hts_RManager
 
doVolcanoPlot() - Method in class object.hts.Hts_RManager
 
DT_ARRAY - Static variable in class JRclient.Rtalk
 
DT_BYTESTREAM - Static variable in class JRclient.Rtalk
 
DT_CHAR - Static variable in class JRclient.Rtalk
 
DT_DOUBLE - Static variable in class JRclient.Rtalk
 
DT_INT - Static variable in class JRclient.Rtalk
 
DT_LARGE - Static variable in class JRclient.Rtalk
this is a flag saying that the contents is large (>0xfffff0) and hence uses 56-bit length field
DT_SEXP - Static variable in class JRclient.Rtalk
 
DT_STRING - Static variable in class JRclient.Rtalk
 
duplicate(int) - Method in class object.microrna.SnipMir
 
duration - Variable in class object.microarray.Project_order
Duration of this Project_order object
dvt_stage - Variable in class object.microarray.Labeling
Developpment stage of this Subject object
dye_cy3 - Variable in class object.microarray.Protocol_labeling
Dye in cy3
dye_cy5 - Variable in class object.microarray.Protocol_labeling
Dye in cy5

E

element - Variable in class object.common.Xhtml
Element Object
ElementMap - Class in object.microarray
Description
ElementMap Object
Infos : KLB - IPMC - 07/2004
ElementMap() - Constructor for class object.microarray.ElementMap
Default constructor
ElementMap(String, String, int, int, int, String, String, String, String, String, String, String, String, String) - Constructor for class object.microarray.ElementMap
Constructs an ElementMap object from several parameters
email - Variable in class object.common.User
E-mail of the User Object
end - Variable in class object.annotation.Cytoband
end of this Cytoband
end - Variable in class object.annotation.Exon
End of the exon on the Chromosome corresponding for the Gene object
end - Variable in class object.annotation.GenomicPosition
End position on the Chromosome
end - Static variable in class object.common.Link
End of a Http Url link ()
energy - Variable in class object.common.RNAfold
energy
energy - Variable in class object.common.RNAhybrid
energy
Enquete - Class in object.common
Description
Enquete object
Infos : KLB - IPMC - 09/2006
Enquete() - Constructor for class object.common.Enquete
Default constructor
Enquete(int) - Constructor for class object.common.Enquete
Constructs a Enquete object from Enquete ID
enquete_id - Variable in class object.common.Enquete
ID of this Enquete Object
enqueteur - Variable in class object.common.Enquete
Enqueteur User Object for this Enquete Object
enrichment_down - Variable in class object.microrna.Mttdata
enrichment_down
enrichment_up - Variable in class object.microrna.Mttdata
enrichment_up
ensembl_id - Variable in class object.annotation.Probeset
ensembl_id
ensemblBase - Variable in class object.annotation.Organism
Blastbase Object corresponding to the Ensembl transcript blastbase of this Organism Object
enst - Variable in class object.microrna.Match
enst
enst - Variable in class object.microrna.Mirna_target
enst
enthalpy - Variable in class object.annotation.Oligo
Enthalpy associated with this Oligo Object
enthalpy - Variable in class object.annotation.Oligo_tiling
enthalpy of Oligo_tiling Object
entropy - Variable in class object.annotation.Oligo
Entropy associated with this Oligo Object
entropy - Variable in class object.annotation.Oligo_tiling
entropy of Oligo_tiling Object
envp - Variable in class object.common.ExecuteCmd
String[] containing the list of the environmental variable used to lanch commandes
eof - Variable in class JRclient.RFileInputStream
set to true once EOF is reached - or more specifically the first time remore fread returns OK and 0 bytes
err - Variable in exception JRclient.RSrvException
 
ERR_access_denied - Static variable in class JRclient.Rtalk
 
ERR_auth_failed - Static variable in class JRclient.Rtalk
 
ERR_conn_broken - Static variable in class JRclient.Rtalk
 
ERR_data_overflow - Static variable in class JRclient.Rtalk
 
ERR_detach_failed - Static variable in class JRclient.Rtalk
 
ERR_inv_cmd - Static variable in class JRclient.Rtalk
 
ERR_inv_par - Static variable in class JRclient.Rtalk
 
ERR_IOerror - Static variable in class JRclient.Rtalk
 
ERR_not_open - Static variable in class JRclient.Rtalk
 
ERR_object_too_big - Static variable in class JRclient.Rtalk
 
ERR_out_of_mem - Static variable in class JRclient.Rtalk
 
ERR_Rerror - Static variable in class JRclient.Rtalk
 
ERR_session_busy - Static variable in class JRclient.Rtalk
 
ERR_unknown_cmd - Static variable in class JRclient.Rtalk
 
ERR_unsupported_cmd - Static variable in class JRclient.Rtalk
 
estMatch - Variable in class object.annotation.Gene
list of number of match EST along the transcript
Estoligo_rel - Class in object.annotation
Description
Describe relations between Oligos object and Ests matchs
Infos : KLB - IPMC - 07/2004
Estoligo_rel() - Constructor for class object.annotation.Estoligo_rel
Default constructor
Estoligo_rel(int, String, String) - Constructor for class object.annotation.Estoligo_rel
Constructs an Estoligo_rel object
EstTissue - Class in object.annotation
Description
EstTissue
Infos : KLB - IPMC - 07/2007
EstTissue() - Constructor for class object.annotation.EstTissue
Default constructor
EstTissue(int) - Constructor for class object.annotation.EstTissue
Construct a Est_tissue Object with a Est_tissue ID
estTissue_id - Variable in class object.annotation.EstTissue
Tissue ID
estTissue_ref - Variable in class object.annotation.EstTissue
Tissue ref
eval(String) - Method in class JRclient.Rconnection
evaluates the given command and retrieves the result
evalue - Variable in class object.annotation.Spodo_hit
evalue
evalue - Variable in class object.microarray.Microarray_project_type
Listing of e-value values for graph specificity drawn for oligos concerning this array
evalue - Variable in class object.microrna.MicroSite
Seed_match searched
event - Variable in class object.common.Diary
event
events - Variable in class object.common.Order
Journal events of the Microarray_order object related to this Order Object
excel_file - Variable in class object.common.Biostats
Path of excel file
ExecuteCmd - Class in object.common
Description
Allow to execute commande and the server system
Infos : KLB - IPMC - 08/2003
ExecuteCmd(String[], String[], String) - Constructor for class object.common.ExecuteCmd
Constructs a ExecuteCmd object
Exon - Class in object.annotation
Description
An Exon object belong to a Gene Object
Infos : KLB - IPMC - 12/2003
Exon() - Constructor for class object.annotation.Exon
Default constructor
Exon(int, int, int, int) - Constructor for class object.annotation.Exon
Constructs an Exon object from several parameters
exon - Variable in class object.annotation.Exon
Order of the exon Object in the composition of the sequence of the Gene object
exon - Variable in class object.annotation.Oligo
not use
expectation - Variable in class object.common.Blast
Value of expectation value for executing Blast program
expectation - Variable in class object.common.BlastTwoSeq
Value of expectation value for executing Blast program
expectation - Variable in class object.common.Project
Expectation of this Project Object, while researching whith Blast all the Oligo Object matching the sequences of the SequenceObject composing the Project
expectation - Variable in class object.common.SessionBlastObject
Expectation for the Blast (e-value)
expected_down - Variable in class object.microrna.Mttdata
expected_down
expected_up - Variable in class object.microrna.Mttdata
expected_up
expectValue - Variable in class object.common.BlastHit
Expect value of the alignment
ext_amount - Variable in class object.microarray.Labeling
RNA available_amount of this Extraction object
ext_bl2seq - Static variable in class object.common.Blast
 
ext_bl2seq - Static variable in class object.common.BlastTwoSeq
 
ext_blast - Static variable in class object.common.Blast
 
ext_concentration - Variable in class object.microarray.Labeling
Concentration of ARN of this Extraction object
ext_oli - Static variable in class object.common.Project
Extension of files concerning oligos files
ext_seq - Static variable in class object.common.BlastTwoSeq
 
ext_seq - Static variable in class object.common.Project
Extension of files concerning sequences files
ext_seq - Static variable in class object.common.SessionBlastObject
Extension for the sequences files
ext_tmp - Static variable in class object.common.Blast
 
ext_tmp - Static variable in class object.common.Project
Extension of files concerning temporary files
ext_tmp - Static variable in class object.common.SessionBlastObject
Extension for the temporary files
ext_xls - Static variable in class object.common.Project
Extension of files concerning excel file generated while sending a mail with informations about oligo selection
externe_id - Variable in class object.annotation.Oligo_externe
externe_id of probe for this Oligo_externe Object
externe_name - Variable in class object.annotation.Oligo_externe
externe_name of probe for this Oligo_externe Object
extraction_ref - Variable in class object.microarray.Labeling
Reference of this Extraction object
extractTiffImage() - Method in class object.microarray.Scan
 

F

fax - Variable in class object.common.Plateforme
Fax number of Plateforme Object
fax - Variable in class object.common.User
Fax number of User object
Feature - Class in object.microarray
Description
Feature Object
Infos : KLB - IPMC - 07/2004
Feature() - Constructor for class object.microarray.Feature
Default constructor
Feature(String, String, String, int, int, int, String, String, String, String, String, String, String, String, String) - Constructor for class object.microarray.Feature
Constructs an Feature object from several parameters
Fichier - Class in object.common
Description
Fichier Object belong to Project_order Object
Infos : KLB - IPMC - 07/2004
Fichier() - Constructor for class object.common.Fichier
Default constructor
Fichier(int) - Constructor for class object.common.Fichier
Constructs a Fichier object from an existing Fichier ID.
Fichier(String, String, String) - Constructor for class object.common.Fichier
Constructs a Fichier object from several parameters.
fichier_id - Variable in class object.common.Fichier
ID of this Fichier object
fichier_ref - Variable in class object.common.Fichier
Reference of this Fichier object
fieldName - Variable in class object.common.OnMouseOver
Fieldnames of OnMouseOver Object
fieldValue - Variable in class object.common.OnMouseOver
FieldValues of OnMouseOver Object
file - Variable in class object.common.Convert
Name of file if query is from an upload file
file - Variable in class object.common.Search
Name of file if query is from an upload file
file - Variable in class object.microarray.Serie
file
file_res - Variable in class object.common.Convert
Name of results file
finalize() - Method in class JRclient.Rconnection
 
findSequence(String, String) - Method in class object.microrna.MicroSite
 
firstname - Variable in class object.common.User
Fistname of the User Object
flag - Variable in class object.microarray.ElementMap
Flag true or false of the spot
flag - Variable in class object.microarray.Feature
Flag true or false of the spot
flag_norm - Variable in class object.microarray.Feature
Flag of feature
flag_str - Variable in class object.microarray.ElementMap
Flag string of the spot
flag_str - Variable in class object.microarray.Feature
Flag string of the spot
flush() - Method in class JRclient.RFileOutputStream
currently (Rserve 0.3) there is no way to force flush on the remote side, hence this function is noop.
focus - Variable in class object.common.CreationPlate
 
focusIndex - Variable in class object.common.CreationPlate
Index for the HTML form concerning input boxes
fold - Variable in class object.microrna.Target
 
fold_image - Variable in class object.common.RNAfold
fold_image
Foq - Class in object.common
Description
Foq Object
Infos : KLB - IPMC - 12/2005
Foq() - Constructor for class object.common.Foq
Default constructor
Foq(int) - Constructor for class object.common.Foq
Constructs a Foq object from Foq ID
foq_id - Variable in class object.common.Foq
ID of Foq Object
formatSequence(String, String) - Method in class object.common.BlastTwoSeq
Check the validity of the sequence entered by the user in the textarea or by uploading a file.
formatSequence(String) - Method in class object.common.SessionBlastObject
This function format sequence received from copy/paste or accession_number in the loadParams() method as a FASTA format
forward(String, HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_common
 
forward(String, HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_hts
 
forward(String, HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_mediante
 
forward(String, HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_medlab
 
forward(String, HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_microrna
 
forward(String, HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_rserve
 
fourBytesToInt(byte[], int) - Static method in class JRclient.jcrypt
 
free_energy - Variable in class object.annotation.Oligo
Free Energy associated with this Oligo Object
free_energy - Variable in class object.annotation.Oligo_tiling
free_energy of Oligo_tiling Object
FValue - Variable in class object.common.Blast
Value of F value for executing Blast program
FValue - Variable in class object.common.BlastTwoSeq
Value of F value for executing Blast program
FValue - Variable in class object.common.SessionBlastObject
F value for the Blast ('T' to ask for blast filter alignment, 'F' for not)

G

gal_file - Variable in class object.microarray.Pattern_file
Path to the file of this Object
gal_file - Variable in class object.microarray.Spotting
.GAL File describing this Spotting Object
genbank_gene_id - Variable in class object.annotation.Gene
genbank gene id of the Gene Object - reference to genbank_gene_id database
genbank_gene_id - Variable in class object.annotation.Probeset
genbank gene id of the Gene Object - reference to genbank_gene_id database
genbank_gene_id - Variable in class object.microrna.Match
genbank_gene_id
genbank_gene_id - Variable in class object.microrna.Mirna_target
genbank_gene_id
genbank_link - Variable in class object.annotation.Gene
ID link from NCBI genbank file to database MIM, MGI, RGD
GenbankRef - Class in object.annotation
Description
GenbankRef Object belong to Gene Object
Infos : KLB - IPMC - 08/2005
GenbankRef() - Constructor for class object.annotation.GenbankRef
Default constructor
GenbankRef(int, int, String, String, String, String) - Constructor for class object.annotation.GenbankRef
Constructs a GenbankRef object
Gene - Class in object.annotation
Description
In fact represent more a Transcript than a Gene
Infos : KLB - IPMC - 08/2003
Gene() - Constructor for class object.annotation.Gene
Default constructor
Gene(int) - Constructor for class object.annotation.Gene
Constructs a Gene object from a Gene ID
NB : the constructor does not load all Vectors of the Gene Object.
Gene(String) - Constructor for class object.annotation.Gene
Constructs a Gene object from Accession number reference
NB : the constructor does not load all Vectors of the Gene Object.
gene - Variable in class object.annotation.Oligo_control
Gene symbol of Oligo_control Object
gene_id - Variable in class object.annotation.Exon
ID of a Gene object owner of this Exon Object
gene_id - Variable in class object.annotation.GenbankRef
ID of the owner Gene object
gene_id - Variable in class object.annotation.Gene
ID of the Gene object
gene_id - Variable in class object.annotation.Genoligo_affy_rel
ID of an existing Gene object
gene_id - Variable in class object.annotation.Genoligo_rel
ID of an existing Gene object
gene_id - Variable in class object.annotation.GoLink
ID of Gene object
gene_id - Variable in class object.annotation.Oligo_adhocRelation
ID of Gene Object
gene_id - Variable in class object.annotation.Probeset
gene id of the Gene Object
gene_id - Variable in class object.common.MapEST
ID of the gene Object
gene_id - Variable in class object.common.SequenceObject
ID of a Gene object if the SequenceObject is associate with an Oligo
gene_name - Variable in class object.microrna.MicroCible
gene_name searched
GeneCart - Class in object.common
Description
GeneCart Objects
Infos : KLB - IPMC - 03/2007
GeneCart() - Constructor for class object.common.GeneCart
Default constructor
GeneCart(User) - Constructor for class object.common.GeneCart
Default constructor
GeneCart(int) - Constructor for class object.common.GeneCart
Constructs a GeneCart Object from a GeneCart ID
genecart - Variable in class object.common.ImageManager
GeneCart Object for this ImageManager Object
genecart_id - Variable in class object.common.GeneCart
ID of GeneCart Object
generif - Variable in class object.annotation.GenbankRef
generif annotation of this GenbankRef object
Genoligo_affy_rel - Class in object.annotation
Description
Resume the relation beetween an Oligo_affy Object and a Gene Object
Infos : KLB - IPMC - 05/2008
Genoligo_affy_rel() - Constructor for class object.annotation.Genoligo_affy_rel
Default constructor
Genoligo_affy_rel(String, String, int, String, String) - Constructor for class object.annotation.Genoligo_affy_rel
Constructs a Genoligo_rel object from several parameters
Genoligo_rel - Class in object.annotation
Description
Resume the relation beetween an Oligo Object and a Gene Object
Infos : KLB - IPMC - 01/2004
Genoligo_rel() - Constructor for class object.annotation.Genoligo_rel
Default constructor
Genoligo_rel(int, int, int, int, double, String) - Constructor for class object.annotation.Genoligo_rel
Constructs a Genoligo_rel object from several parameters
genomicPosition - Variable in class object.annotation.Gene
GenomicPosition Object concerning this Gene Object
GenomicPosition - Class in object.annotation
Description
GenomicPosition Object
Infos : KLB - IPMC - 02/2006
GenomicPosition() - Constructor for class object.annotation.GenomicPosition
Default constructor
GenomicPosition(Organism, String, String, int, int, int) - Constructor for class object.annotation.GenomicPosition
Constructs a GenomicPosition object
genomicPosition - Variable in class object.annotation.Oligo_adhoc_match
GenomicPosition concerning this Oligo_adhoc_match Object
genotype - Variable in class object.microarray.Labeling
Genotype of this Subject object
geo - Variable in class object.common.Public_database
GEO reference of this Public_database Object
geo - Variable in class object.microarray.Microarray_project_type
GEO accession number
geo_extract - Variable in class object.microarray.Labeling_type
GEO default extraction protocol of this Labeling_type object
geo_hyb - Variable in class object.microarray.Labeling_type
GEO default hybridization protocol of this Labeling_type object
geo_id - Variable in class object.microarray.GeoSerie
geo_id
geo_id_ref - Variable in class object.microarray.Feature
ID_REF for GEO submission
geo_label - Variable in class object.microarray.Labeling_type
GEO default labeling protocol of this Labeling_type object
geo_nucleicacid - Variable in class object.microarray.Labeling_type
GEO default type of nucleic acid of this Labeling_type object
geo_ref - Variable in class object.microarray.Nucleic_acid_type
Reference of this Nucleic_acid_type object for GEO
GeoSerie - Class in object.microarray
Description
External laboratories owner of Array Objects
Infos : KLB - IPMC - 08/2003
GeoSerie() - Constructor for class object.microarray.GeoSerie
Default constructor
GeoSerie(String, String, String, int, Microarray_project_type) - Constructor for class object.microarray.GeoSerie
constructor
getAc_ref() - Method in class object.common.Foq
Corrective action reference
getAccession() - Method in class object.annotation.Oligo_adhoc
Accession of this Oligo_adhoc Object
getAccession() - Method in class object.annotation.Oligo_affy
Accession of probe for this Oligo_affy Object
getAccession() - Method in class object.annotation.Oligo_control
Accession number of Oligo_control Object
getAccession() - Method in class object.annotation.Spodo_hit
accession
getAccession() - Method in class object.common.SessionBlastObject
Accession number of an existing Gene Object
getAccession() - Method in class object.microarray.MageProtocol
accession of this MageProtocol Object
getAccession_number() - Method in class object.annotation.Gene
Accession number of the Gene Object - refernce to a Bio Database like Refseq
getAccession_number() - Method in class object.annotation.Genoligo_affy_rel
accession_number
getAccession_number() - Method in class object.annotation.Oligo_annotation
Accession number asociated to this relation
getAccession_number() - Method in class object.annotation.Probeset
accession_number
getAccessionOne() - Method in class object.common.BlastTwoSeq
Accession number one
getAccessionTwo() - Method in class object.common.BlastTwoSeq
Accession number two
getAction() - Method in class object.common.Journal
Action performed by the User
getAction_corrective() - Method in class object.common.Foq
Is there a corrective action launch whith this Foq Object
getAction_ok() - Method in class object.common.Foq
Efficacity of action
getAdd_fact() - Method in class object.common.User
Billing address of User object
getAdd_livr() - Method in class object.common.User
Sending address of User object
getAdresse() - Method in class object.common.Plateforme
Address of Plateforme Object
getAdresse() - Method in class object.common.User
Address of User object
getAe_if_cy3() - Method in class object.microarray.Protocol_labeling
Reference of this Protocol_labeling object for Arrayexpress in cy3
getAe_if_cy5() - Method in class object.microarray.Protocol_labeling
Reference of this Protocol_labeling object for Arrayexpress in cy5
getAe_ref() - Method in class object.microarray.Nucleic_acid_type
Reference of this Nucleic_acid_type object for ArrayExpress
getAe_ref() - Method in class object.microarray.Protocol_hybridization
Reference of this Protocol_hybridization object for ArrayExpress
getAgilent_design() - Method in class object.microarray.Microarray_project_type
agilent_design (i.e. 8x15k, 4x44k, 1x44k or 1x22k)
getAlign() - Method in class object.microrna.MatchMCB
align
getAlignment() - Method in class object.common.RNAfold
alignment
getAlignment() - Method in class object.common.RNAhybrid
alignment
getAlignmentBl2seq(Sequence, Sequence, BlastHit, int, Gene, String) - Method in class object.common.Spidey
This function return a graph concerning alignment from two sequences
getAlignmentSequenceFastaStyle(BlastHit) - Method in class object.common.Spidey
This function return a graph concerning blast result alignment from a BlastHit Object, with FASTA sytle
getAlignmentSequenceHit(BlastHit) - Method in class object.common.Spidey
This function return a graph concerning blast result alignment from a BlastHit Object
getAlignmentSize() - Method in class object.common.BlastHit
Alignment size
getAllAddress() - Method in class object.common.Common
This function return a Vector containing email String of all Users Object.
getAllChromosome(int) - Method in class object.common.Common
This function returns a Vector containing all the Chromosome Object for the Organism received
getAllChromosomes() - Method in class object.annotation.Organism
Return all Chromosomes object for this Organism Object
getAllClient() - Method in class object.common.Common
This function returns a Vector containing ToolBox Object concerning User Object
getAllCytoband() - Method in class object.annotation.Chromosome
This function return a vector containing all Cytoband object for this Chromosome Object
ordered by start position across the Chromosome Object.
getAllDiary() - Method in class object.common.Common
This function returns a Vector containing all the Diary Object
getAllEnquete() - Method in class object.common.Common
This function returns a Vector containing ToolBox Object concerning Enquete Object
getAllEstTissue() - Method in class object.common.Common
This function return a Vector containing all EstTissue object define in database.
getAllFoq() - Method in class object.common.Common
This function returns a Vector containing Foq Object
getAllGenes() - Method in class object.annotation.Chromosome
This function return a vector containing all Genes object for this Chromosome Object
getAllGenes() - Method in class object.annotation.Cytoband
Return all Genes object for this Cytoband
getAllGeoSerie() - Method in class object.common.Common
 
getAllGOterm() - Method in class object.common.Common
 
getAllMicroarray_project_type(int) - Method in class object.common.Common
Allowed to return all Microarray_project_type in the Database concerning an Organism ID
getAllMirna() - Method in class object.common.Common
 
getAllMirna_mature() - Method in class object.common.Common
This function returns a Vector containing ToolBox Object concerning all Mirna_mature Objects
getAllMoIDForUser(int) - Method in class object.common.Common
This function returns a vector containing ToolBox Object containing informations concerning Microarray_order
Objects belonging to the User Object received.
getAllOk() - Method in class object.common.Blast
This boolean is true if the Blast program was execute well
getAllOrders() - Method in class object.common.Common
This function return a Vector containing Order Objects concerning all the Microarray_order stored in Database, ordered by state and date_attribution
getAllOrders(int, String) - Method in class object.common.Common
 
getAllPlateforme() - Method in class object.common.Common
This function returns a vector containing all Plateforme Objects stored in database.
getAllProject_order() - Method in class object.common.User
This function return a Vector containing all the Project_order Object of this User
getAllProject_orderForPF(int) - Method in class object.common.Common
This function returns a vector containing ToolBox Object concerning Project_order Objects belonging to the Plateforme Object received.
getAllProjectObject() - Method in class object.common.User
This function return a Vector containing all the Projects of this User
getAllRefPlaques384_ForDilution() - Method in class object.common.Common
This function returns a String of all the 384 Plate wich are not diluted
getAllUserColleague(int) - Method in class object.common.Common
This function allowed to get all the Colleagues of a User
getAllUserForPF(int) - Method in class object.common.Common
This function returns a vector containing ToolBox Object concerning User Objects belonging to the Plateforme Object received.
getAllUsers() - Method in class object.common.Common
This function returns a vector containing all User Objects stored in database.
getAmount() - Method in class object.hts.Hts_minseqe
Amount concerning this Hts_minseqe object
getAmount_hyb() - Method in class object.microarray.Hybridization
Amount of RNA concerning this Hybridization object
getAmount_input() - Method in class object.microarray.Labeling
ARN Amount input of this Labeling object
getAmount_output() - Method in class object.microarray.Labeling
ARN Amount output of this Labeling object
getAmpli_amount() - Method in class object.microarray.Labeling
RNA available_amount after amplification
getAmpli_concentration() - Method in class object.microarray.Labeling
Concentration of ARN after amplification
getANForGID(int) - Method in class object.common.Common
This function returns the accession number for the gene_id received
getAnnotation() - Method in class object.annotation.Oligo_control
Annotation of Oligo_control Object
getAppli() - Method in class object.common.ImageManager
External application reference for download file (directory : 'file')
getApv_cutoff() - Method in class object.microrna.MicroTopTable
adjusted p.value cutoff
getArray_1() - Method in class object.common.ImageManager
Int concerning the first microarray for graph visualization (directory : 'graph')
getArray_2() - Method in class object.common.ImageManager
Int concerning the second microarray for graph visualization (directory : 'graph')
getArray_labo_id() - Method in class object.microarray.ArrayLabo
ID of ArrayLabo object
getArray_labo_name() - Method in class object.microarray.ArrayLabo
Name of ArrayLabo object
getArrayexpress() - Method in class object.common.Public_database
ArrayExpress reference of this Public_database Object
getArrayexpress() - Method in class object.microarray.Labeling_type
arrayexpress reference of this Labeling_type object
getArrayexpress() - Method in class object.microarray.Microarray_project_type
ArrayExpress accession number
getArrayLabo() - Method in class object.microarray.Microarray_project_type
ArrayLabo Object owner of this Array object
getArrayQuality() - Method in class object.microarray.Microarray
arrayQuality
getAttribute() - Method in class JRclient.REXP
get attribute of the REXP.
getAuthor() - Method in class object.microrna.Mirna_reference
author
getAuthors() - Method in class object.annotation.GenbankRef
Authors of this GenbankRef object
getAuto_mature() - Method in class object.microrna.Mcbmatch
auto_mature
getAuto_mature() - Method in class object.microrna.MicroCible
micro_name searched
getAuto_mature() - Method in class object.microrna.Mirna_mature
auto_mature
getAuto_mature() - Method in class object.microrna.Mirna_target
auto_mature
getAuto_matureForMature_acc(String) - Method in class object.common.Common
 
getAuto_mirna() - Method in class object.microrna.Mirna
auto_mirna
getAveExpr() - Method in class object.microrna.Mttdata
aveExpr
getAverage() - Method in class object.microarray.Feature
 
getAvgexpr() - Method in class object.microrna.MicroTopTable
avgexpr
getB_cutoff() - Method in class object.microrna.MicroTopTable
b_cutoff
getBackground() - Method in class object.common.Biostats
Background normalization method of Biostats Object
getBackground() - Method in class object.common.Rstat
Background normalization method of Biostats Object
getBatchNumber() - Method in class object.microarray.Microarray
batchNumber of the Microarray Object
getBcr_file() - Method in class object.microarray.Spotting
.BCR File describing this Spotting Object
getBinaryLength() - Method in class JRclient.REXP
Calculates the length of the binary representation of the REXP including all headers.
getBinaryRepresentation(byte[], int) - Method in class JRclient.REXP
Stores the REXP in its binary (ready-to-send) representation including header into a buffer and returns the index of the byte behind the REXP.
getBiomaterial() - Method in class object.hts.Hts_minseqe
 
getBiostats_file() - Method in class object.common.Biostats
Path of biostats file
getBiostats_id() - Method in class object.common.Biostats
ID of Biostats Object
getBiostats_ref() - Method in class object.common.Biostats
Reference of Biostats Object
getBlast() - Method in class object.common.BlastTwoSeq
Blast object in which we are going to store the Blast results
getBlast() - Method in class object.common.SessionBlastObject
Blast Object containing informations concerning the Blast process
getBlastbase() - Method in class object.annotation.Specificity
BlastBase Object concerning this Specificity Object
getBlastbase() - Method in class object.common.SessionBlastObject
BlastBase Object concerning the Blast Base against which the Sequence will be compare
getBlastbase_id() - Method in class object.common.BlastBase
ID of BlastBase object
getBlastbase_name() - Method in class object.common.BlastBase
Name of BlastBase object
getBlastbase_type() - Method in class object.common.BlastBase
Type of BlastBase object
getBlastOligo() - Method in class object.common.Project
Blast Object, describing the match beetween Mediante oligos and the SequenceObject Objects of the Project
getBlastParameters(String) - Method in class object.common.Common
This function returns a select box for an HTML form describing the parameters for the execution of a Blast
getBloc() - Method in class object.common.DisplayParams
Bloc number asked for image display
getBloc() - Method in class object.microarray.ElementMap
Bloc in which the oligo is located
getBloc() - Method in class object.microarray.Feature
Bloc in which the oligo is located
getBlocsWithSymbol(String) - Method in class object.microarray.Spotting
 
getBody() - Method in class JRclient.RList
get body xpression (CDR)
getBRLMM_file() - Method in class object.microarray.Scan
 
getBvalue() - Method in class object.common.ImageManager
Bvalue for features filtration
getCdf() - Method in class object.microrna.Target
cdf
getCdf_down() - Method in class object.microrna.Mttdata
cdf_down
getCdf_up() - Method in class object.microrna.Mttdata
cdf_up
getCEL_file() - Method in class object.microarray.Scan
 
getCell_type() - Method in class object.microarray.Labeling
cell_type corresponding to this Subject object
getCh1() - Method in class object.microarray.Serie
ch1
getCh2() - Method in class object.microarray.Serie
ch2
getCheckIfIsAnOption(String) - Method in class object.hts.Hts_sample
 
getCHP_file() - Method in class object.microarray.Scan
 
getChr_nb() - Method in class object.annotation.Organism
Number of chromosomes of the Organism Object
getChromosome() - Method in class object.annotation.GenomicPosition
Chromosome Object concerned by this GenomicPosition Object
getChromosome() - Method in class object.microrna.Mstdata
chromosome
getChromosome_id() - Method in class object.annotation.Chromosome
ID of Chromosome object
getChromosome_id() - Method in class object.annotation.Cytoband
Chromosome owner of this Cytoband
getChromosome_id() - Method in class object.annotation.GenomicPosition
Chromosome ID concerned by this GenomicPosition Object
getChromosome_id() - Method in class object.common.Search
ID of a Chromosome Object in the case of a cytoband type search
getChromosome_name() - Method in class object.annotation.Chromosome
Description of this Chromosome
getChromosomeGraph(int, int) - Method in class object.common.Spidey
This function return the graph of a Chromosome Object received as a parameter.
getClauseWhere(String, String) - Method in class object.common.Search
This function parse the query attribute and return an SQL where clause well-formated.
getClient() - Method in class object.common.Enquete
ID of User object who get the contatc whith the client
getClient_id() - Method in class object.common.Contact_client
ID of User Object who is the client
getCmd() - Method in class JRclient.Rpacket
get command
getColor() - Method in class object.common.Point
Color of this Point Object
getColor() - Method in class object.microarray.Labeling_type
Color of this Labeling_type object
getColor() - Method in class object.microarray.SpotType
color
getColumn() - Method in class object.annotation.Oligo_rel
Column of the oligo in the Plate Object (i.e. 1)
getColumn() - Method in class object.microarray.ElementMap
Column in Bloc in which the oligo is located
getColumn() - Method in class object.microarray.Feature
Column in Bloc in which the oligo is located
getCommande_id() - Method in class object.common.Commande
ID of Commande object
getCommande_ref() - Method in class object.common.Commande
Reference of Commande object
getComment() - Method in class object.common.Order
Comments of this Microarray_order send by production
getComment() - Method in class object.microarray.Hybridization
Comments of this Hybridization object
getComment() - Method in class object.microarray.Spotting
Comment concerning this Spotting Object
getComments() - Method in class object.common.Journal
Comments added by the User cocnerning the action performed
getCommon_name() - Method in class object.annotation.Organism
Common name or Organism object
getCon() - Method in class common.sql.PgsqlConnector
Return Conn Object
getConcentration() - Method in class object.microarray.Plate
Oligo concentration of this Plate object
getConcentration_bank() - Method in class object.hts.Hts_minseqe
 
getConcentration_sample() - Method in class object.hts.Hts_minseqe
 
getCont() - Method in class JRclient.Rpacket
get content
getContact(String, String, String, String, String) - Method in class object.common.Common
 
getContact_client_id() - Method in class object.common.Contact_client
ID of Contact_client Object
getContactClient(int) - Method in class object.common.Common
This function returns a Vector containing Contact_client Object concerning client_id received (user_id).
getContent() - Method in class JRclient.REXP
get raw content.
getContext() - Method in class object.annotation.Oligo_adhoc_match
Genomic context for this Oligo_adhoc_match Object
getContig_end() - Method in class object.microrna.Mirna_chromosome
contig_end
getContig_start() - Method in class object.microrna.Mirna_chromosome
contig_start
getControl_type() - Method in class object.microarray.Control
Control_type Object concerning this Control Object
getControl_type_id() - Method in class object.microarray.Control_type
ID of Control_type Object
getControl_type_ref() - Method in class object.microarray.Control_type
Reference of Control_type Object
getControlColor() - Method in class object.microarray.Scan
 
getCoord() - Method in class object.annotation.Chromosome
Coord of this Chromosome on th e HTML map displayed in the Chromosome visualisation application part
getCoord2() - Method in class object.annotation.Chromosome
Coord of this Chromosome on the HTML map displayed in the Viewer manager chromosome application part
getCouleur() - Method in class object.common.DisplayParams
Color asked for image display
getCount() - Method in class object.microrna.Target
count
getCT_idForMID(int) - Method in class object.common.Common
This function returns a control_type_id for the microarray_id received,
in case of this Microarray Object is a Control Object.
getCurrentPage() - Method in class object.common.Project
Current page of the Project which is viewing by the User in the oligo selection part
getCurrentReference() - Method in class object.common.Attribution
Referrence of microarray or hts_sample
getCy3_bruit() - Method in class object.microarray.ElementMap
Cy3 Signal Background of the spot
getCy3_bruit() - Method in class object.microarray.Feature
Cy3 Signal Background of the spot
getCy3_median() - Method in class object.microarray.ElementMap
Cy3 Signal of the spot
getCy3_median() - Method in class object.microarray.Feature
Cy3 Signal of the spot
getCy5_bruit() - Method in class object.microarray.ElementMap
Cy5 Signal Background of the spot
getCy5_bruit() - Method in class object.microarray.Feature
Cy5 Signal Background of the spot
getCy5_median() - Method in class object.microarray.ElementMap
Cy5 Signal of the spot
getCy5_median() - Method in class object.microarray.Feature
Cy5 Signal of the spot
getCy_pmol() - Method in class object.microarray.Labeling
Cy pmol for this Extraction Object
getCytoband_id() - Method in class object.annotation.Cytoband
ID of Cytoband object
getCytoband_id() - Method in class object.common.Search
ID of Cytoband Object in the case of a cytoband type search
getCytoband_ref() - Method in class object.annotation.Cytoband
Description of this Cytoband
getCytobandGraph(Cytoband) - Method in class object.common.Spidey
This function return the graph of a Cytoband Object received as a parameter.
getDatabase() - Method in class object.common.Blast
Database name
getDatas(Hashtable, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class object.microarray.Quantification_file
 
getDate(String) - Method in class common.beans.locale.LocaleBean
Returns the specified date String converted to a Date, parsed as defined by the currently selected locale.
getDate() - Method in class object.common.Contact_client
Date of contact client
getDate() - Method in class object.common.CreationPlate
Date of the creation Plate Object process
getDate() - Method in class object.common.Diary
date
getDate() - Method in class object.common.Foq
Date of Foq creation
getDate() - Method in class object.common.Journal
Date of this Journal Object
getDate() - Method in class object.common.Project
Creation date of this Project Object
getDate() - Method in class object.common.ProjectObject
Date of creation of this Project
getDate() - Method in class object.hts.Hts_minseqe
Creation date of this Hts_minseqe Object
getDate() - Method in class object.hts.Hts_result
Creation date of this hts_result object
getDate() - Method in class object.hts.Hts_run
Date of the hts_run Object
getDate_attribution() - Method in class object.common.Attribution
Attribution Date
getDate_attribution() - Method in class object.hts.Hts_sample
Attribution Date for this Hts_sample Object
getDate_attribution() - Method in class object.microarray.Microarray
Attribution Date for this Microarray Object
getDate_control() - Method in class object.microarray.Control
Date of this control
getDate_creation() - Method in class object.microarray.Plate
Creation date of this Plate object
getDate_delivery() - Method in class object.common.Order
Delivery date of this Microarray_order
getDate_dilution() - Method in class object.microarray.Plate384
Date of the dilution process
getDate_enquete() - Method in class object.common.Enquete
Date of contact client
getDate_expiration() - Method in class object.microarray.Microarray
Expiration Date for this Microarray Object
getDate_extraction() - Method in class object.microarray.Labeling
Date of creation of this Extraction object
getDate_hyb() - Method in class object.microarray.Hybridization
Creation date of this Hybridization object
getDate_labeling() - Method in class object.microarray.Labeling
Creation Date this Labeling object
getDate_order() - Method in class object.common.Order
Ordering date of this Microarray_order
getDate_prevision() - Method in class object.common.Order
Prevision date of this Microarray_order
getDate_project_order() - Method in class object.microarray.Project_order
Creation date of this Project_order object
getDate_sample() - Method in class object.microarray.Labeling
Creation date of this Sample object
getDate_scan() - Method in class object.microarray.Scan
Creation date of this Scan object
getDate_spotting() - Method in class object.microarray.Spotting
Date of the Spotting Object
getDate_subject() - Method in class object.microarray.Labeling
Creation date of this Subject object
getDate_wish() - Method in class object.common.Order
Wishing reception date of this Microarray_order
getDateString(Date) - Method in class common.beans.locale.LocaleBean
Returns the specified Date converted to a String, formatted as defined by the currently selected locale.
getDecodedValue(String) - Method in class common.beans.locale.LocaleBean
This method returns a new String created from the specified String, encoded as 8859_1 converted to the currently set charset.
getDefaultLocale() - Method in class common.beans.locale.LocaleBean
Returns a Locale for the default language.
getDemande() - Method in class object.common.Contact_client
Client question or problem
getDescription() - Method in class object.annotation.Gene
Description of the Gene object in the bio-litterature
getDescription() - Method in class object.annotation.Oligo_adhoc
Description concerning this Oligo_adhoc Object
getDescription() - Method in class object.annotation.Oligo_adhoc_match
Description concerning this Oligo_adhoc_match Object
getDescription() - Method in class object.annotation.Probeset
description
getDescription() - Method in class object.annotation.Spodo_hit
description
getDescription() - Method in class object.common.BlastBase
Description of BlastBase object
getDescription() - Method in class object.common.GeneCart
Description reference for this GeneCart Object
getDescription() - Method in class object.common.IdDescriptionObject
Description reference of the ID for the IdDescriptionObject Object
getDescription() - Method in class object.common.Project
Description of this Project Object
getDescription() - Method in class object.common.ProjectObject
Description of this Project
getDescription() - Method in class object.common.Public_database
Description of Public_database Object
getDescription() - Method in class object.hts.Hts_analysis
Description of this Hts_analysis object
getDescription() - Method in class object.hts.Hts_analysis_parameter
description
getDescription() - Method in class object.hts.Hts_pipeline_outfile
description
getDescription() - Method in class object.hts.Hts_pipeline_parameter
description
getDescription() - Method in class object.hts.Hts_type
Description of this Microarray_project_type object
getDescription() - Method in class object.microarray.Microarray_project_type
Description of this Microarray_project_type object
getDescription() - Method in class object.microarray.Project_order
Description of this Project_order object
getDescription() - Method in class object.microrna.Mirna
description
getDiluant() - Method in class object.common.Dilution
Type of liquid used for the dilution
getDiluant() - Method in class object.microarray.Plate384
Diluant use for the dilution of the oligos in this Plate384
getDirectory() - Method in class object.common.ImageManager
Type of datas to display at screen, could be :
- 'select' : selection of microarrays
- 'imag' : visualization of image of microarray quantification
- 'cart' : download of gene datas according to the gene cart
- 'file' : download of pre-formatted files for external applications
- 'chro' : visuallization of genes cart on a chromosome map
- 'graphe' : visualization of graphs concerning microarrays selected
- 'image' : modification of quantification image light and contrast
getDisease() - Method in class object.microarray.Labeling
Disease of this Subject object
getDisplayParams() - Method in class object.common.ImageManager
DisplayParams Object contains informations about displaying images (directory : 'file')
getDNA(String) - Method in class object.microrna.MicroSite
 
getDouble(String) - Method in class common.beans.locale.LocaleBean
Returns the specified number String converted to a double, parsed as defined by the currently selected locale.
getDuration() - Method in class object.microarray.Project_order
Duration of this Project_order object
getDvt_stage() - Method in class object.microarray.Labeling
Developpment stage of this Subject object
getDye_cy3() - Method in class object.microarray.Protocol_labeling
Dye in cy3
getDye_cy5() - Method in class object.microarray.Protocol_labeling
Dye in cy5
getEmail() - Method in class object.common.User
E-mail of the User Object
getEnd() - Method in class object.annotation.Cytoband
end of this Cytoband
getEnd() - Method in class object.annotation.Exon
End of the exon on the Chromosome corresponding for the Gene object
getEnd() - Method in class object.annotation.GenomicPosition
End position on the Chromosome Object concerned by this GenomicPosition Object
getEnergy() - Method in class object.common.RNAfold
energy
getEnergy() - Method in class object.common.RNAhybrid
energy
getEnquete_id() - Method in class object.common.Enquete
ID of Contact_client Object
getEnqueteur() - Method in class object.common.Enquete
Enqueteur User Object for this Enquete Object
getEnrichement_down() - Method in class object.microrna.Mttdata
enrichment_down
getEnrichement_up() - Method in class object.microrna.Mttdata
enrichment_up
getEnsembl_id() - Method in class object.annotation.Probeset
ensembl_id
getEnsemblBase() - Method in class object.annotation.Organism
Blastbase Object corresponding to the Ensembl transcript blastbase of this Organism Object
getENSG(String) - Method in class object.common.Common
This function returns the ensg and description from an enst reference
getEnst() - Method in class object.microrna.Match
enst
getEnst() - Method in class object.microrna.Mirna_target
enst
getEnthalpy() - Method in class object.annotation.Oligo
Enthalpy associated with this Oligo Object
getEnthalpy() - Method in class object.annotation.Oligo_tiling
enthalpy of Oligo_tiling Object
getEntropy() - Method in class object.annotation.Oligo
Entropy associated with this Oligo Object
getEntropy() - Method in class object.annotation.Oligo_tiling
entropy of Oligo_tiling Object
getError() - Method in class object.common.ExecuteCmd
Allowed to see in the log file of the server all the errors of the commande line executed
getEstMatch() - Method in class object.annotation.Gene
list of number of match EST along the transcript
getEstTissue_id() - Method in class object.annotation.EstTissue
estTissue_id
getEstTissue_ref() - Method in class object.annotation.EstTissue
estTissue_ref
getEvalue() - Method in class object.annotation.Spodo_hit
evalue
getEvalue() - Method in class object.microarray.Microarray_project_type
Listing of e-value values for graph specificity drawn for oligos concerning this array
getEvalue() - Method in class object.microrna.MicroSite
evalue
getEvent() - Method in class object.common.Diary
event
getEvents(Vector) - Method in class object.common.Common
 
getEvents() - Method in class object.common.Order
Journal events of the Microarray_order object related to this Order Object
getExcel_file() - Method in class object.common.Biostats
Path of excel file
getExon() - Method in class object.annotation.Exon
Order of the exon Object in the composition of the sequence of the Gene object
getExon() - Method in class object.annotation.Oligo
not use
getExpectation() - Method in class object.common.Blast
Value of expectation value for executing Blast program
getExpectation() - Method in class object.common.BlastTwoSeq
Value of expectation value for executing Blast program
getExpectation() - Method in class object.common.Project
Expectation of this Project Object, while researching whith Blast all the Oligo Object matching the sequences of the SequenceObject composing the Project
getExpectation() - Method in class object.common.SessionBlastObject
Expectation for the Blast (e-value)
getExpected_down() - Method in class object.microrna.Mttdata
expected_repressed
getExpected_up() - Method in class object.microrna.Mttdata
expected_expressed
getExpectValue() - Method in class object.common.BlastHit
Expect value of the alignment
getExt_amount() - Method in class object.microarray.Labeling
RNA available_amount of this Extraction object
getExt_concentration() - Method in class object.microarray.Labeling
Concentration of ARN of this Extraction object
getExterne_id() - Method in class object.annotation.Oligo_externe
externe_id of probe for this Oligo_externe Object
getExterne_name() - Method in class object.annotation.Oligo_externe
externe_name of probe for this Oligo_externe Object
getExtraction_ref() - Method in class object.microarray.Labeling
Reference of this Extraction object
getFax() - Method in class object.common.Plateforme
Fax number of Plateforme Object
getFax() - Method in class object.common.User
Fax number of User object
getFichier_id() - Method in class object.common.Fichier
ID of this Fichier object
getFichier_ref() - Method in class object.common.Fichier
Reference of this Fichier object
getFile() - Method in class object.common.Convert
Name of file if query is from an upload file
getFile() - Method in class object.common.Search
Name of file if query is from an upload file
getFile() - Method in class object.microarray.Serie
file
getFile_res() - Method in class object.common.Convert
Name of results file
getFileName(String) - Method in class object.common.Common
This function returns the name of the file of the path reveiced
getFileNameNoExt(String) - Method in class object.common.Common
This function returns the name of the file of the path reveiced
getFirstGeneForOID(int) - Method in class object.common.Common
This function return the first Gene Object matching the Oligo Object from the oligo_id received
getFirstname() - Method in class object.common.User
Fistname of the User Object
getFlag() - Method in class object.microarray.ElementMap
Flag true or false of the spot
getFlag() - Method in class object.microarray.Feature
Flag true or false of the spot
getFlag_norm() - Method in class object.microarray.Feature
 
getFlag_str() - Method in class object.microarray.ElementMap
Flag string of the spot
getFlag_str() - Method in class object.microarray.Feature
Flag string of the spot
getFloat(String) - Method in class common.beans.locale.LocaleBean
Returns the specified number String converted to a float, parsed as defined by the currently selected locale.
getFocus() - Method in class object.common.CreationPlate
Index for the HTML form concerning input boxes
getFocusIndex() - Method in class object.common.CreationPlate
 
getFold() - Method in class object.microrna.Target
fold
getFold_image() - Method in class object.common.RNAfold
fold_image
getFoq_id() - Method in class object.common.Foq
ID of Foq Object
getFree_energy() - Method in class object.annotation.Oligo
Free Energy associated with this Oligo Object
getFree_energy() - Method in class object.annotation.Oligo_tiling
Free_energy Oligo_tiling Object
getFValue() - Method in class object.common.Blast
Value of F value for executing Blast program
getFValue() - Method in class object.common.BlastTwoSeq
Value of F value for executing Blast program
getFValue() - Method in class object.common.SessionBlastObject
F value for the Blast ('T' to ask for blast filter alignment, 'F' for not)
getGal_file() - Method in class object.microarray.Pattern_file
Path to the file of this Object
getGal_file() - Method in class object.microarray.Spotting
.GAL File describing this Spotting Object
getGal_fileFromMID(int) - Method in class object.common.Common
This function return the gal file a the Spotting Object of the Microarray Object ID received
getGenbank_gene_id() - Method in class object.annotation.Gene
genbank_gene id of the Gene Object - reference to genbank_gene_id database
getGenbank_gene_id() - Method in class object.annotation.Probeset
genbank_gene_id
getGenbank_gene_id(String) - Method in class object.common.Common
This function returns the genbank_gene_id and description from a refseq reference
getGenbank_gene_id() - Method in class object.microrna.Match
genbank_gene_id
getGenbank_gene_id() - Method in class object.microrna.Mirna_target
gene_id
getGenbank_link() - Method in class object.annotation.Gene
ID link from NCBI genbank file to database MIM, MGI, RGD
getGene() - Method in class object.annotation.Oligo_control
Gene symbol of Oligo_control Object
getGene_id() - Method in class object.annotation.Exon
ID of a Gene object owner of this Exon Object
getGene_id() - Method in class object.annotation.GenbankRef
ID of the owner Gene object
getGene_id() - Method in class object.annotation.Gene
ID of the Gene object
getGene_id() - Method in class object.annotation.Genoligo_affy_rel
ID of an existing Gene object
getGene_id() - Method in class object.annotation.Genoligo_rel
ID of an existing Gene object
getGene_id() - Method in class object.annotation.GoLink
ID of Gene object
getGene_id() - Method in class object.annotation.Oligo_adhocRelation
ID of Gene Object
getGene_id() - Method in class object.annotation.Probeset
gene_id
getGene_id() - Method in class object.common.MapEST
Number of match
getGene_id() - Method in class object.common.SequenceObject
ID of a Gene object if the SequenceObject is associate with an Oligo
getGene_name() - Method in class object.microrna.MicroCible
gene_name searched
getGenecart() - Method in class object.common.ImageManager
GeneCart Object for this ImageManager Object
getGenecart_id() - Method in class object.common.GeneCart
ID of GeneCart Object
getGeneCartForUser(int) - Method in class object.common.Common
This function returns a vector containing ToolBox Object of GeneCart Object owned by the User received.
getGenerif() - Method in class object.annotation.GenbankRef
Generif annotation of this GenbankRef object
getGenomicPosition() - Method in class object.annotation.Gene
GenomicPosition Object concerning this Gene Object
getGenomicPosition() - Method in class object.annotation.Oligo_adhoc_match
GenomicPosition concerning this Oligo_adhoc_match Object
getGenotype() - Method in class object.microarray.Labeling
Genotype of this Subject object
getGeo() - Method in class object.common.Public_database
GEO reference of this Public_database Object
getGeo() - Method in class object.microarray.Microarray_project_type
GEO accession number
getGeo_extract() - Method in class object.microarray.Labeling_type
GEO default extraction protocol of this Labeling_type object
getGeo_hyb() - Method in class object.microarray.Labeling_type
GEO default hybridization protocol of this Labeling_type object
getGeo_id() - Method in class object.microarray.GeoSerie
geo_id of GeoSerie object
getGeo_id_ref() - Method in class object.microarray.Feature
ID_ref for GEO submission
getGeo_label() - Method in class object.microarray.Labeling_type
GEO default labeling protocol of this Labeling_type object
getGeo_nucleicacid() - Method in class object.microarray.Labeling_type
GEO default type of nucleic acid of this Labeling_type object
getGeo_ref() - Method in class object.microarray.Nucleic_acid_type
Reference of this Nucleic_acid_type object for GEO
getGEODescription() - Method in class object.microarray.Hybridization
 
getGEODescription() - Method in class object.microarray.Scan
 
getGi() - Method in class object.annotation.Estoligo_rel
List of Gi number corresponding to the refseq accession number of ESTs
getGIDForAN(String) - Method in class object.common.Common
This function returns the gene ID for the accession_number received
getGIDForSymbol(String, String) - Method in class object.common.Common
This function returns the Mediante gene ID for the symbol and organism ID received
getGiFromRefseq(String) - Method in class object.common.Common
This function returns the gi number for the refseq reference received
getGo_acc() - Method in class object.annotation.Term
Gene Ontology accession
getGoFrequence(int) - Method in class object.common.Common
 
getGps_file() - Method in class object.microarray.Scan
Path to quantification settings file for this Scan object
getGrade() - Method in class object.microarray.Labeling
Cancer grade of this Subject object
getGroupe(String, String, double, double) - Method in class object.common.ImageManager
 
getGUwobble() - Method in class object.microrna.MicroCible
GUwobble
getHash() - Method in class object.common.GeneCart
Listing of the symbols or oligos IDs for this GeneCart Object
getHashAdhoc() - Method in class object.common.Common
This function return a Hashtable containing Oligo_annotation Objects.
getHashBeadToSeq() - Method in class object.hts.MaFile
 
getHashBlastConfiguration() - Method in class object.common.Xhtml
This function return a Hashtable containing all informations concerning Blast Object configuration
getHashBlocs() - Method in class object.microarray.Quantification_file
Hashtable containing Features Objects on the microarray hybridization image ordered with Microarrays selected slide_codes and then by blocs
getHashBSData() - Method in class object.common.Biostats
This function return a Hashtable containing data contains in the this.biostats_file file.
getHashCalcul() - Method in class object.common.ImageManager
Hashtable containing values of calcul asked by user
getHashColor() - Method in class object.common.ImageManager
Hashtable containing values of color mapping
getHashCols() - Method in class object.common.Biostats
Hashtable containing first line of biostats files
getHashColumns() - Method in class object.microarray.Pattern_file
Columns
getHashColumns() - Method in class object.microarray.Quantification_file
Columns for this search
getHashCoord() - Method in class object.microarray.Quantification_file
Hashtable containing Coordinates of spots on the microarray hybridization image ordered with Microarrays selected slide_codes
getHashCourbes() - Method in class object.common.ImageManager
 
getHashData() - Method in class object.microrna.TargetPrediction
Results for this search
getHashDatas() - Method in class object.common.ImageManager
Hashtable containing Quantification_file Object
getHashDown() - Method in class object.microrna.Mttdata
hashDown
getHashExtensions() - Method in class object.common.Xhtml
This function return a Hashtable containing all informations concerning Extensions configuration
getHashFeatures() - Method in class object.microarray.Quantification_file
Features for this Quantification_file Object
getHashFile() - Method in class object.common.ImageManager
Hashtable containing Files path downloadables
getHashFiles() - Method in class object.hts.Hts_RManager
Hashtable containing Listing of available files for this Hts_RManager query
getHashGenes() - Method in class object.microrna.MicroCible
Hash containing genes
getHashGenoligo_affy_rel() - Method in class object.common.Search
Hashtable of Genoligo_affy_rel Objects found with this search
getHashGenoligo_rel() - Method in class object.annotation.Sonde
Hashtable containing relation with Gene Object concerning this Sonde Object
getHashGoFrequence() - Method in class object.microrna.MapTarget
hashGoFrequence
getHashGroupLabel() - Method in class object.hts.Hts_RManager
Hashtable containing Hts_sample group labels
getHashID() - Method in class object.microarray.Pattern_file
IDs
getHashIDtoAcc(Microarray_project_type) - Method in class object.common.Common
This function return a Hashtable containing the symbol of gene symbol.
getHashImage() - Method in class object.common.ImageManager
Hashtable containing Images path displayed on screen
getHashKeys() - Method in class object.microrna.MapTarget
hashKeys
getHashKeyToAxon(int, int) - Method in class object.microarray.Quantification_file
 
getHashMailConfiguration() - Method in class object.common.Xhtml
This function return a Hashtable containing all informations concerning Mail configuration parameters.
getHashMaMatch() - Method in class object.hts.MaFile
 
getHashMap() - Method in class object.common.ImageManager
Hashtable containing Html Maps for Images displayed on screen
getHashMap_toID(Microarray_project_type) - Method in class object.common.Common
This function return a Hashtable containing the correspondance between
the reference of External Microarray Object as Agilent or comming from
other Plateforme as Evry or Strasbourg and the Oligo_externe or Oligo Object.
getHashMcbdata() - Method in class object.microrna.MicroCible
Results for this search
getHashMcbmatch() - Method in class object.microrna.Mcbdata
hashMcbMatch
getHashMicros() - Method in class object.microrna.MicroCible
Hash containing microRNAs
getHashMirna_target() - Method in class object.annotation.Gene
Hashtable of Mirna_target for this Gene object
getHashMirna_target() - Method in class object.microrna.Mirna_mature
hashMirna_target
getHashMstdata() - Method in class object.microrna.MicroSite
Results for this search
getHashMttdata() - Method in class object.microrna.MicroTopTable
hashMttdata
getHashName() - Method in class object.microarray.Pattern_file
Names
getHashOIDForControl() - Method in class object.common.Common
This function return a Hashtable containing the correspondance between
the reference of External Microarray Object as Agilent or comming from
other Plateforme as Evry or Strasbourg and the Oligo_externe or Oligo Object.
getHashOligo_annotation(boolean) - Method in class object.common.Common
This function return a Hashtable containing Oligo_annotation Objects.
getHashOligoArrayConfiguration() - Method in class object.common.Xhtml
This function return a Hashtable containing all informations concerning OligoArray Object configuration
getHashOligoPosition() - Method in class object.microarray.Plate
Hashtable of Oligo_rel Object for this Plate object
getHashOligosAffy() - Method in class object.annotation.Gene
Hashtable of Oligo_affy Object matching this Gene object
getHashOligosExternes() - Method in class object.annotation.Gene
Hashtable of Oligo_externe Object matching this Gene object
getHashOutFile() - Method in class object.hts.Hts_pipeline
hashOutFile
getHashParameter() - Method in class object.hts.Hts_analysis
hashParameter
getHashParameter() - Method in class object.hts.Hts_pipeline
hashParameter
getHashPlate96() - Method in class object.common.CreationPlate
Hashtable containing Plate 96 Object concerning with this creation Plate Object process
getHashPoints() - Method in class object.common.ImageManager
This function proceed to the creation of the Hashtable needed for the makeImage function of ImageManager.
getHashPointsToptable() - Method in class object.common.ImageManager
This function proceed to the creation of the Hashtable needed for the makeImage function of ImageManager.
getHashPosition() - Method in class object.microarray.Spotting
 
getHashPredicted() - Method in class object.microrna.Mttdata
hashPredicted
getHashRefGenmate() - Method in class object.common.CreationPlate
Hashtable containing reference slide code of new Plate 384 in creation
getHashScore() - Method in class object.microarray.Feature
 
getHashSequenceObject() - Method in class object.common.SessionBlastObject
Hashtable of Sequences needed to blast
getHashSpecificity() - Method in class object.annotation.Sonde
Hashtable containing specificity informations concerning this Sonde Object
getHashSpideyConfiguration() - Method in class object.common.Xhtml
This function return a Hashtable containing all informations concerning Spidey Objects configuration
getHashSymbol() - Method in class object.microrna.Mttdata
vectorSymbol
getHashSymbols() - Method in class object.microarray.Quantification_file
Hashtable containing Gene Symbols and IDs of spots on the microarray hybridization image ordered with Microarrays selected slide_codes
getHashtableBlastHit() - Method in class object.common.Blast
Hashtable containing the list of the BlastHit object results of the Blast
getHashTarget() - Method in class object.microrna.MapTarget
hashTarget
getHashTissues() - Method in class object.common.MapEST
hashTissues
getHashTTData() - Method in class object.common.Toptable
 
getHashUp() - Method in class object.microrna.Mttdata
hashUp
getHead() - Method in class JRclient.RList
get head xpression (CAR)
getHeader() - Method in class object.microarray.SerieFile
header of SerieFile object
getHeader() - Method in class object.microarray.SpotTypeFile
header of SpotTypeFile object
getHeaders() - Method in class object.microarray.Pattern_file
Headers of patter_file Object
getHistology() - Method in class object.microarray.Labeling
Cancer histology of this Subject object
getHistopathology_number() - Method in class object.hts.Hts_minseqe
 
getHitId() - Method in class object.common.BlastHit
Hit id for the corresponding alignment
getHitLink(BlastBase, String) - Method in class object.common.Link
Return a link to the database selected with type parameter concatenate with the ID received
getHitLink(String, String) - Method in class object.common.Link
Return a link to the database selected with type parameter concatenate with the ID received
getHitSequence() - Method in class object.common.BlastHit
Hit sequence
getHitStartPosition() - Method in class object.common.BlastHit
Start position on the hit sequence
getHitStopPosition() - Method in class object.common.BlastHit
Stop position on the hit sequence
getHowWeNormalized() - Method in class object.microarray.Quantification_file
The way we have normalized Datas
getHts_analysis() - Method in class object.hts.Hts_RManager
Hts_analysis to performs
getHts_analysis_id() - Method in class object.hts.Hts_analysis
ID of this Hts_analysis object
getHts_analysis_ref() - Method in class object.hts.Hts_analysis
Reference of this Hts_analysis object
getHts_extraction() - Method in class object.hts.Hts_minseqe
Hts extraction protocol used for this Hts_minseqe object
getHts_extraction_id() - Method in class object.hts.Hts_extraction
ID of this Hts_extraction object
gethts_extraction_ref() - Method in class object.hts.Hts_extraction
Reference of this Hts_extraction object
getHts_minseqe() - Method in class object.hts.Hts_sample
 
getHts_minseqe_id() - Method in class object.hts.Hts_minseqe
ID of this Hts_minseqe Object
getHts_minseqe_ref() - Method in class object.hts.Hts_minseqe
Reference of this Hts_minseqe Object
getHts_order_id() - Method in class object.hts.Hts_sample
ID of Hts_order Object for this Hts_sample Object
getHts_pipeline() - Method in class object.hts.Hts_result
hts_pipeline Object of hts_result Object
getHts_pipeline_id() - Method in class object.hts.Hts_pipeline
ID of this Hts_pipeline object
getHts_pipeline_ref() - Method in class object.hts.Hts_pipeline
Reference of this Hts_pipeline object
getHts_pipeline_type() - Method in class object.hts.Hts_pipeline
Type of this Hts_pipeline object
getHts_pipeline_type_required() - Method in class object.hts.Hts_analysis
hts_pipeline_type_required
getHts_quantification() - Method in class object.hts.Hts_minseqe
Hts quantification protocol used for this Hts_minseqe object
getHts_quantification_id() - Method in class object.hts.Hts_quantification
ID of this Hts_quantification object
gethts_quantification_ref() - Method in class object.hts.Hts_quantification
Reference of this Hts_quantification object
getHts_result_id() - Method in class object.hts.Hts_result
ID of this Hts_result object
getHts_result_ref() - Method in class object.hts.Hts_result
Reference of this hts_result object
getHts_run_id() - Method in class object.hts.Hts_run
ID of Hts_run object
getHts_run_id() - Method in class object.hts.Hts_sample
ID of Hts_run Object for this Hts_sample Object
getHts_run_ref() - Method in class object.hts.Hts_run
Reference of Hts_run object
getHts_sample_id() - Method in class object.hts.Hts_minseqe
Hts_sample ID asssociated to this Hts_minseqe Object
getHts_sample_id() - Method in class object.hts.Hts_result
ID of the Hts_sample Object related to this Hts_result object
getHts_sample_id() - Method in class object.hts.Hts_sample
ID of Hts_sample object
getHts_sample_ref() - Method in class object.hts.Hts_sample
Reference of Hts_sample object
getHts_type() - Method in class object.common.Order
Hts_type of this Hts_sample object
getHts_type() - Method in class object.hts.Hts_pipeline
Hts_type of this Hts_pipeline object
getHts_type() - Method in class object.hts.Hts_RManager
Hts_type to performs
getHts_type() - Method in class object.hts.Hts_run
Hts_type of this Hts_run object
getHts_type() - Method in class object.hts.Hts_sample
Hts_type of this Hts_run object
getHts_type_id() - Method in class object.hts.Hts_type
ID of this Hts_type object
getHts_type_ref() - Method in class object.hts.Hts_type
Reference of this Hts_type object
getHtsInfos(String, String, String) - Method in class object.common.Common
This function return a Hashtable containing informations concerning
the production of Hts samples among the different plateforms.
getHuman_quota() - Method in class object.annotation.EstTissue
human_quota
getHybridization() - Method in class object.microarray.Microarray
Hybridization Object for this Microarray Object
getHybridization_id() - Method in class object.microarray.Hybridization
ID of this Hybridization object
getHybridization_id() - Method in class object.microarray.Labeling
ID of the corresponding Hybridization Object
getId() - Method in class object.annotation.Specificity
ID of a Sonde Object
getId(String) - Method in class object.common.Common
 
getId() - Method in class object.common.IdDescriptionObject
ID of base reference of the IdDescriptionObject Object
getId() - Method in class object.microarray.SpotType
id
getIdentity() - Method in class object.annotation.Genoligo_rel
Percentage of identity of the Oligo Object on the sequence of the Gene Object
getIdentity() - Method in class object.annotation.Oligo_adhocRelation
Percent identity of the match
getIdentity() - Method in class object.annotation.Spodo_hit
identity
getImage() - Method in class object.common.Commande
Name of image describing the Commande object when seeing Oligos description
getImage_ch1() - Method in class object.microarray.Scan
Path to Channel 1 image of this Scan object
getImage_ch2() - Method in class object.microarray.Scan
Path to Channel 2 image of this Scan object
getImage_map() - Method in class object.common.Graph
image_map
getImage_path() - Method in class object.common.Graph
image_path
getImage_tosplit() - Method in class object.microarray.Scan
Path to tiff image with both channels of this Scan object
getImageTif() - Method in class object.microarray.Scan
Name of Image tiff from which the GPR is derived
getImg() - Method in class object.annotation.OligoHit
Image representing the OligoHit at the screen
getImgA() - Method in class object.microrna.MicroTopTable
imgA
getImgB() - Method in class object.microrna.MicroTopTable
imgB
getImgDOWN() - Method in class object.microrna.MicroTopTable
imgDOWN
getImgM() - Method in class object.microrna.MicroTopTable
imgM
getImgUP() - Method in class object.microrna.MicroTopTable
imgUP
getIndex(String) - Method in class object.common.Project
This function check if the Accession number received is not already in the vectorSequenceObject Vector
getInformation() - Method in class object.annotation.Oligo_adhoc
Informations concerning this Oligo_adhoc Object (pcr production for IPMC 5k array)
getInitialisation() - Method in class object.common.BlastTwoSeq
boolean : true if our query for align two sequence worked well
getInitialisation() - Method in class object.common.Search
boolean control if the initialization of the Search Object is OK
getInitialisation() - Method in class object.common.SessionBlastObject
Boolean : true if the initialization is OK, false if not
getInput() - Method in class object.common.ExecuteCmd
Allowed to see in the log file of the server all the output of the commande line executed
getInt(String) - Method in class common.beans.locale.LocaleBean
Returns the specified number String converted to a int, parsed as defined by the currently selected locale.
getInt(byte[], int) - Static method in class JRclient.Rtalk
converts bit-wise stored int in Intel-endian form into Java int
getInterslide() - Method in class object.common.Biostats
Interslide normalization method of Biostats Object
getInterslide() - Method in class object.common.Rstat
Interslide normalization method of Biostats Object
getIntraslide() - Method in class object.common.Biostats
Intraslide normalization method of Biostats Object
getIntraslide() - Method in class object.common.Rstat
Intraslide normalization method of Biostats Object
getIs_384SuiteBcr_ok() - Method in class object.microarray.Spotting
 
getIs_accessionOne() - Method in class object.common.BlastTwoSeq
boolean : true if we want to align the first sequence from the database
getIs_accessionTwo() - Method in class object.common.BlastTwoSeq
boolean : true if we want to align the second sequence from the database
getIs_active() - Method in class object.common.Project
True if the Project Object is an Active Project
getIs_active() - Method in class object.common.ProjectObject
'Y' or 'N' in function of the activity of this Project
getIs_active() - Method in class object.hts.Hts_sample
True if this Hts_sample Object is active
getIs_active() - Method in class object.microarray.Microarray
True if this Microarray Object is active
getIs_active() - Method in class object.microarray.Plate
True if this Plate object is already active
getIs_adhoc() - Method in class object.annotation.Oligo_rel
True if the oligo is an Oligo_adhoc Object
getIs_adhoc() - Method in class object.microarray.ElementMap
if this oligo is an adhoc oligo
getIs_adhoc() - Method in class object.microarray.Feature
if this oligo is an adhoc oligo
getIs_admin() - Method in class object.common.User
Boolean : true if the User object is a plateform administrator of the interface
getIs_admin_plateforme() - Method in class object.common.Plateforme
Plateforme administrator indication (option for production)
getIs_affy() - Method in class object.common.Toptable
is_affy
getIs_affy() - Method in class object.microarray.Microarray_project_type
Is this microarray is a microarray from Affymetrix
getIs_allowed(int, int) - Method in class object.common.Common
This function returns a boolean concerning the possibility to see a Project_order for a User Object.
getIs_analysis() - Method in class object.hts.Hts_sample
True if a hts_result is referenced as a analysis pipeline for this Hts_sample Object
getIs_best_oligo(int) - Method in class object.common.Common
This function returns a boolean corresponding to the fact that the oligo received is a "best" oligo
getIs_blast_proceeded() - Method in class object.common.SequenceObject
Boolean : true when we have already launch the Mediante Oligo Blast for this SequenceObject
getIs_cleanup() - Method in class object.hts.Hts_minseqe
 
getIs_collaboration() - Method in class object.common.Order
If this order is coming from a collaborative work (i.e. no facture)
getIs_control() - Method in class object.annotation.Oligo_rel
True if the oligo is an Oligo_control Object
getIs_control() - Method in class object.microarray.ElementMap
if this oligo is an oligo control
getIs_control() - Method in class object.microarray.Feature
if this oligo is an oligo control
getIs_devis() - Method in class object.common.User
Boolean : true if the User object is administratif
getIs_diluted() - Method in class object.microarray.Plate384
True if this Plate384 have been diluted
getIs_experiment() - Method in class object.microarray.Microarray
True if a hybridization is referenced for this Microarray Object
getIs_externe() - Method in class object.microarray.ElementMap
if this oligo is an external oligo
getIs_externe() - Method in class object.microarray.Feature
if this oligo is an external oligo
getIs_first() - Method in class object.common.Search
boolean control for the Web interface, first time we call a search it is true
getIs_first() - Method in class object.common.SessionBlastObject
Boolean control, true if it is the first time we ask for the Blast interface, false if not
getIs_found() - Method in class object.common.Search
boolean : true when the search found at least one Gene Object, and false if not
getIs_found() - Method in class object.microrna.MicroCible
boolean : true when the search found at least one Gene Object, and false if not
getIs_gu() - Method in class object.microrna.MatchMCB
match with GU
getIs_gz() - Method in class object.hts.Hts_pipeline_outfile
is_gz
getIs_hybrid() - Method in class object.common.Order
If hybridization must be perform by platforme
getIs_hybrid() - Method in class object.common.User
Boolean : true if the User object is a hybridizator
getIs_in_replaceMode() - Method in class object.microarray.Spotting
 
getIs_load() - Method in class object.microarray.MicroarrayElement
Boolean true if the MicroarrayElement is load and false if not.
getIs_local_ordered(int) - Method in class object.common.Common
This function returns a boolean corresponding to the existence of an oligo in the Local set ordered
getIs_matching() - Method in class object.common.SequenceObject
Boolean : true when the Oligo associate match the sequence of this SequenceObject, false if not
getIs_matching() - Method in class object.hts.Hts_sample
True if a hts_result is referenced as a matching pipeline for this Hts_sample Object
getIs_medlab() - Method in class object.common.User
Boolean : true if the User object can connect to Medlab interface
getIs_micro() - Method in class object.microarray.Microarray_project_type
Is this microarray is a microarray of microRNAs
getIs_minseqe() - Method in class object.hts.Hts_sample
True if a Hts_minseqe is referenced for this Hts_sample Object
getIs_mir_probe() - Method in class object.annotation.Oligo_externe
is_mir_probe
getIs_national_ordered(int) - Method in class object.common.Common
This function returns a boolean corresponding to the existence of an oligo in the National set ordered
getIs_normalized() - Method in class object.microarray.Microarray
True if this Microarray Object is active
getIs_normalized() - Method in class object.microarray.Quantification_file
boolean to know if this object is normalized too
getIs_open() - Method in class object.common.Order
Boolean descibing if this Microarray_order is opened in the Project_order Object
getIs_open() - Method in class object.common.Project
True if this Project Object is open is the current User session
getIs_open() - Method in class object.microarray.Project_order
Boolean true if this Project_order object is open in the Board Object containing this Project_order Object
getIs_order() - Method in class object.hts.Hts_analysis
Type of Object for this Hts_analysis object is Hts_order Object
getIs_orderable() - Method in class object.hts.Hts_type
True if Hts_type object is orderable
getIs_orderable() - Method in class object.microarray.Microarray_project_type
True if the microarray_project_type is orderable
getIs_owner() - Method in class object.common.Project
True if User curently viewing the Project in the Web Interface is the owner, false if not
getIs_prod() - Method in class object.common.User
Boolean : true if the User object is a microarray productor
getIs_production() - Method in class object.common.Plateforme
If the Plateforme plateforme is a microarray production platforme
getIs_quantif() - Method in class object.hts.Hts_sample
True if hts_result Object of all type matchig, reads and analysis pipelines are referenced for this Hts_sample Object
getIs_quantif() - Method in class object.microarray.Microarray
True if a scan is referenced for this Microarray Object
getIs_reads() - Method in class object.hts.Hts_sample
True if a hts_result is referenced as a reads pipeline for this Hts_sample Object
getIs_real_control() - Method in class object.annotation.Oligo_control
Indicate if this Oligo_control Object is a real control ('Y') or a lost oligo ('N')
getIs_rmq() - Method in class object.common.User
Boolean : true if the User object is a Quality Manager
getIs_sample() - Method in class object.hts.Hts_analysis
Type of Object for this Hts_analysis object is Hts_sample Object
getIs_save() - Method in class object.common.Rstat
is_save
getIs_select() - Method in class object.annotation.Genoligo_rel
Caracteristic of the selection or not of this relation for the Gene Object.
getIs_selected(int) - Method in class object.common.Common
This function returns a boolean corresponding to the existence of an oligo in the Local set ordered
getIs_spottable() - Method in class object.microarray.Microarray_project_type
True if the microarray_project_type is spottable
getIs_superadmin() - Method in class object.common.User
Boolean : true if the User object is super-administrator of the interface
getIs_tiling() - Method in class object.microarray.ElementMap
if this oligo is a tiling oligo
getIs_tiling() - Method in class object.microarray.Feature
if this oligo is a tiling oligo
getIs_update() - Method in class object.common.Order
If this order has been updated
getIs_viewable() - Method in class object.microarray.ArrayLabo
Indicate if we can display in Mediante probes sequences informations positions
getIs_viewable() - Method in class object.microarray.Microarray
True if a scan and a hybridization are referenced for this Microarray Object
getIs_viewable() - Method in class object.microarray.Microarray_project_type
Is this microarray can be viewed in Multi_PF oligo nucleotides comparison
getIs_viewer() - Method in class object.common.Project
True if User curently viewing the Project in the Web Interface is a viewer, false if not
getIs_writer() - Method in class object.common.Project
True if User curently viewing the Project in the Web Interface is the writer, false if not
getJournal() - Method in class object.annotation.GenbankRef
Journal of this GenbankRef object
getJournal() - Method in class object.microrna.Mirna_reference
journal
getKeyword_id() - Method in class object.common.Keyword
ID of a Keyword object
getKeyword_ref() - Method in class object.common.Keyword
Reference of a Keyword object
getLabel() - Method in class object.hts.Hts_sample
 
getLabeling_ch1() - Method in class object.microarray.MicroarrayElement
labeling_ch1 reference of the Microarray object corresponding to this MicroarrayElement
getLabeling_ch1() - Method in class object.microarray.Scan
Labeling reference for Channel 1
getLabeling_ch2() - Method in class object.microarray.MicroarrayElement
labeling_ch2 reference of the Microarray object corresponding to this MicroarrayElement
getLabeling_ch2() - Method in class object.microarray.Scan
Labeling reference for Channel 2
getLabeling_id() - Method in class object.microarray.Labeling
ID of this Labeling object
getLabeling_ref() - Method in class object.microarray.Labeling
Reference of this Labeling object
getLabeling_type() - Method in class object.microarray.Labeling
Labeling type of this Labeling object
getLabeling_type_ch1() - Method in class object.microarray.Scan
Labeling_type Object for Channel 1 of this Scan Object
getLabeling_type_ch2() - Method in class object.microarray.Scan
Labeling_type Object for Channel 1 of this Scan Object
getLabeling_type_id() - Method in class object.microarray.Labeling_type
ID of this Labeling_type object
getLabeling_type_ref() - Method in class object.microarray.Labeling_type
Refrence of this Labeling_type object
getLabels() - Method in class object.microarray.Hybridization
 
getLabels() - Method in class object.microarray.Microarray
 
getLabels() - Method in class object.microarray.Scan
 
getLabRefList() - Method in class object.common.ImageManager
String[] containing distinct labeling references among the Project_order Object concerned
getLanguage() - Method in class common.beans.locale.LocaleBean
Returns the language code for the currently selected locale.
getLastError() - Method in class JRclient.Rconnection
get last error string
getLastname() - Method in class object.common.User
Lastname of the User Object
getLatin_name() - Method in class object.annotation.Organism
Latin name or Organism Object
getLegende() - Method in class object.common.Convert
legende
getLen(byte[], int) - Static method in class JRclient.Rtalk
converts bit-wise stored length from a header.
getLength() - Method in class object.annotation.Chromosome
Length of this Chromosome
getLetter_a() - Method in class object.microarray.Plate_transfert_type
Letter_A string for Description of transfert from 96 plate
getLetter_b() - Method in class object.microarray.Plate_transfert_type
Letter_B string for Description of transfert from 96 plate
getLimma_M() - Method in class object.common.Biostats
Path of Limma M normalized file
getLink() - Method in class object.annotation.OligoHit
First link of the OligoHit ---> details of the Oligo
getLink(String, String) - Method in class object.common.Link
Return a link to the database selected with type parameter concatenate with the ID received
getLink(String, String, String) - Method in class object.common.Link
Return a link to the database selected with type parameter concatenate with the GI and Refseq AN received
getLink(String, Organism, String) - Method in class object.common.Link
Return a link to the database selected
getLink(GenomicPosition) - Method in class object.common.Link
Return a link corresponding to the GenomicPosition Object received
getLink(String, String, int) - Method in class object.common.Link
 
getLink(int, int, int) - Method in class object.microarray.Feature
 
getLink2() - Method in class object.annotation.OligoHit
Second link of the OligoHit ---> selection of the Oligo for the SequenceObject Object
getLinks() - Method in class object.hts.Hts_sample
 
getLinks() - Method in class object.microarray.Microarray
 
getLinkTargetPrediction(String, int) - Method in class object.common.Link
 
getListePlate384() - Method in class object.common.Dilution
 
getListing() - Method in class object.common.Attribution
Listing of microarrays or Hts_sample references in attribution
getListing() - Method in class object.common.GeneCart
Listing of the symbols or oligos IDs for this GeneCart Object
getListing() - Method in class object.hts.Hts_run
 
getListing() - Method in class object.microarray.Spotting
 
getLocale() - Method in class common.beans.locale.LocaleBean
Returns a Locale.
GetLocalTextTag - Class in common.tags.generic
 
GetLocalTextTag() - Constructor for class common.tags.generic.GetLocalTextTag
 
getLogFC() - Method in class object.common.ImageManager
logFC for features filtration
getLogfc() - Method in class object.microrna.MicroTopTable
logfc
getLogFC() - Method in class object.microrna.Mttdata
logFC
getLogin() - Method in class object.common.User
Login of the User Object
getLogratio() - Method in class object.microarray.Feature
 
getLong(String) - Method in class common.beans.locale.LocaleBean
Returns the specified number String converted to a long, parsed as defined by the currently selected locale.
getLong(byte[], int) - Static method in class JRclient.Rtalk
converts bit-wise Intel-endian format into long
getLongueur() - Method in class object.annotation.Gene
Length of the Gene sequence
getLongueur() - Method in class object.annotation.OligoHit
Longueur Of the OligoHit
getLst_genes_down() - Method in class object.microrna.MicroTopTable
lst_genes_down
getLst_genes_up() - Method in class object.microrna.MicroTopTable
lst_genes_up
getMainEstTissue() - Method in class object.common.Common
This function return a Hashtable containing the main est_tissue_id for the EstTissue which are not main EstTissue.
getMamap() - Method in class object.annotation.Sonde
Mamap
getMap() - Method in class object.annotation.Gene
map for images
getMap() - Method in class object.common.MapEST
map for images
getMapEST() - Method in class object.annotation.Gene
MapEST Object of this Gene Object
getMapEST() - Method in class object.annotation.Oligo
MapEST Object of this Oligo Object
getMapName() - Method in class object.annotation.OligoHit
Html Map string wich separate the image in two parts : for first link (link attribute) and second link -link2 attribute
getMapTargetDown() - Method in class object.microrna.Mttdata
MapTargetDown
getMapTargetUp() - Method in class object.microrna.Mttdata
MapTargetUp
getMark() - Method in class object.microarray.Labeling
Mark type for this Labeling Object
getMask_A() - Method in class object.common.Toptable
mask_A
getMask_id() - Method in class object.common.Toptable
mask_id
getMask_M() - Method in class object.common.Toptable
mask_M
getMask_name() - Method in class object.common.Toptable
mask_name
getMature_acc() - Method in class object.microrna.MicroTopTable
auto_mature
getMature_acc() - Method in class object.microrna.Mirna_mature
mature_acc
getMature_acc() - Method in class object.microrna.Mirna_target
mature_acc
getMature_acc() - Method in class object.microrna.Mttdata
mature_acc
getMature_acc() - Method in class object.microrna.TargetPrediction
auto_mature
getMature_name() - Method in class object.microrna.Mcbmatch
mature_name
getMature_name() - Method in class object.microrna.Mirna_mature
mature_name
getMature_name() - Method in class object.microrna.Mirna_target
mature_name
getMature_name() - Method in class object.microrna.Mttdata
mature_name
getMedline() - Method in class object.microrna.Mirna_reference
medline
getMega(int) - Method in class object.common.Common
This function make the conversion beetween sequence base size and MegaBase size
getMessage() - Method in exception JRclient.RSrvException
 
getMessage() - Method in class object.common.Attribution
Information message displayed in JSP
getMessage() - Method in class object.common.BlastTwoSeq
Information message
getMessage() - Method in class object.common.Board
Message concerning this Board Object
getMessage() - Method in class object.common.CreationPlate
Information message in case of error during the process
getMessage() - Method in class object.common.Dilution
Information message in case of error during the process
getMessage() - Method in class object.common.Project
Information message concerning this project (update at each step of the modifications of this project)
getMessage() - Method in class object.common.Rstat
Message information
getMessage() - Method in class object.common.Search
Information message concerning the search
getMessage() - Method in class object.common.SessionBlastObject
Informations message concerning the Blast proceed
getMessage() - Method in class object.hts.Hts_result
Information message in case of error during the process
getMessage() - Method in class object.hts.Hts_RManager
Message information
getMessage() - Method in class object.hts.Hts_run
Message for user information
getMessage() - Method in class object.microarray.Scan
Information message in case of error during the process
getMessage() - Method in class object.microarray.Spotting
 
getMessage() - Method in class object.microrna.MicroCible
Information message concerning the search
getMfe_cutoff() - Method in class object.microrna.MicroCible
mfe_cutoff
getMfe_cutoff() - Method in class object.microrna.MicroTopTable
mfe_cutoff
getMicro() - Method in class object.common.RNAhybrid
micro
getMicro() - Method in class object.microrna.MatchMCB
micro
getMicro_list() - Method in class object.microrna.MicroSite
micro_list
getMicroarray() - Method in class object.microarray.MicroarrayElement
Microarray object corresponding to this MicroarrayElement
(might be not initialized most of the time)
getMicroarray(String) - Method in class object.microarray.Project_order
 
getMicroarray_id() - Method in class object.microarray.Control
ID of Microarray Object with which the control has been done
getMicroarray_id() - Method in class object.microarray.Hybridization
Microarray ID asssociated to this Hybridization object
getMicroarray_id() - Method in class object.microarray.Microarray
ID of Microarray object
getMicroarray_id() - Method in class object.microarray.MicroarrayElement
ID of the Microarray object corresponding to this MicroarrayElement
getMicroarray_id() - Method in class object.microarray.Scan
ID of the Microarray Object related to this Scan object
getMicroarray_order_id() - Method in class object.microarray.Microarray
Microarray_project_type Object for this Microarray Object
getMicroarray_order_id() - Method in class object.microarray.Microarray_project_type
Default Microarray_order ID concerning the quality control associated to the microarray_project_type
getMicroarray_orderLabel(int) - Method in class object.common.Common
This function returns a description string of the Microarray_order Objects ID received.
getMicroarray_project_type() - Method in class object.annotation.Oligo_adhoc
Microarray_project_type Object owner of this Oligo_adhoc Object
getMicroarray_project_type() - Method in class object.annotation.Oligo_externe
Microarray_project_type Object owner of this Oligo_adhoc Object
getMicroarray_project_type() - Method in class object.common.Order
Microarray_project_type of this Microarray_order
getMicroarray_project_type() - Method in class object.microarray.GeoSerie
microarray_project_type of GeoSerie object
getMicroarray_project_type() - Method in class object.microarray.Microarray
Microarray_project_type Object for this Microarray Object
getMicroarray_project_type() - Method in class object.microarray.Spotting
Microarray project type in spotting
getMicroarray_project_type_id() - Method in class object.microarray.Microarray_project_type
ID of this Microarray_project_type object
getMicroarray_project_type_ref() - Method in class object.microarray.Microarray_project_type
Reference of this Microarray_project_type object
getMicroarray_type() - Method in class object.microarray.Microarray
Microarray_type Object for this Microarray Object
getMicroarray_type_id() - Method in class object.microarray.Microarray_type
ID of Microarray_type object
getMicroarray_type_ref() - Method in class object.microarray.Microarray_type
Name of the Microarray_type Object
getMicroarrayInfos(String, String, String) - Method in class object.common.Common
This function return a Hashtable containing informations concerning
the production of Microarrays among the different plateforms.
getMicroCible() - Method in class object.microrna.SnipMir
MicroCible
getMicrocibleLink(String, String, String, String, String, int) - Method in class object.common.Link
 
getMiddleSequence(String, String) - Method in class object.common.Spidey
This function return a string concerning alignment of two sequences from a Blast process.
getMiddleSequenceFont(String, String) - Method in class object.common.Spidey
This function return a string concerning alignment of two sequences from a Blast process.
getMirbaseTargetLink(String, String, String) - Method in class object.common.Link
 
getMirna() - Method in class object.microrna.Mirna_mature
mirna
getMirna_acc() - Method in class object.microrna.Mirna
mirna_acc
getMirna_id() - Method in class object.microrna.Mirna
mirna_id
getMirna_target_tool_id() - Method in class object.microrna.MapTarget
mirna_target_tool_id
getMix_ref() - Method in class object.hts.Hts_result
Reference for mix sequenced
getMouse_quota() - Method in class object.annotation.EstTissue
mouse_quota
getMPTForRefAndPF(String, int) - Method in class object.common.Common
This function returns the ID of the Microarray_project_type Object identified by both parameters.
getMultiplier() - Method in class object.microarray.Microarray_project_type
 
getMyFiles() - Method in class object.common.Rstat
String[] containing Listing of available files for this Rstat query
getName() - Method in class object.annotation.Oligo_tiling
name of Oligo_tiling Object
getName() - Method in class object.annotation.Term
Gene Ontology description of the accession
getName() - Method in class object.common.ToolBox
Name of the ToolBox object
getName() - Method in class object.common.ToolBoxString
Name of the ToolBoxString object
getName() - Method in class object.hts.Hts_analysis_parameter
name
getName() - Method in class object.hts.Hts_pipeline_outfile
name
getName() - Method in class object.hts.Hts_pipeline_parameter
name
getName() - Method in class object.microarray.Feature
Name of Oligo object of this Feature
getName() - Method in class object.microarray.MageProtocol
name of this MageProtocol Object
getName() - Method in class object.microarray.SpotType
name
getName() - Method in class object.microrna.Mstdata
name
getNb() - Method in class object.annotation.Estoligo_rel
Number of match
getNb() - Method in class object.common.Attribution
Number of arrays or hts samples to attribute to the Order Object
getNb_all() - Method in class object.annotation.Histology
Reference of Categorie Object
getNb_all_down() - Method in class object.microrna.MicroTopTable
 
getNb_all_up() - Method in class object.microrna.MicroTopTable
 
getNb_bloc() - Method in class object.common.ImageManager
Numero of the bloc to display at the screen
getNb_bloc() - Method in class object.microarray.Pattern_file
Number of bloc
getNb_bloc() - Method in class object.microarray.Quantification_file
Number of bloc
getNb_bloc_column() - Method in class object.microarray.Pattern_file
Number of column of bloc
getNb_bloc_row() - Method in class object.microarray.Pattern_file
Number of row of bloc
getNb_column() - Method in class object.microarray.Pattern_file
Number of column in each block
getNb_column() - Method in class object.microarray.Quantification_file
Number of column in each block
getNb_est() - Method in class object.annotation.Sonde
Number of ESTs matching the Sonde Object
getNb_fields() - Method in class object.common.Convert
nb_fields returns
getNb_gene() - Method in class object.microrna.MicroTopTable
 
getNb_gene_a() - Method in class object.microrna.MicroTopTable
 
getNb_gene_filt() - Method in class object.microrna.MicroTopTable
 
getNb_identity() - Method in class object.annotation.Spodo_hit
nb_identity
getNb_lame() - Method in class object.microarray.Spotting
Number of Microarray create in this spotting session
getNb_match() - Method in class object.microrna.MicroCible
Number of match between microRNAs and genes for this search
getNb_microarray() - Method in class object.common.Order
Number of microarrays ordered (ex :in case of 4x44k pattern = 4 x this.nb_slide) in this Microarray_order
getNb_microarray() - Method in class object.microarray.GeoSerie
nb_microarray of GeoSerie object
getNb_microarray_more() - Method in class object.common.Order
Number of microarrays rest to attribute to this Microarray_order by the IPMC production
getNb_microarray_ok() - Method in class object.common.Order
Number of microarrays with informations loaded concerning the Microarray_order object related to this Order Object
getNb_neoplasia() - Method in class object.annotation.Histology
Reference of Categorie Object
getNb_normal() - Method in class object.annotation.Histology
ID of Categorie Object
getNb_predict() - Method in class object.microrna.Mttdata
nb_predict
getNb_row() - Method in class object.microarray.Pattern_file
Number of row in each block
getNb_row() - Method in class object.microarray.Quantification_file
Number of row in each block
getNb_sample() - Method in class object.common.Order
Number of sample in this Hts_order Object
getNb_sample() - Method in class object.hts.Hts_run
Number of sample create in this hts_run Object
getNb_sample_more() - Method in class object.common.Order
Number of sample in this Hts_order Object to add to close this Hts_order Object
getNb_slide() - Method in class object.common.Order
Number of unique slide ordered in this Microarray_order
getNb_unknown() - Method in class object.annotation.Histology
Reference of Categorie Object
getNb_use() - Method in class object.microarray.Plate
Number of time this Plate object have been used for Microarray Object production
getNb_xhybrid_string() - Method in class object.annotation.Sonde
This function returns a string corresponding to the xhybrid_max attribute
getNbResultsParPAge() - Method in class object.common.Project
Number of SeqeuenceObject displayed per page in the Oligo selection part
getNbResultsParPAge() - Method in class object.common.Search
Number of results to show in one page in the web interface
getNeedToConvert() - Method in class object.microarray.Spotting
 
getNucleic_acid_type() - Method in class object.hts.Hts_minseqe
Nucleic acid type of this Hts_minseqe object
getNucleic_acid_type() - Method in class object.microarray.Labeling
Nucleic acid type of this Extraction object
getNucleic_acid_type_id() - Method in class object.microarray.Nucleic_acid_type
ID of this Nucleic_acid_type object
getNucleic_acid_type_ref() - Method in class object.microarray.Nucleic_acid_type
Reference of this Nucleic_acid_type object
getNumber(String) - Method in class common.beans.locale.LocaleBean
Returns the specified String as a Number, parsed based on the currently selected locale.
getNumber() - Method in class object.microarray.Serie
number
getNumberOfIdentities() - Method in class object.common.BlastHit
Number of identities
getNumberString(double) - Method in class common.beans.locale.LocaleBean
Returns the specified number converted to a String, formatted as defined by the currently selected locale.
getOligo_adhoc_id() - Method in class object.annotation.Oligo_adhocRelation
ID of oligo_adhoc object
getOligo_adhoc_id() - Method in class object.microrna.Mttdata
oligo_adhoc_id
getOligo_control_id() - Method in class object.annotation.Oligo_control
ID of Oligo_control Object
getOligo_id() - Method in class object.annotation.Genoligo_rel
ID of an existing Oligo object
getOligo_id() - Method in class object.annotation.Oligo_annotation
ID of Oligo_adhoc object associated to this relation
getOligo_id() - Method in class object.annotation.Oligo_rel
ID of the Oligo, Oligo_adhoc or Oligo_control Object associated with this relation
getOligo_id() - Method in class object.common.Point
ID of the Oligo Object associated with this Point Object
getOligo_id() - Method in class object.common.SequenceObject
ID of an Oligo object if the SequenceObject is associate with an Oligo
getOligo_id() - Method in class object.microarray.ElementMap
ID of Oligo object of this ElementMap
getOligo_id() - Method in class object.microarray.Feature
ID of Oligo object of this Feature
getOligo_id_str() - Method in class object.microarray.ElementMap
Oligo ID string object of this ElementMap
getOligo_id_str() - Method in class object.microarray.Feature
Oligo ID string object of this Feature
getOligo_tiling_id() - Method in class object.annotation.Oligo_tiling
ID of Oligo_tiling Object
getOligoBase() - Method in class object.annotation.Organism
Blastbase Object corresponding to the Oligo blastbase of this Organism Object
getOligoGraph() - Method in class object.common.SequenceObject
Blast Graph for this sequence against our Mediante Oligo Object Database
getOligoGraphMap() - Method in class object.common.SequenceObject
Map for Blast Graph for this sequence against our Mediante Oligo Object Database
getOnlyCart() - Method in class object.common.ImageManager
True if only genes in cart must be displayed on the visualization graph (directory : 'graph')
getOnMouseOver() - Method in class object.annotation.OligoHit
Label of the OligoHit
getOptions() - Method in class object.hts.Hts_analysis_parameter
options
getOptions() - Method in class object.hts.Hts_pipeline_parameter
options
getOrder() - Method in class object.common.Attribution
Order Object in microarray attribution
getOrder_id() - Method in class object.common.Journal
ID of order_id Object related to this journal Object
getOrder_id() - Method in class object.common.Order
order_id
getOrder_ref(int, String) - Method in class object.common.Common
This function return the mo_ref parameter of the Microarray_order Object received.
getOrder_ref() - Method in class object.common.Order
order_ref
getOrder_stats() - Method in class object.hts.Hts_order
Stats of order Object
getOrder_type(int) - Method in class object.common.Common
Return the Order_type for an Order Object
getOrder_type() - Method in class object.common.Order
order_type
getOrderedKeys() - Method in class object.common.Convert
IDs search searched as user request
getOrderForPlateforme() - Method in class object.common.Common
This function return a Vector containing Order Objects concerning all the Microarray_order waiting for plateforme attribution
getOrdre_id() - Method in class object.common.SequenceObject
ID of an Oligo object if the SequenceObject is associate with an Oligo
getOrdre_id() - Method in class object.microarray.Microarray
ordre_id of this Microarray Object in the Spotting Object
getOrganism() - Method in class object.annotation.GenomicPosition
Organism concerned by this GenomicPosition Object
getOrganism() - Method in class object.annotation.Oligo_annotation
Organism common name string associated to this relation
getOrganism() - Method in class object.annotation.Oligo_control
Organism common name of Oligo_control Object
getOrganism() - Method in class object.common.Project
Organism Object of this Project Object
getOrganism() - Method in class object.common.Public_database
Organism owner of the Public_database Object
getOrganism() - Method in class object.hts.Hts_minseqe
Organism corresponding to this Hts_minseqe object
getOrganism() - Method in class object.microarray.Labeling
Organism corresponding to this Subject object
getOrganism() - Method in class object.microarray.Microarray_project_type
Organism Object concerned by this Microarray_project_type object
getOrganism() - Method in class object.microarray.Plate
Organism Object concerning this Plate object
getOrganism() - Method in class object.microrna.MicroSite
Organism
getOrganism() - Method in class object.microrna.TargetPrediction
Organism
getOrganism_gene() - Method in class object.microrna.MicroCible
Organism for transcripts search
getOrganism_id() - Method in class object.annotation.Chromosome
Organism owner of this Chromosome
getOrganism_id() - Method in class object.annotation.Organism
ID of Organism object
getOrganism_id() - Method in class object.annotation.Sonde
ID of Organism Object related to this Sonde Object
getOrganism_id() - Method in class object.common.BlastBase
ID of Organism object
getOrganism_id() - Method in class object.common.Convert
ID of the Organism concerning by the search
getOrganism_id() - Method in class object.common.ProjectObject
ID of Organism of this Project
getOrganism_id() - Method in class object.common.Search
ID of the Organism concerning by the search
getOrganism_id() - Method in class object.microrna.Mcbdata
symbol
getOrganism_id() - Method in class object.microrna.Mirna_mature
organism_id
getOrganisme() - Method in class object.common.User
Organism
getOrigin() - Method in class object.microarray.Labeling
Origin of this Subject object
getOverlap_sense() - Method in class object.microrna.Mirna_context
overlap_sense
getOverlap_type() - Method in class object.microrna.Mirna_context
overlap_type
getOwner() - Method in class object.microarray.GeoSerie
owner of GeoSerie object
getPageName(String) - Method in class common.beans.locale.LocaleBean
Returns a version of the specified page name with a language/country suffix for the currently selected locale.
getParameter(String) - Method in class common.beans.locale.LocaleBean
Returns the first all value for the specified parameter, parsed using the currently specified charset.
getParameterNames() - Method in class common.beans.locale.LocaleBean
Returns an Enumeration of all parameter names.
getParameters(HttpServletRequest) - Method in class common.tags.generic.UseLocaleBundleTag
Returns a Hashtable with all HTTP parameters from an HttpServetRequest.
getParameters() - Method in class object.microarray.MageProtocol
parameters of this MageProtocol Object
getParameterValues(String) - Method in class common.beans.locale.LocaleBean
Returns an array of all values for the specified parameter, parsed using the currently specified charset.
getParent_id() - Method in class object.annotation.Oligo_adhoc
ID of parent of this Oligo_adhoc Object
getPassword() - Method in class object.common.User
Password of the User Object
getPath() - Method in class object.hts.Hts_pipeline_outfile
path
getPath() - Method in class object.hts.MaFile
 
getPath_fichier() - Method in class object.common.Fichier
Relative path to file of this Fichier object
getPathFichier() - Method in class object.common.Blast
Path of the file where the sequence to Blast are store
getPattern_file() - Method in class object.microarray.Spotting
 
getPattern_file(Pattern_file) - Method in class object.microarray.Spotting
 
getPays() - Method in class object.common.User
Country of User object
getPdf_file() - Method in class object.common.Biostats
Path of R script file
getPearson(Hashtable) - Method in class object.common.ImageManager
 
getPercentageIdentity() - Method in class object.common.BlastHit
Percentage of identity
getPid_pref() - Method in class object.common.Order
Preference choice of user concerning plateforme
getPlate384Ref() - Method in class object.common.Dilution
Slide_code of the Plate384 Object in dilution
getPlate96_id() - Method in class object.annotation.Oligo_rel
ID of the Plate96 if we are talking about Plate384 position
getPlate_A1() - Method in class object.microarray.Plate384
ID of a Plate96 Object part of this Plate384 Object
getPlate_A2() - Method in class object.microarray.Plate384
ID of a Plate96 Object part of this Plate384 Object
getPlate_B1() - Method in class object.microarray.Plate384
ID of a Plate96 Object part of this Plate384 Object
getPlate_B2() - Method in class object.microarray.Plate384
ID of a Plate96 Object part of this Plate384 Object
getPlate_id() - Method in class object.annotation.Oligo_rel
ID of Plate Object associated with this relation
getPlate_id() - Method in class object.microarray.Plate
ID of this Plate object
getPlate_ref() - Method in class object.microarray.Plate
Reference of this Plate object
getPlate_transfert_type() - Method in class object.microarray.Plate384
Type of transfert from plate96 Object
getPlate_transfert_type_desc() - Method in class object.microarray.Plate_transfert_type
Description of the Plate_transfert_type Object
getPlate_transfert_type_id() - Method in class object.microarray.Plate_transfert_type
ID of Plate_transfert_type object
getPlate_type() - Method in class object.microarray.Plate
Plate_type Object of this Plate object
getPlate_type_id() - Method in class object.microarray.Plate_type
ID of Plate_type object
getPlate_type_ref() - Method in class object.microarray.Plate_type
Reference of the Plate_type Object
getPlateforme() - Method in class object.common.Order
Plateforme where order is ordered
getPlateforme() - Method in class object.common.User
If this User Object belong to a Plateforme Object
getPlateforme() - Method in class object.hts.Hts_type
Plateforme where Hts_type is performed
getPlateforme() - Method in class object.microarray.Microarray_project_type
Plateforme Object of this Microarray_project_type Object
getPlateforme() - Method in class object.microarray.Spotting
Plateforme owner of this Spotting object
getPlateforme_id() - Method in class object.common.Plateforme
ID of Plateforme Object
getPlateforme_ref() - Method in class object.common.Plateforme
Ref of Plateforme Object
getPmt_ch1() - Method in class object.microarray.Scan
PMT used for Channel 1 mesures for this Scan object
getPmt_ch2() - Method in class object.microarray.Scan
PMT used for Channel 2 mesures for this Scan object
getPO_IDForMO_ID(int) - Method in class object.common.Common
This function return the project_order_id parameter of the Project_order Object owning the Microarray_order received.
getPopSize(int) - Method in class object.common.Common
 
getPopsize() - Method in class object.microrna.MapTarget
popsize
getPosition() - Method in class object.annotation.Genoligo_rel
Start position of the Oligo Object on the sequence of the Gene Object
getPosition() - Method in class object.annotation.Oligo_adhocRelation
Position of oligo_adhoc object sequence on the Gene object sequence
getPosition() - Method in class object.annotation.Oligo_control
Position of Oligo_control Object on the associated gene
getPosition() - Method in class object.annotation.Oligo_rel
Position of the oligo in the Plate Object (i.e.
getPosition() - Method in class object.microrna.MatchMCB
position
getPrecision() - Method in class object.common.Foq
Precision concerning the type of Foq Object
getPrefam_acc() - Method in class object.microrna.Mttdata
prefam_acc
getPrefam_id() - Method in class object.microrna.Mttdata
prefam_id
getPremir() - Method in class object.microrna.Mstdata
premir
getPremir_end() - Method in class object.microrna.Mstdata
premir_end
getPremir_start() - Method in class object.microrna.Mstdata
premir_start
getProbe_set_id() - Method in class object.annotation.Genoligo_affy_rel
probe_set_id
getProbe_set_id() - Method in class object.annotation.Oligo_affy
probe_set_id of probe for this Oligo_affy Object
getProbeset_id() - Method in class object.annotation.Probeset
probeset_id
getProbleme() - Method in class object.common.Foq
Problem observed
getProject() - Method in class object.common.SessionObject
Project Object
getProject_id() - Method in class object.common.Project
ID of Project Object
getProject_id() - Method in class object.common.ProjectObject
ID of Project object
getProject_id() - Method in class object.common.SequenceObject
ID of an Oligo object if the SequenceObject is associate with an Oligo
getProject_order() - Method in class object.common.Board
Project_order for this Board Object
getProject_order() - Method in class object.common.ImageManager
Project_order Object concerning this ImageManager Object
getProject_order() - Method in class object.hts.Hts_RManager
project_order
getProject_order_id() - Method in class object.common.Biostats
ID of Project_order Object owner of this analysis
getProject_order_id() - Method in class object.common.Order
ID of the Project_order Object to which belong this Microarray_order object
getProject_order_id() - Method in class object.common.Rstat
project_order_id
getProject_order_id() - Method in class object.common.Toptable
ID of Project_order Object owner of this analysis
getProject_order_id() - Method in class object.microarray.Project_order
ID of this Project_order object
getProject_order_ref() - Method in class object.common.Order
Project_order_ref of Project Object related to the Microarray_order object related to this Order Object
getProject_order_ref() - Method in class object.microarray.Project_order
Reference of this Project_order object
getProjectForUser(int) - Method in class object.common.Common
This function returns a vector containing ToolBox Object of Project Object owned by the User received.
getProtein_id() - Method in class object.annotation.Gene
ID from protein from NCBI genbank file
getProtein_id() - Method in class object.annotation.Probeset
protein_id
getProtocol_amplification() - Method in class object.microarray.Labeling
Protocol_amplification Object used for this Extraction object
getProtocol_amplification_id() - Method in class object.microarray.Protocol_amplification
ID of Protocol_amplification Object
getProtocol_amplification_ref() - Method in class object.microarray.Protocol_amplification
Reference of Protocol_amplification Object
getProtocol_extraction() - Method in class object.hts.Hts_minseqe
Extraction protocol used for this Hts_minseqe object
getProtocol_extraction() - Method in class object.microarray.Labeling
Extraction protocol used for this Extraction object
getProtocol_extraction_id() - Method in class object.microarray.Protocol_extraction
ID of this Protocol_extraction object
getProtocol_extraction_ref() - Method in class object.microarray.Protocol_extraction
Reference of this Protocol_extraction object
getProtocol_hybridization() - Method in class object.microarray.Hybridization
Protocol_hybridization Object of this Hybridization object
getProtocol_hybridization_id() - Method in class object.microarray.Protocol_hybridization
ID of this Protocol_hybridization object
getProtocol_hybridization_ref() - Method in class object.microarray.Protocol_hybridization
Reference of this Protocol_hybridization object
getProtocol_labeling() - Method in class object.microarray.Labeling
Labeling protocol used for this Labeling object
getProtocol_labeling_id() - Method in class object.microarray.Protocol_labeling
ID of this Protocol_labeling object
getProtocol_labeling_ref() - Method in class object.microarray.Protocol_labeling
Reference of this Protocol_labeling object
getProvider_id() - Method in class object.microarray.Provider
ID of Provider object
getProvider_ref() - Method in class object.microarray.Provider
Name of the Provider Object
getPsl_coord() - Method in class object.annotation.Sonde
PSL Genome Coordinates
getPublic_database_id() - Method in class object.common.Public_database
ID of Public_database Object
getPubmed() - Method in class object.annotation.GenbankRef
Reference of this GenbankRef object
getPvalue() - Method in class object.common.RNAhybrid
pvalue
getPvalue() - Method in class object.microrna.Match
pvalue
getPvalue() - Method in class object.microrna.Mirna_target
pvalue
getQuantif_file() - Method in class object.microarray.Quantification_file
Path to the file of this Object
getQuantif_file() - Method in class object.microarray.Scan
Path to quantification file for this Scan object
getQuantification_file() - Method in class object.microarray.Scan
Quantification_file object associated with this Scan object
getQuery() - Method in class object.common.Search
Query string to search in the list of the type_recherche attribute
getQueryId() - Method in class object.common.BlastHit
Query id for the corresponding alignment
getQuerySequence() - Method in class object.common.BlastHit
Query sequence
getQueryStartPosition() - Method in class object.common.BlastHit
Start position on the query sequence
getQueryStopPosition() - Method in class object.common.BlastHit
Stop position on the query sequence
getQuestion_1() - Method in class object.common.Enquete
Question number 1
getQuestion_10() - Method in class object.common.Enquete
Question number 10
getQuestion_2() - Method in class object.common.Enquete
Question number 2
getQuestion_3() - Method in class object.common.Enquete
Question number 3
getQuestion_4() - Method in class object.common.Enquete
Question number 4
getQuestion_5() - Method in class object.common.Enquete
Question number 5
getQuestion_6() - Method in class object.common.Enquete
Question number 6
getQuestion_7() - Method in class object.common.Enquete
Question number 7
getQuestion_8() - Method in class object.common.Enquete
Question number 8
getQuestion_9() - Method in class object.common.Enquete
Question number 9
getQuestion_9plus() - Method in class object.common.Enquete
Question number 9plus
getR_script() - Method in class object.common.Biostats
Path of R script file
getRatio() - Method in class object.microarray.ElementMap
Ratio Signal of the spot
getRatio() - Method in class object.microarray.Feature
Ratio Signal of the spot
getRatio_230() - Method in class object.hts.Hts_minseqe
 
getRatio_280() - Method in class object.hts.Hts_minseqe
 
getRayon() - Method in class object.microarray.ElementMap
rayon of the oligo on the Tiff image
getRayon() - Method in class object.microarray.Feature
rayon of the oligo on the Tiff image
getReal_micro_seq(String) - Method in class object.microrna.MicroCible
 
getRef() - Method in class object.microarray.SpotType
ref
getRefseq() - Method in class object.annotation.Estoligo_rel
Refseq accession number of ESTs
getRefseqBase() - Method in class object.annotation.Organism
Blastbase Object corresponding to the Refseq transcript blastbase of this Organism Object
getRegion() - Method in class object.microrna.MicroCible
gene region searched
getReponse() - Method in class object.common.Contact_client
Answer done to the client
getRequestErrorDescription() - Method in exception JRclient.RSrvException
 
getRequestErrorDescription(int) - Method in exception JRclient.RSrvException
 
getRequestReturnCode() - Method in exception JRclient.RSrvException
 
getResponsable() - Method in class object.common.Plateforme
Production administrator of the Plateforme Object
getResults() - Method in class object.common.Convert
Results of conversion
getRev_start() - Method in class object.microrna.Mstdata
rev_start
getReverse(String) - Method in class object.microrna.MicroCible
 
getReverse(String) - Method in class object.microrna.MicroSite
 
getRight() - Method in class object.common.Board
Right on this Project_order
getRin() - Method in class object.hts.Hts_minseqe
 
getRin_number() - Method in class object.microarray.Labeling
RNA integrity number for this Extraction object
getRnafold() - Method in class object.microrna.MatchMCB
rnafold
getRnafold() - Method in class object.microrna.Mstdata
rnafold
getRnahybrid() - Method in class object.microrna.MatchMCB
rnahybrid
getRnahybrid() - Method in class object.microrna.Mstdata
rnahybrid
getRng_id() - Method in class object.common.Order
RNG ID of the Microarray_order object related to this Order Object
getRounded(double) - Method in class object.common.Common
 
getRounded2(double) - Method in class object.common.Common
 
getRounded4(double) - Method in class object.common.Common
 
getRow() - Method in class object.annotation.Oligo_rel
Row of the oligo in the Plate Object (i.e.
getRow() - Method in class object.microarray.ElementMap
Row in Bloc in which the oligo is located
getRow() - Method in class object.microarray.Feature
Row in Bloc in which the oligo is located
getRstat() - Method in class object.common.ImageManager
Rstat
getSample_ref() - Method in class object.microarray.Labeling
Reference of this Sample object
getSanger_id() - Method in class object.annotation.Oligo_adhoc_match
Sanger_id for this Oligo_adhoc_match Object
getSanger_ref() - Method in class object.annotation.Oligo_adhoc_match
Sanger_ref for this Oligo_adhoc_match Object
getScan_id() - Method in class object.microarray.Scan
ID of this Scan object
getScan_ref() - Method in class object.microarray.Scan
Reference of this Scan object
getScanForMicroarray_id(int) - Method in class object.common.Common
This function returns a Scan Object according to the microarray_id received
getScanner_id() - Method in class object.microarray.Scanner
ID of this Scanner object
getScanner_ref() - Method in class object.microarray.Scanner
Reference of this Scanner object
getScore() - Method in class object.annotation.Oligo
not use
getScore() - Method in class object.annotation.Spodo_hit
score
getScore() - Method in class object.common.BlastHit
Score of the corresponding alignment
getSearch() - Method in class object.common.SessionObject
Search Object
getSeed_size() - Method in class object.microrna.MicroCible
Seed size searched
getSeed_start() - Method in class object.microrna.MicroCible
Seed start searched
getSeed_stop() - Method in class object.microrna.MicroCible
Seed stop searched
getSeedsWobble(String) - Method in class object.microrna.MicroCible
 
getSelectBoxColor(String, String) - Method in class object.common.Common
 
getSens() - Method in class object.annotation.Oligo_tiling
sens of this Oligo_tiling Object
getSEQForAN(String) - Method in class object.common.Common
This function returns the sequence for the accession number received
getSEQForGID(int) - Method in class object.common.Common
This function returns the sequence for the gene_id received
getSEQForOligo_adhoc_id(String) - Method in class object.common.Common
This function returns the sequence for the sonde reference received
getSeqOne() - Method in class object.common.BlastTwoSeq
The sequence entered in the first textarea of our form
getSeqToFold(String, String) - Method in class object.microrna.MicroCible
 
getSeqTwo() - Method in class object.common.BlastTwoSeq
The sequence entered in the second textarea of our form
getSequence() - Method in class object.annotation.Gene
RNA sequence of this Gene object
getSequence() - Method in class object.annotation.Oligo_control
Sequence of Oligo_control Object
getSequence() - Method in class object.annotation.Oligo_tiling
Sequence of Oligo_tiling Object
getSequence() - Method in class object.annotation.Sonde
Sequence of the Sonde Object
getSequence() - Method in class object.common.RNAfold
sequence
getSequence() - Method in class object.common.SequenceObject
Sequence object from Biojava API
getSequence() - Method in class object.microrna.Mcbdata
sequence
getSequence() - Method in class object.microrna.Mcbmatch
sequence
getSequence() - Method in class object.microrna.MicroCible
sequence
getSequence() - Method in class object.microrna.Mstdata
sequence
getSequence_name() - Method in class object.common.SequenceObject
Name of the sequenceObject Object
getSequenceBase() - Method in class object.annotation.Organism
Blastbase Object corresponding to the Mediante transcript blastbase of this Organism Object
getSequenceBR() - Method in class object.annotation.Sonde
This function returns the oligo_adhoc sequence fetch by 60
getSequenceOne() - Method in class object.common.BlastTwoSeq
Sequence object for our first sequence to align
getSequenceTwo() - Method in class object.common.BlastTwoSeq
Sequence object for our second sequence to align
getSerie_file() - Method in class object.common.Biostats
Path of serie file
getSerie_ok() - Method in class object.common.Rstat
serie_ok true when serie file has been validated
getSerieFile() - Method in class object.common.Rstat
Serie file
getServerVersion() - Method in class JRclient.Rconnection
get server version as reported during the handshake.
getShort_accession() - Method in class object.annotation.Oligo_adhoc
Short Accession of this Oligo_adhoc Object
getShort_slide_code() - Method in class object.microarray.Microarray
Short slide code of the Microarray Object
getShortName() - Method in class object.microarray.Feature
Short Name of Oligo object of this Feature
getShortref() - Method in class object.annotation.Genoligo_affy_rel
shortref
getShortref() - Method in class object.annotation.Probeset
shortref
getShortRef() - Method in class object.hts.Hts_type
ShortRef of this Microarray_project_type object
getShortRef() - Method in class object.microarray.Microarray_project_type
ShortRef of this Microarray_project_type object
getSid_for_mid(int) - Method in class object.common.Common
 
getSize() - Method in class object.annotation.Genoligo_rel
size of the Oligo Object on the sequence of the Gene Object
getSize() - Method in class object.annotation.Oligo_adhocRelation
Size of match of the oligo_adhoc on the Gene
getSize_of_support() - Method in class object.common.Attribution
Number of arrays or hts samples currently to attribute to the Order Object
getSize_spot() - Method in class object.common.ImageManager
Size of spot for features illustration
getSlide_code(String, int) - Method in class object.common.Common
This function returns the slide code of the Microarray ID from which we received
getSlide_code() - Method in class object.microarray.Microarray
Code of the Microarray Object
getSlide_code() - Method in class object.microarray.MicroarrayElement
Slide_code of the Microarray object corresponding to this MicroarrayElement
getSlide_codeForMicroarray_id(int) - Method in class object.common.Common
This function returns the slide code of the Microarray ID received
getSnip_sequence() - Method in class object.microrna.SnipMir
snip_sequence
getSoftware_id() - Method in class object.microrna.MicroTopTable
software_id
getSolution() - Method in class object.common.Foq
Action anwser to the problem observed
getSolvant() - Method in class object.microarray.Plate
Solvant use for this Plate object
getSonde(String, int, int) - Method in class object.microrna.MicroCible
 
getSonde_id() - Method in class object.annotation.Sonde
ID of Sonde Object
getSonde_type() - Method in class object.microrna.MicroSite
sonde_type
getSonde_type_id() - Method in class object.annotation.Sonde
ID of Sonde type
getSpecificity() - Method in class object.annotation.Specificity
String describing this Specificity Object
getSpo_ref() - Method in class object.microarray.Microarray_project_type
Spotting ref of this Microarray_project_type object for spotting from other Plateformes
getSpotter() - Method in class object.microarray.Spotting
Spotter Object
getSpotter_id() - Method in class object.microarray.Spotter
ID of Spotter object
getSpotter_ref() - Method in class object.microarray.Spotter
Reference of Spotter Object
getSpotting_id() - Method in class object.microarray.Control
ID of Spotting Object for which the control has been done
getSpotting_id() - Method in class object.microarray.Microarray
Spotting Object for this Microarray Object
getSpotting_id() - Method in class object.microarray.MicroarrayElement
ID of the Spotting Object parent of the Microarray object corresponding to this MicroarrayElement
getSpotting_id() - Method in class object.microarray.Spotting
ID of Spotting object
getSpotting_ref() - Method in class object.microarray.Spotting
Reference of Spotting object
getSpottype_file() - Method in class object.common.Biostats
Path of spottype file
getSpotTypeFile() - Method in class object.common.Rstat
Spot type file
getStade() - Method in class object.microarray.Labeling
Cancer stade of this Subject object
getStart() - Method in class object.annotation.Cytoband
Start of this Cytoband
getStart() - Method in class object.annotation.Exon
Start of the exon on the Chromosome corresponding for the Gene object
getStart() - Method in class object.annotation.GenomicPosition
Start position on the Chromosome Object concerned by this GenomicPosition Object
getStart() - Method in class object.microrna.Mstdata
start
getStat() - Method in class JRclient.Rpacket
get status code of last response
getState() - Method in class object.common.Order
State of this Microarray_order, it can be 'send', 'biostat', 'hybrid', 'prod', 'devis', 'reject', 'cancel' or 'wait'
getStepFourDone() - Method in class object.microarray.Spotting
 
getStepOneDone() - Method in class object.common.Attribution
Flag set to true when step one is done
getStepOneDone() - Method in class object.microarray.Spotting
 
getStepThreeDone() - Method in class object.microarray.Spotting
 
getStorage() - Method in class object.microarray.Plate
Strorage used for this Plate object
getStorage_id() - Method in class object.microarray.Storage
ID of Storage object
getStorage_ref() - Method in class object.microarray.Storage
Name of the Storage Object
getStrand() - Method in class object.annotation.GenomicPosition
Strand for this GenomicPosition Object
getStrand() - Method in class object.microrna.Mirna_chromosome
strand
getStringViewers(int) - Method in class object.common.Project
This function return the list of viewers concerning this project Object
getSubject_ref() - Method in class object.microarray.Labeling
Reference of this Subject object
getSupportedLocale(Locale[]) - Method in class common.beans.locale.LocaleBean
Returns the first Locale that matches a supported language, or the default Locale if no match.
getSupportInfo() - Method in class object.common.Order
 
getSValue() - Method in class object.common.Blast
Value of S value for executing Blast program
getSValue() - Method in class object.common.BlastTwoSeq
Value of S value for executing Blast program
getSValue() - Method in class object.common.SessionBlastObject
S value for the Blast ( '1' is single strain (direct), '2' for single strain (indirect), '3' for both)
getSymbol() - Method in class object.annotation.Gene
Gene symbol (name)
getSymbol() - Method in class object.annotation.Genoligo_affy_rel
Symbol
getSymbol() - Method in class object.annotation.Oligo_annotation
Gene symbol associated to this relation
getSymbol() - Method in class object.annotation.Probeset
symbol
getSymbol() - Method in class object.common.Point
Gene symbol associated with this Point Object
getSymbol() - Method in class object.microarray.ElementMap
Symbol of Oligo object of this ElementMap
getSymbol() - Method in class object.microrna.Match
symbol
getSymbol() - Method in class object.microrna.Mcbdata
symbol
getSymbol() - Method in class object.microrna.Mirna_target
symbol
getSymbol() - Method in class object.microrna.TargetPrediction
symbol
getSymbolForGeneList(String) - Method in class object.common.Common
This function returns a String containing distinct gene symbol from Gene Object
belonging to the Project Object with the ID received as a String.
getSymbolForGO(int, String) - Method in class object.common.Common
This function returns a String containing distinct gene symbol for gene Ontology term
getSymbolForMirna_mature(String) - Method in class object.common.Common
This function returns a String containing distinct gene symbol of gene predicted as target of the Mirna_mature auto_mature received
for mirna_target_tool_id = 4 (default).
getSymbolForOAID(int) - Method in class object.common.Common
This function returns the annotation for the oligo_adhoc_id received
getSymbolSearch() - Method in class object.common.DisplayParams
List of string symbol asked for image display, without internal modifications
getSynonym() - Method in class object.annotation.Gene
Gene symbol (synonyms)
getTag() - Method in class JRclient.RList
get tag xpression
getTaille() - Method in class object.annotation.Sonde
Length of the sequence of the Sonde Object
getTarget() - Method in class object.common.RNAhybrid
target
getTarget() - Method in class object.microrna.MatchMCB
target
getTargetScanLink(String, String, String) - Method in class object.common.Link
 
getTaxonomy_id() - Method in class object.annotation.Organism
Taxonomy ID from external database (9606 from Homo Sapiens and 10090 for Mus musculus)
getTelephone() - Method in class object.common.Plateforme
Phone number of Plateforme Object
getTelephone() - Method in class object.common.User
Phone number of the User Object
getTemperature() - Method in class object.microarray.Hybridization
Temperature for this Hybridization
getTemps() - Method in class object.microarray.Hybridization
Duration for this Hybridization
getTemps_creation() - Method in class object.common.CreationPlate
Time of creation plate (not use)
getTemps_creation() - Method in class object.microarray.Plate384
Creation time for the Plate384 creation process
getTerm() - Method in class object.annotation.GoLink
Term describing the Gene Ontology link with the gene
getTerm() - Method in class object.microrna.Target
Term of the Target Object
getTestHash() - Method in class object.common.Common
This function return a Hashtable containing the ID and REF of Plate Object from plate SQL table.
getText(String) - Method in class common.beans.locale.LocaleBean
Returns the text resource for the specified key, with the best match for the currently selected locale.
getText() - Method in class object.microarray.MageProtocol
text of this MageProtocol Object
getTexteEmail(String) - Method in class object.common.Common
 
getTIP_BG() - Method in class object.common.OnMouseOver
Background color of Tips
getTIP_FONT() - Method in class object.common.OnMouseOver
Font of Tips
getTissue() - Method in class object.hts.Hts_minseqe
Tissue Object from which this Hts_minseqe object come from
getTissue() - Method in class object.microarray.Labeling
Tissue Object from which this Sample object come from
getTissue_id() - Method in class object.annotation.Tissue
Tissue ID
getTissue_ref() - Method in class object.annotation.Tissue
Tissue ref
getTitle() - Method in class object.microarray.GeoSerie
title of GeoSerie object
getTitle() - Method in class object.microrna.Mirna_reference
title
getTITLE_BG() - Method in class object.common.OnMouseOver
Background color of Title
getTITLE_FONT() - Method in class object.common.OnMouseOver
Font of Title
getTitre() - Method in class object.annotation.GenbankRef
Title of this GenbankRef object
getTm() - Method in class object.annotation.Oligo_tiling
Tm of Oligo_tiling Object
getTm() - Method in class object.annotation.Sonde
Melting temperature of the Sonde Object
getTmpDir() - Method in class object.common.Biostats
tmp DIR in case of Mediante online Rstat production
getToolBoxHts_analysis(int) - Method in class object.common.Common
 
getToolBoxHts_pipeline(int) - Method in class object.common.Common
 
getToolBoxHts_run(int) - Method in class object.common.Common
 
getToolBoxMicroarray(String, int) - Method in class object.common.Common
This function returns a Vector containing ToolBox Object concerning all the Spotting Object not yet Cross linked
getToolBoxSpotting(int, boolean) - Method in class object.common.Common
This function returns a Vector containing ToolBox Object concerning all the Spotting Object associated to the ID of Plateforme Object received
getToptable() - Method in class object.common.ImageManager
Toptable for features filtration
getToptable_file() - Method in class object.common.Toptable
Path of Toptable file
getToptable_gene() - Method in class object.microrna.MicroTopTable
toptable_gene
getToptable_id() - Method in class object.common.Toptable
ID of Toptable Object
getToptable_image() - Method in class object.common.Toptable
Path of Toptable image
getToptable_micro() - Method in class object.microrna.MicroTopTable
toptable_micro
getToptable_ref() - Method in class object.common.Toptable
reference of Toptable Object
getToptableForUser(User) - Method in class object.common.Common
 
getTranscript_id() - Method in class object.microrna.Mirna_context
transcript_id
getTranscript_name() - Method in class object.microrna.Mirna_context
transcript_name
getTranscript_source() - Method in class object.microrna.Mirna_context
transcript_source
getTreatment() - Method in class object.hts.Hts_minseqe
 
getTwoMuch() - Method in class object.common.Search
boolean : true when the search found two much Gene Objects ( limit is attribute : NB_MAX_RESULTS)
getTwoMuch() - Method in class object.microrna.MicroCible
boolean : true when the search found two much Gene Objects ( limit is attribute : NB_MAX_RESULTS)
getTxt_file() - Method in class object.microarray.Spotting
.TXT File describing this Spotting Object
getType() - Method in class JRclient.REXP
get xpression type (see XT_.. constants) of the content.
getType() - Method in class object.annotation.Term
Type of this Gene Ontology term
getType() - Method in class object.common.Biostats
Type of normalized files
getType() - Method in class object.hts.Hts_analysis_parameter
type
getType() - Method in class object.hts.Hts_pipeline_parameter
type
getType() - Method in class object.microarray.MageProtocol
type of this MageProtocol Object
getType() - Method in class object.microarray.Scan
Type of scan
getType_contact() - Method in class object.common.Contact_client
Type contact (mail or phone)
getType_convert() - Method in class object.common.Convert
Type of conversion
getType_fichier() - Method in class object.common.Fichier
Type of this Fichier object
getType_file() - Method in class object.microarray.Quantification_file
Type of the file (Agilent or Genepix)
getType_foq() - Method in class object.common.Foq
Type of the Foq Object
getType_graphe() - Method in class object.common.ImageManager
Type of graph for visualization (directory : 'graph')
getType_recherche() - Method in class object.common.Search
Type of search to proceed (can be : id_reference, keyword, geneOntology or cytoband)
getUnigene_id() - Method in class object.annotation.Gene
Unigene reference for this Gene Object - Unigene Database
getUnite() - Method in class object.common.User
Unite
getUnreleased() - Method in class object.microarray.GeoSerie
unreleased
getUser() - Method in class object.common.Board
User owner of this Board Object
getUser() - Method in class object.common.Board_user
 
getUser() - Method in class object.common.GeneCart
User owner of this GeneCart Object
getUser() - Method in class object.common.Keyword
User owner of this Keyword Object
getUser() - Method in class object.common.Order
User owner of the Microarray_order object related to this Order Object
getUser() - Method in class object.common.SessionObject
User object, user curently browsing the web Interface
getUser() - Method in class object.hts.Hts_sample
User owner of this Hts_sample Object
getUser() - Method in class object.microarray.Microarray
User owner of this Microarray Object
getUser() - Method in class object.microarray.Plate
User who have created this Plate object
getUser() - Method in class object.microarray.Project_order
User owner of this Project_order object
getUser() - Method in class object.microarray.Spotting
User of this Spotting
getUser_dest_id() - Method in class object.common.Foq
ID of User Object for which the Foq Object is destinate
getUser_dilution() - Method in class object.microarray.Plate384
User that have been proceeded to the dilution process
getUser_hybrid() - Method in class object.common.Order
ID of user going to hybridize the microarrays for this order
getUser_id() - Method in class object.common.Contact_client
ID of User object who get the contatc whith the client
getUser_id() - Method in class object.common.Convert
ID of the Organism concerning by the search
getUser_id() - Method in class object.common.Foq
ID of User Object who describe the Foq Object
getUser_id() - Method in class object.common.ImageManager
ID of User owning this ImageManager Object
getUser_id() - Method in class object.common.Journal
ID of User owner of this journal Object
getUser_id() - Method in class object.common.Rstat
user_id
getUser_id() - Method in class object.common.User
ID of User object
getUser_id() - Method in class object.hts.Hts_RManager
user_id
getUser_idForMPT_id(int) - Method in class object.common.Common
This function return the User ID parameter of a User Object owner of
the Default Microarray_order Object for this Microarray_project_type Object received.
getUser_idForProject_order_id(int) - Method in class object.common.Common
This function returns the User Object ID owner of the Project_order Object ID received.
getUser_owner() - Method in class object.common.Project
ID of User Object owner of this Project Object
getUser_owner() - Method in class object.common.ProjectObject
ID of the User owner of this Project
getUser_viewer() - Method in class object.common.Project
String of IDs of User curently viewer of this Project Object
getUser_writer() - Method in class object.common.Project
ID of User Object curently the only writer for this Project Object
getUser_writer() - Method in class object.common.ProjectObject
ID of the User currently writer of this Project
getValidPathFile(String) - Method in class object.common.Common
 
getValue() - Method in class object.common.ToolBox
value of the ToolBox object
getValue() - Method in class object.common.ToolBoxString
value of the ToolBoxString object
getValue() - Method in class object.hts.Hts_analysis_parameter
value
getValue() - Method in class object.hts.Hts_pipeline_parameter
value
getVariableInfo(TagData) - Method in class common.tags.generic.UseLocaleBundleTagExtraInfo
 
getVectorAdminBiol() - Method in class object.common.Plateforme
This function return a Vector of String concerning Globals administrators e-mails for this Platforme Object.
getVectorAdministrator() - Method in class object.common.Plateforme
This function return a Vector of String concerning Plateforme administrators e-mails for this Platforme Object.
getVectorAdministratorDevis() - Method in class object.common.Plateforme
This function return a Vector of String concerning devis administrators e-mails for this Platforme Object.
getVectorAnnotations() - Method in class object.annotation.Gene
Vector of GoLink Object for this Gene object
getVectorBiostats() - Method in class object.microarray.Project_order
Vector of Biostats object associated in this Project_order object
getVectorCMD() - Method in class object.common.Rstat
Vector containing Command to R
getVectorCMD() - Method in class object.hts.Hts_RManager
Vector containing Command to R
getVectorCommande() - Method in class object.annotation.Oligo
Vector of Commande Object in which this Oligo have been ordered
getVectorControl() - Method in class object.microarray.Spotting
Vector of Control Object in this Spotting Object
getVectorControl(Vector) - Method in class object.microarray.Spotting
 
getVectorCytobands() - Method in class object.annotation.Gene
Vector of Cytoband Object for this Gene object
getVectOrderedNames() - Method in class object.hts.Hts_pipeline
vectOrderedNames
getVectorExons() - Method in class object.annotation.Gene
Vector of Exons Object which composed this Gene object
getVectorGenbankRef() - Method in class object.annotation.Gene
Vector of GenbankRef Object for this Gene object
getVectorGenes() - Method in class object.common.Search
Vector of Gene Objects found with this search
getVectorGenoligo_rel() - Method in class object.annotation.Sonde
Vector containing relation with Gene Object concerning this Sonde Object
getVectorHitOrdre() - Method in class object.common.Blast
Vector containing the order of the sequence in which the Blast program proceed
getVectorHts_order() - Method in class object.hts.Hts_RManager
Vector containing Hts_order Objects
getVectorHts_order() - Method in class object.microarray.Project_order
Vector of Hts_order object associated in this Project_order object
getVectorHts_result() - Method in class object.hts.Hts_sample
Hts_result(s) Vector for this Hts_sample Object
getVectorHts_sample() - Method in class object.common.Attribution
Vector of Hts_sample Object in attribution
getVectorHts_sample() - Method in class object.hts.Hts_order
Vector containing Hts_sample Objects corresponding this Hts_order
getVectorHts_sample() - Method in class object.hts.Hts_RManager
Vector containing Hts_sample Objects
getVectorHts_sample() - Method in class object.hts.Hts_run
Vector of Hts_sample Object creating by this Hts_run Object
getVectorHybridator(int) - Method in class object.common.Plateforme
This function return a Vector of String concerning hybriddators e-mails for this Platforme Object.
getVectorInfos() - Method in class object.annotation.Oligo_control
This function return a Vector of informations concerning this Oligo_control Object.
getVectorInfos() - Method in class object.annotation.Oligo_tiling
This function return a Vector of informations concerning this Oligo_control Object.
getVectorInfos(Gene) - Method in class object.annotation.Sonde
This function returns a Vector with the list of the Informations available for this Oligo object.
getVectorJournal() - Method in class object.common.Order
Vector containing journal actions event for this order Object
getVectorKeys() - Method in class object.microrna.MapTarget
vectorKeys
getVectorKeys() - Method in class object.microrna.MicroCible
Vector of keys ordered
getVectorKeys() - Method in class object.microrna.MicroSite
Vector of keys ordered
getVectorKeys() - Method in class object.microrna.MicroTopTable
Vector of keys ordered
getVectorKeys() - Method in class object.microrna.TargetPrediction
Vector of keys ordered
getVectorKeyword() - Method in class object.microarray.Project_order
Vector of Keyword object associated in this Project_order object
getVectorKeywords(User) - Method in class object.common.Common
This function returns a Vector containing Keyword Objects for User Object received
getVectorLabeling() - Method in class object.microarray.Hybridization
Vector of Labeling used for this Hybridization Object
getVectorMatch() - Method in class object.microrna.Mttdata
vectorMatch
getVectorMatch() - Method in class object.microrna.Target
vectorMatch
getVectorMatchMCB() - Method in class object.microrna.Mcbmatch
vectorMatchMCB
getVectorMicroarray() - Method in class object.common.Attribution
Vector of Microarray Object in attribution
getVectorMicroarray() - Method in class object.common.Rstat
Vector containing Microarrays Objects corresponding this Microarray_order
getVectorMicroarray() - Method in class object.microarray.Microarray_order
Vector containing Microarrays Objects corresponding this Microarray_order
getVectorMicroarray() - Method in class object.microarray.Spotting
Vector of Microarray Object creating by this Spotting Object
getVectorMicroarray_order() - Method in class object.microarray.Project_order
Vector of Microarray_order object associated in this Project_order object
getVectorMicroarray_project_type() - Method in class object.common.Common
 
getVectorMicroarrayForPlateforme(Plateforme) - Method in class object.common.Common
This function returns a Vector containing ToolBox Object concerning microarray Object produced by Plateforme Object received
getVectorMicroarrays() - Method in class object.common.ImageManager
Vector containing Microarray Objects selected for visualization
getVectorMirna_chromosome() - Method in class object.microrna.Mirna
vectorMirna_chromosome
getVectorMirna_context() - Method in class object.microrna.Mirna
vectorMirna_context
getVectorMirna_mature() - Method in class object.annotation.Oligo_adhoc
 
getVectorMirna_reference() - Method in class object.microrna.Mirna
vectorMirna_reference
getVectorMirna_target() - Method in class object.microrna.MapTarget
vectorMirna_target
getVectorMPTForPF(String, Plateforme) - Method in class object.common.Common
This function returns a Vector containing ToolBox Object concerning type Object received for the Plateforme Object received.
getVectorOligo_adhocRelation() - Method in class object.annotation.Gene
Vector of PcrRelation Object for this Gene object
getVectorOligos() - Method in class object.annotation.Gene
Vector of Oligo Object matching this Gene object
getVectorOrdered() - Method in class object.microrna.TargetPrediction
Vector of name ordered
getVectorPlate() - Method in class object.microarray.Spotting
 
getVectorPlate384() - Method in class object.common.Dilution
Vector of Plate384 Object concerning by this dilution process
getVectorPlate384() - Method in class object.microarray.Spotting
Vector of Plate384 Object concerning this Spotting Object
getVectorPO(User) - Method in class object.common.Common
This function returns a Vector containing toolBox Object of Project_order owned by the User Object received order by date_project_order
getVectorPO_view(User) - Method in class object.common.Common
This function returns a Vector containing toolBox Object of Project_order visualisable by the User Object received order by date_project_order
getVectorPOForUser(int) - Method in class object.common.Common
This function return a Vector containing ToolBox Object of Project_order Objects (project_order_id, project_order_ref) owning by the user received
getVectorProductor() - Method in class object.common.Plateforme
This function return a Vector of String concerning microarrays productors e-mails for this Platforme Object.
getVectorProject_order() - Method in class object.common.Board_user
vectorProject_order for this Board Object
getVectorScan() - Method in class object.microarray.Microarray
Scan(s) Vector for this Microarray Object
getVectorSequence() - Method in class object.microrna.MicroSite
Vector of sequence
getVectorSequenceObject() - Method in class object.common.Project
Vector containing the order of SequenceObject composing this Project Object in which we have to display the SequenceObject in the web interface
getVectorSequenceOrdre() - Method in class object.common.SessionBlastObject
Vector of Sequences needed to blast in the order of the user
getVectorSerie() - Method in class object.microarray.SerieFile
Vector of Serie of SerieFile object
getVectorSlideList(String, ImageManager) - Method in class object.common.Common
This function return a Vector containing slide_code of Microarray Objects contained in the Project_order of the ImageManager Object and not selected in the vectorMicroarrays parameter of the ImageManager Object.
getVectorSondes() - Method in class object.common.Search
Vector of Sondes Objects found with this search
getVectorSpodo_hits() - Method in class object.annotation.Oligo_adhoc
 
getVectorSpotType() - Method in class object.microarray.SpotTypeFile
Vector of spotType of SpotTypeFile object
getVectorToolBox(String) - Method in class object.common.Common
This function returns a Vector containing ToolBox Object concerning type Object received.
getVectorToptable() - Method in class object.microarray.Project_order
Vector of Toptable object associated in this Project_order object
getViewers() - Method in class object.common.Project
This function return the list of the viewers of the Project Object separated by '
'
getVille() - Method in class object.common.User
Town of User object
getVille_fact() - Method in class object.common.User
Billing town of User object
getVille_livr() - Method in class object.common.User
Sending town of User object
getVolume() - Method in class object.common.CreationPlate
Volume from Plate 96 to Plate 384
getVolume() - Method in class object.common.Dilution
Volume of the dilution
getVolume() - Method in class object.microarray.Plate
Volume of oligo in this Plate object
getVrk_file() - Method in class object.microarray.Spotting
.VRK File describing this Spotting Object
getVsm_file() - Method in class object.microarray.Spotting
.VSM File describing this Spotting Object
getWavelength() - Method in class object.microarray.Labeling_type
wavelength default of this Labeling_type object
getWhatIsValue() - Method in class object.microarray.Quantification_file
The meaning of The Value (feature.getLogratio())
getWorkingDIR() - Method in class object.common.Rstat
workingDIR
getWorkingDIR() - Method in class object.hts.Hts_RManager
workingDIR
getWValue() - Method in class object.common.Blast
Value of W value for executing Blast program
getWValue() - Method in class object.common.BlastTwoSeq
Value of W value for executing Blast program
getWValue() - Method in class object.common.SessionBlastObject
W value for the Blast (length of minmal identical word to find)
getX() - Method in class object.common.Point
X coord on the microarray for this Point Object
getX_coord() - Method in class object.microarray.ElementMap
X_coord of the oligo on the Tiff image
getX_coord() - Method in class object.microarray.Feature
X_coord of the oligo on the Tiff image
getX_pos() - Method in class object.annotation.EstTissue
x_pos
getXhybrid() - Method in class object.annotation.Specificity
X_hybridation concerning this Specificity Object
getXhybrid_max() - Method in class object.annotation.Sonde
H_HYBRID value for this Sonde Object
getXhybridMatch() - Method in class object.annotation.Gene
list of Xhybrid match along the transcript
getXsome() - Method in class object.microrna.Mirna_chromosome
xsome
getY() - Method in class object.common.Point
Y coord on the microarray for this Point Object
getY_coord() - Method in class object.microarray.ElementMap
Y_coord of the oligo on the Tiff image
getY_coord() - Method in class object.microarray.Feature
Y_coord of the oligo on the Tiff image
getY_pos() - Method in class object.annotation.EstTissue
y_pos
getZipcode() - Method in class object.common.User
Zipcode of User object
getZipcode_fact() - Method in class object.common.User
Billing Zipcode of User object
getZipcode_livr() - Method in class object.common.User
Sending Zipcode of User object
gi - Variable in class object.annotation.Estoligo_rel
List of Gi number corresponding to the refseq accession number of ESTs
giveTo(int) - Method in class object.common.Project
This function allowed to give the Project to an other user, only called if the user is the owner or the current writer
go_acc - Variable in class object.annotation.Term
Gene Ontology accession
GoLink - Class in object.annotation
Description
Resume the relation between a Gene and the Term of the Gene Ontology
Infos : KLB - IPMC - 12/2003
GoLink() - Constructor for class object.annotation.GoLink
Default constructor
GoLink(int, Term) - Constructor for class object.annotation.GoLink
Constructs a GoLink object from a gene_id and a Term from the Gene Ontology
gps_file - Variable in class object.microarray.Scan
Path to quantification settings file for this Scan object
grade - Variable in class object.microarray.Labeling
Cancer grade of this Subject object
Graph - Class in object.common
Description
Graph object
Infos : KLB - IPMC - 05/2008
Graph() - Constructor for class object.common.Graph
Default constructor
GUwobble - Variable in class object.microrna.MicroCible
true if search concerns GU wobble match

H

h - Variable in class JRclient.RList
usual assumption is that both head and body are xpressions containing vectors.
hash - Variable in class object.common.GeneCart
hashtable containing Symbol and Oligo IDs
hashBeadToSeq - Variable in class object.hts.MaFile
 
hashBlocs - Variable in class object.microarray.Quantification_file
Datas
hashCalcul - Variable in class object.common.ImageManager
Hashtable containing values of calcul asked by user
hashColor - Static variable in class object.common.ImageManager
 
hashCols - Variable in class object.common.Biostats
Hashtable containing first line of biostats files
hashColumns - Variable in class object.microarray.Pattern_file
Columns
hashColumns - Variable in class object.microarray.Quantification_file
Columns
hashCoord - Variable in class object.microarray.Quantification_file
Datas
hashData - Variable in class object.microrna.TargetPrediction
Results for this search
hashDatas - Variable in class object.common.ImageManager
Hashtable containing Quantification_file Object
hashDown - Variable in class object.microrna.Mttdata
hashDown
hashFeatures - Variable in class object.microarray.Quantification_file
Datas
hashFile - Variable in class object.common.ImageManager
Hashtable containing Files path downloadables
hashFiles - Variable in class object.hts.Hts_RManager
Hashtable containing Listing of available files for this Hts_RManager query
hashGenes - Variable in class object.microrna.MicroCible
 
hashGenoligo_affy_rel - Variable in class object.common.Search
Hashtable of Genoligo_affy_rel Objects found with this search
hashGenoligo_rel - Variable in class object.annotation.Sonde
Hashtable containing relation with Gene Object concerning this Sonde Object
hashGoFrequence - Variable in class object.microrna.MapTarget
hashKeys
hashGroupLabel - Variable in class object.hts.Hts_RManager
Hashtable containing Hts_sample group labels
hashID - Variable in class object.microarray.Pattern_file
IDs
hashImage - Variable in class object.common.ImageManager
Hashtable containing Images path displayed on screen
hashKeys - Variable in class object.microrna.MapTarget
hashKeys
hashLegend - Static variable in class object.common.ImageManager
 
hashMaMatch - Variable in class object.hts.MaFile
 
hashMap - Variable in class object.common.ImageManager
Hashtable containing Html Maps for Images displayed on screen
hashMcbdata - Variable in class object.microrna.MicroCible
Results for this search
hashMcbmatch - Variable in class object.microrna.Mcbdata
hashMcbMatch
hashMicros - Variable in class object.microrna.MicroCible
 
hashMirna_target - Variable in class object.annotation.Gene
Hash of Target with key is the tool of target prediction
hashMirna_target - Variable in class object.microrna.Mirna_mature
Hash of Target with key is the tool of target prediction
hashMstdata - Variable in class object.microrna.MicroSite
Results for this search
hashMttdata - Variable in class object.microrna.MicroTopTable
 
hashName - Variable in class object.microarray.Pattern_file
Names
hashOligoPosition - Variable in class object.microarray.Plate
Hashtable of Oligo_rel Object for this Plate object
hashOligosAffy - Variable in class object.annotation.Gene
Hashtable of Oligo_affy Object matching this Gene object
hashOligosExternes - Variable in class object.annotation.Gene
Hashtable of Oligo_externe Object matching this Gene object
hashOutFile - Variable in class object.hts.Hts_pipeline
 
hashParameter - Variable in class object.hts.Hts_analysis
 
hashParameter - Variable in class object.hts.Hts_pipeline
 
hashPlate96 - Variable in class object.common.CreationPlate
Hashtable containing Plate 96 Object concerning with this creation Plate Object process
hashPosition - Variable in class object.microarray.Spotting
 
hashPredicted - Variable in class object.microrna.Mttdata
hashPredicted
hashRefGenmate - Variable in class object.common.CreationPlate
Hashtable containing reference slide code of new Plate 384 in creation
hashRefNumber - Variable in class object.microarray.Pattern_file
RefNumber
hashScore - Variable in class object.microarray.Feature
Hashtable of score for this feature
hashSequenceObject - Variable in class object.common.SessionBlastObject
Hashtable of Sequences needed to blast
hashSpecificity - Variable in class object.annotation.Sonde
Hashtable containing specificity informations concerning this Sonde Object
hashStarts - Variable in class object.microrna.MicroCible
 
hashSymbol - Variable in class object.microrna.Mttdata
accession
hashSymbols - Variable in class object.microarray.Quantification_file
Datas
hashtableBlastHit - Variable in class object.common.Blast
Hashtable containing the list of the BlastHit object results of the Blast
hashTarget - Variable in class object.microrna.MapTarget
hashTarget
hashTissues - Variable in class object.common.MapEST
hashTissues
hashUp - Variable in class object.microrna.Mttdata
hashUp
head - Variable in class JRclient.RList
xpressions containing head and body.
header - Variable in class object.microarray.SerieFile
header of SerieFile Object
header - Variable in class object.microarray.SpotTypeFile
header of SpotTypeFile Object
headers - Variable in class object.microarray.Pattern_file
Headers of patter_file Object
Histology - Class in object.annotation
Description
Histology of tissue
Infos : KLB - IPMC - 07/2004
Histology() - Constructor for class object.annotation.Histology
Default constructor
histology - Variable in class object.microarray.Labeling
Cancer histology of this Subject object
histopathology_number - Variable in class object.hts.Hts_minseqe
 
hitId - Variable in class object.common.BlastHit
Hit id for the corresponding alignment
hitSequence - Variable in class object.common.BlastHit
Hit sequence
hitStartPosition - Variable in class object.common.BlastHit
Start position on the hit sequence
hitStopPosition - Variable in class object.common.BlastHit
Stop position on the hit sequence
host - Variable in class JRclient.Rconnection
 
host - Variable in class JRclient.RSession
 
howWeNormalized - Variable in class object.microarray.Quantification_file
 
HPERM_OP(int, int, int) - Static method in class JRclient.jcrypt
 
href_microcible_1 - Static variable in class object.common.Link
Http Url link to Internal Microcible
href_microcible_2 - Static variable in class object.common.Link
 
href_microcible_3 - Static variable in class object.common.Link
 
href_microcible_4 - Static variable in class object.common.Link
 
href_microcible_5 - Static variable in class object.common.Link
 
href_mirbasetarget_1 - Static variable in class object.common.Link
Http Url link to TargetScan 5.0
href_mirbasetarget_2 - Static variable in class object.common.Link
 
href_mirbasetarget_3 - Static variable in class object.common.Link
 
href_targetscan_1 - Static variable in class object.common.Link
Http Url link to TragetScan 5.0
href_targetscan_2 - Static variable in class object.common.Link
 
href_targetscan_3 - Static variable in class object.common.Link
 
href_targetscan_4 - Static variable in class object.common.Link
 
href_tp_1 - Static variable in class object.common.Link
 
href_tp_2 - Static variable in class object.common.Link
 
hrefEnsg - Static variable in class object.common.Link
Http Url link to Ensembl database for viewing a Homo sapiens Gene details
hrefEnsgMouse - Static variable in class object.common.Link
Http Url link to Ensembl database for viewing a Mus musculus Gene details
hrefEnsgRattus - Static variable in class object.common.Link
Http Url link to Ensembl database for viewing a Mus musculus Gene details
hrefEnst - Static variable in class object.common.Link
Http Url link to Ensembl database for viewing a Homo sapiens Transcript details
hrefEnstMouse - Static variable in class object.common.Link
Http Url link to Ensembl database for viewing a Mus musculus Transcript details
hrefEnstRattus - Static variable in class object.common.Link
Http Url link to Ensembl database for viewing a Mus musculus Transcript details
hrefEST - Static variable in class object.common.Link
Http Url link to NCBI website to see EST details
hrefGb_gene_id - Static variable in class object.common.Link
Http Url link to GENBANK_GENE_ID database for viewing GENBANK_GENE id cluster details
hrefGBLink_mgi - Static variable in class object.common.Link
Http Url link to MGD database
hrefGBLink_mim - Static variable in class object.common.Link
Http Url link to OMIM database
hrefGBLink_rgd - Static variable in class object.common.Link
Http Url link to RGD database
hrefGenbank_gene_id - Static variable in class object.common.Link
Http Url link to NCBI website to see Gene details
hrefGeneCard - Static variable in class object.common.Link
Http Url link to GENE CARDS
hrefGi - Static variable in class object.common.Link
Http Url link to NCBI website to see GI details
hrefGo - Static variable in class object.common.Link
Http Url link to GO(Gene Ontology) database
hrefMICIB_1 - Static variable in class object.common.Link
Http Url link to IPMC CIBLE tool
hrefMICIB_2 - Static variable in class object.common.Link
 
hrefMiranda - Static variable in class object.common.Link
Http Url link to Sanger institute to see Miranda targets
hrefMiRNAMAP_1 - Static variable in class object.common.Link
Http Url link to miRNA MAP 2.0
hrefMiRNAMAP_2 - Static variable in class object.common.Link
 
hrefmiRNASanger - Static variable in class object.common.Link
Http Url link to Sanger website miRNA informations
hrefProtein - Static variable in class object.common.Link
Http Url link to NCBI for protein
hrefPubmed - Static variable in class object.common.Link
Http Url link to NCBI website to see PUbmed publication
hrefRefseq - Static variable in class object.common.Link
Http Url link to NCBI website to see Refseq accession number details
hrefSRS_1 - Static variable in class object.common.Link
Http Url link to SwissProt SRS
hrefSRS_2 - Static variable in class object.common.Link
 
hrefSRS_3 - Static variable in class object.common.Link
 
hrefUCSC_1 - Static variable in class object.common.Link
Http Url link to UCSC genome browser
hrefUCSC_2 - Static variable in class object.common.Link
 
hrefUnigene - Static variable in class object.common.Link
Http Url link to Unigene database for viewing cluster Unigene id detail, first part
hrefUnigene2 - Static variable in class object.common.Link
 
hrefUnigeneEST - Static variable in class object.common.Link
Http Url link to NCBI website to see Unigene est profiler system
Hts_analysis - Class in object.hts
Description
Hts_analysis Object
Infos : KLB - IPMC - 12/2009
Hts_analysis() - Constructor for class object.hts.Hts_analysis
Default constructor
Hts_analysis(int) - Constructor for class object.hts.Hts_analysis
Constructs a Hts_analysis object from an existing Hts_analysis ID
hts_analysis - Variable in class object.hts.Hts_RManager
 
hts_analysis_id - Variable in class object.hts.Hts_analysis
ID of this Hts_analysis object
Hts_analysis_parameter - Class in object.hts
Description
Hts_analysis_parameter Object
Infos : KLB - IPMC - 09/2009
Hts_analysis_parameter() - Constructor for class object.hts.Hts_analysis_parameter
Default constructor
Hts_analysis_parameter(String, String, String, String, String) - Constructor for class object.hts.Hts_analysis_parameter
Constructs a Hts_analysis_parameter object
hts_analysis_ref - Variable in class object.hts.Hts_analysis
Reference of this Hts_analysis object
Hts_extraction - Class in object.hts
Description
Hts_extraction Object belong to Hts_extraction Object
Infos : KLB - IPMC - 09/2009
Hts_extraction() - Constructor for class object.hts.Hts_extraction
Default constructor
Hts_extraction(int) - Constructor for class object.hts.Hts_extraction
Constructs a Hts_extraction object from an existing Hts_extraction ID.
hts_extraction - Variable in class object.hts.Hts_minseqe
Hts extraction protocol used for this Hts_minseqe object
hts_extraction_id - Variable in class object.hts.Hts_extraction
ID of this Hts_extraction object
hts_extraction_ref - Variable in class object.hts.Hts_extraction
Reference of this Hts_extraction object
Hts_minseqe - Class in object.hts
Description
Infos : KLB - IPMC - 09/2009
Hts_minseqe() - Constructor for class object.hts.Hts_minseqe
Default constructor
Hts_minseqe(int) - Constructor for class object.hts.Hts_minseqe
Constructs an Hts_minseqe object from an existing Hts_minseqe ID
hts_minseqe - Variable in class object.hts.Hts_sample
Hts_minseqe of this Hts_sample object
hts_minseqe_id - Variable in class object.hts.Hts_minseqe
ID of this Hts_minseqe Object
hts_minseqe_ref - Variable in class object.hts.Hts_minseqe
Reference of this Hts_minseqe Object
Hts_order - Class in object.hts
Description
Hts_order Object
Infos : KLB - IPMC - 05/2009
Hts_order() - Constructor for class object.hts.Hts_order
Default constructor
Hts_order(int) - Constructor for class object.hts.Hts_order
Constructs a Hts_order object from an existing Hts_order ID
Hts_order(String) - Constructor for class object.hts.Hts_order
Constructs a Hts_order object from an existing Hts_order reference
hts_order_id - Variable in class object.hts.Hts_sample
ID of Hts_order Object for this Hts_sample Object
Hts_pipeline - Class in object.hts
Description
Hts_pipeline Object
Infos : KLB - IPMC - 09/2009
Hts_pipeline() - Constructor for class object.hts.Hts_pipeline
Default constructor
Hts_pipeline(int) - Constructor for class object.hts.Hts_pipeline
Constructs a Hts_pipeline object from an existing Hts_pipeline ID
hts_pipeline - Variable in class object.hts.Hts_result
hts_pipeline Object of hts_result Object
hts_pipeline_id - Variable in class object.hts.Hts_pipeline
ID of this Hts_pipeline object
Hts_pipeline_outfile - Class in object.hts
Description
Hts_pipeline_outfile Object
Infos : KLB - IPMC - 09/2009
Hts_pipeline_outfile() - Constructor for class object.hts.Hts_pipeline_outfile
Default constructor
Hts_pipeline_outfile(String, String, String) - Constructor for class object.hts.Hts_pipeline_outfile
Constructs a Hts_pipeline_outfile object
Hts_pipeline_parameter - Class in object.hts
Description
Hts_pipeline_parameter Object
Infos : KLB - IPMC - 09/2009
Hts_pipeline_parameter() - Constructor for class object.hts.Hts_pipeline_parameter
Default constructor
Hts_pipeline_parameter(String, String, String, String, String) - Constructor for class object.hts.Hts_pipeline_parameter
Constructs a Hts_pipeline_outfile object
hts_pipeline_ref - Variable in class object.hts.Hts_pipeline
Reference of this Hts_pipeline object
hts_pipeline_type - Variable in class object.hts.Hts_pipeline
Type of this Hts_pipeline object
hts_pipeline_type_required - Variable in class object.hts.Hts_analysis
hts_pipeline_type_required
hts_quantification - Variable in class object.hts.Hts_minseqe
Hts quantification protocol used for this Hts_minseqe object
Hts_quantification - Class in object.hts
Description
Hts_quantification Object belong to Hts_extraction Object
Infos : KLB - IPMC - 09/2009
Hts_quantification() - Constructor for class object.hts.Hts_quantification
Default constructor
Hts_quantification(int) - Constructor for class object.hts.Hts_quantification
Constructs a Hts_quantification object from an existing Hts_quantification ID.
hts_quantification_id - Variable in class object.hts.Hts_quantification
ID of this Hts_quantification object
hts_quantification_ref - Variable in class object.hts.Hts_quantification
Reference of this Hts_quantification object
Hts_result - Class in object.hts
Description
Hts_result Object
Infos : KLB - IPMC - 09/2009
Hts_result() - Constructor for class object.hts.Hts_result
Default constructor
Hts_result(int) - Constructor for class object.hts.Hts_result
Constructs an Scan object from an existing Hts_result ID
hts_result_id - Variable in class object.hts.Hts_result
ID of this Hts_result object
hts_result_ref - Variable in class object.hts.Hts_result
Reference of this hts_result object
Hts_RManager - Class in object.hts
Description
A Hts_RManager object allow to perform R queies for Hts Objects
Infos : KLB - IPMC - 10/2008
Hts_RManager(int) - Constructor for class object.hts.Hts_RManager
Default constructor
Hts_run - Class in object.hts
Description
Hts_run Object
Infos : KLB - IPMC - 05/2009
Hts_run() - Constructor for class object.hts.Hts_run
Default constructor
Hts_run(int) - Constructor for class object.hts.Hts_run
Constructs a Hts_run object from Hts_run ID
hts_run_id - Variable in class object.hts.Hts_run
ID of Hts_run object
hts_run_id - Variable in class object.hts.Hts_sample
ID of Hts_run Object for this Hts_sample Object
hts_run_ref - Variable in class object.hts.Hts_run
Reference of Hts_run object
Hts_sample - Class in object.hts
Description
Hts_sample Object
Infos : KLB - IPMC - 05/2009
Hts_sample() - Constructor for class object.hts.Hts_sample
Default constructor
Hts_sample(int) - Constructor for class object.hts.Hts_sample
Constructs a Hts_sample object from Hts_sample ID
Hts_sample(String) - Constructor for class object.hts.Hts_sample
Constructs a Hts_sample object from Hts_sample ref
hts_sample_id - Variable in class object.hts.Hts_minseqe
Hts_sample ID asssociated to this Hts_minseqe Object
hts_sample_id - Variable in class object.hts.Hts_result
ID of the Hts_sample Object related to this Hts_result object
hts_sample_id - Variable in class object.hts.Hts_sample
ID of Hts_sample object
hts_sample_ref - Variable in class object.hts.Hts_sample
Reference of Hts_sample object
hts_type - Variable in class object.common.Order
Hts_type of this Hts_sample object
hts_type - Variable in class object.hts.Hts_pipeline
Hts_type of this Hts_pipeline object
hts_type - Variable in class object.hts.Hts_RManager
 
hts_type - Variable in class object.hts.Hts_run
Hts_type default of this Hts_run object : not saved
hts_type - Variable in class object.hts.Hts_sample
Hts_type of this Hts_sample object
Hts_type - Class in object.hts
Description
Hts_type Object
Infos : KLB - IPMC - 05/2009
Hts_type() - Constructor for class object.hts.Hts_type
Default constructor
Hts_type(int) - Constructor for class object.hts.Hts_type
Constructs a Hts_type object from an existing Hts_type ID
hts_type_id - Variable in class object.hts.Hts_type
ID of this Hts_type object
hts_type_ref - Variable in class object.hts.Hts_type
Reference of this Hts_type object
http - Static variable in class servlets.Proxy
 
http - Static variable in class servlets.Proxy_common
 
http - Static variable in class servlets.Proxy_hts
 
http - Static variable in class servlets.Proxy_mediante
 
http - Static variable in class servlets.Proxy_medlab
 
http - Static variable in class servlets.Proxy_microrna
 
http - Static variable in class servlets.Proxy_rserve
 
human_quota - Variable in class object.annotation.EstTissue
 
Hybridization - Class in object.microarray
Description
Concern all biological experiment than we do on with a Microarray Object
Infos : KLB - IPMC - 02/2004
Hybridization() - Constructor for class object.microarray.Hybridization
Default constructor
Hybridization(int) - Constructor for class object.microarray.Hybridization
Constructs an Hybridization object from an existing Hybridization ID
hybridization - Variable in class object.microarray.Microarray
Hybridization Object for this Microarray Object
hybridization_id - Variable in class object.microarray.Hybridization
ID of this Hybridization Object
hybridization_id - Variable in class object.microarray.Labeling
ID of the corresponding Hybridization Object
HypDistanceCalculator - Class in object.common
This class calculates cumulative Hypergeometric distances, used for p-value calculations.
HypDistanceCalculator() - Constructor for class object.common.HypDistanceCalculator
 

I

id - Variable in class common.tags.generic.UseLocaleBundleTag
 
id - Variable in class JRclient.RFactor
IDs (content: Integer) each entry corresponds to a case, ID specifies the category
id - Variable in class object.annotation.Specificity
ID of a Sonde Object
id - Variable in class object.common.IdDescriptionObject
ID of base reference of the IdDescriptionObject Object
id - Variable in class object.microarray.SpotType
id
IdDescriptionObject - Class in object.common
Description
Object with key/value, use for the generation of ToolBox HTML form
Infos : KLB - IPMC - 08/2003
IdDescriptionObject() - Constructor for class object.common.IdDescriptionObject
Default constructor
identity - Variable in class object.annotation.Genoligo_rel
Percentage of identity of the Oligo Object on the sequence of the Gene Object
identity - Variable in class object.annotation.Oligo_adhocRelation
Percent identity of the match
identity - Variable in class object.annotation.Spodo_hit
identity
image - Variable in class object.common.Commande
Name of image describing the Commande object when seeing Oligos description
image_ch1 - Variable in class object.microarray.Scan
Path to Channel 1 image of this Scan object
image_ch2 - Variable in class object.microarray.Scan
Path to Channel 2 image of this Scan object
image_map - Variable in class object.common.Graph
image_map
image_path - Variable in class object.common.Graph
image_path
image_tosplit - Variable in class object.microarray.Scan
Path to tiff image with both channels of this Scan object
ImageManager - Class in object.common
Description
ImageManager Object is used to access data from quantification file and
display it at the screen in the Microarray data managment web interface
Infos : KLB - IPMC - 08/2003
ImageManager() - Constructor for class object.common.ImageManager
Default constructor
ImageManager(int, Project_order) - Constructor for class object.common.ImageManager
Constructs an ImageManager object
imageTif - Variable in class object.microarray.Scan
 
img - Variable in class object.annotation.OligoHit
Image representing the OligoHit at the screen
imgA - Variable in class object.microrna.MicroTopTable
 
imgB - Variable in class object.microrna.MicroTopTable
 
imgDOWN - Variable in class object.microrna.MicroTopTable
 
imgM - Variable in class object.microrna.MicroTopTable
 
imgUP - Variable in class object.microrna.MicroTopTable
 
impair - Static variable in class object.common.Spidey
Image for impair exon
inactive() - Method in class object.microarray.Plate
This function incative the Plate Object in database (not use).
indexError - Variable in class object.common.Rstat
 
information - Variable in class object.annotation.Oligo_adhoc
Informations concerning this Oligo_adhoc Object (pcr production for IPMC 5k array)
init(ServletConfig) - Method in class servlets.Proxy
 
init(ServletConfig) - Method in class servlets.Proxy_common
 
init(ServletConfig) - Method in class servlets.Proxy_hts
 
init(ServletConfig) - Method in class servlets.Proxy_mediante
 
init(ServletConfig) - Method in class servlets.Proxy_medlab
 
init(ServletConfig) - Method in class servlets.Proxy_microrna
 
init(ServletConfig) - Method in class servlets.Proxy_rserve
 
initAgilent(Microarray_project_type, String[], String) - Method in class object.microarray.Quantification_file
 
initApplicationConfiguration() - Method in class servlets.Proxy
 
initFileListing() - Method in class object.common.Rstat
 
initGenepix(Microarray_project_type, String[], String, String, String, String) - Method in class object.microarray.Quantification_file
 
initGenes() - Method in class object.microrna.MicroCible
 
initGO(String, int) - Method in class object.microrna.MapTarget
init GO annotation for target of this auto_mature
initGO(Hashtable, Hashtable, int) - Method in class object.microrna.MapTarget
init GO annotation for target listed in hashSymbol
initHashMttdata() - Method in class object.microrna.MicroTopTable
 
initialisation - Variable in class object.common.BlastTwoSeq
boolean : true if our query for align two sequence worked well
initialisation - Variable in class object.common.Search
boolean control if the initialization of the Search Object is OK
initialisation - Variable in class object.common.SessionBlastObject
Boolean : true if the initialization is OK, false if not
initMicros() - Method in class object.microrna.MicroCible
 
initSequence() - Method in class object.microrna.MicroSite
 
initSequenceFromFile(String, String) - Method in class object.common.BlastTwoSeq
Initialize the sequence object of the BlastTwoSeq object if the query of the user is by uploading a file.
initSerieFile() - Method in class object.common.Rstat
 
initSpotTypeFile() - Method in class object.common.Rstat
 
initWorkingDIR() - Method in class object.common.Rstat
 
initWorkingDIR() - Method in class object.hts.Hts_RManager
 
insertAction(String, String) - Method in class object.common.User
This function insert into the Action table a new line concerning the actions performed by the user in Mediante/Medlab applications
insertConnexion(String, String) - Method in class object.common.User
This function insert into the Connexion table a new line concerning the connexion of this user to Mediante application
interslide - Variable in class object.common.Biostats
Interslide normalization method of Biostats Object
interslide - Variable in class object.common.Rstat
Interslide normalization method of Biostats Object
intraslide - Variable in class object.common.Biostats
Intraslide normalization method of Biostats Object
intraslide - Variable in class object.common.Rstat
Intraslide normalization method of Biostats Object
intToFourBytes(int, byte[], int) - Static method in class JRclient.jcrypt
 
is - Variable in class JRclient.Rconnection
 
is - Variable in class JRclient.Rtalk
 
is_384SuiteBcr_ok - Variable in class object.microarray.Spotting
 
is_accessionOne - Variable in class object.common.BlastTwoSeq
boolean : true if we want to align the first sequence from the database
is_accessionTwo - Variable in class object.common.BlastTwoSeq
boolean : true if we want to align the second sequence from the database
is_active - Variable in class object.common.Project
True if the Project Object is an Active Project
is_active - Variable in class object.common.ProjectObject
'Y' or 'N' in function of the activity of this Project
is_active - Variable in class object.hts.Hts_sample
True if this Hts_sample Object is active
is_active - Variable in class object.microarray.Microarray
True if this Microarray Object is active
is_active - Variable in class object.microarray.Plate
True if this Plate object is already active
is_adhoc - Variable in class object.annotation.Oligo_rel
True if the oligo is an Oligo_adhoc Object
is_adhoc - Variable in class object.microarray.ElementMap
if this oligo is an adhoc oligo
is_adhoc - Variable in class object.microarray.Feature
if this oligo is an adhoc oligo
is_admin - Variable in class object.common.User
Boolean : true if the User object is a plateform administrator of the interface
is_admin_plateforme - Variable in class object.common.Plateforme
Plateforme administrator indication (option for production)
is_affy - Variable in class object.common.Toptable
is_affy
is_affy - Variable in class object.microarray.Microarray_project_type
Is this microarray is a microarray from Affymetrix suplier
is_analysis - Variable in class object.hts.Hts_sample
True if a hts_result is referenced as a analysis pipeline for this Hts_sample Object
is_blast_proceeded - Variable in class object.common.SequenceObject
Boolean : true when we have already launch the Mediante Oligo Blast for this SequenceObject
is_cleanup - Variable in class object.hts.Hts_minseqe
 
is_collaboration - Variable in class object.common.Order
If this Order is coming from a collaborative work (i.e. no facture)
is_control - Variable in class object.annotation.Oligo_rel
True if the oligo is an Oligo_control Object
is_control - Variable in class object.microarray.ElementMap
if this oligo is an oligo control
is_control - Variable in class object.microarray.Feature
if this oligo is an oligo control
is_devis - Variable in class object.common.User
Boolean : true if the User object is administratif
is_diluted - Variable in class object.microarray.Plate384
True if this Plate384 have been diluted
is_experiment - Variable in class object.microarray.Microarray
True if a hybridization is referenced for this Microarray Object
is_externe - Variable in class object.microarray.ElementMap
if this oligo is an external oligo
is_externe - Variable in class object.microarray.Feature
if this oligo is an external oligo
is_first - Variable in class object.common.Search
boolean control for the Web interface, first time we call a search it is true
is_first - Variable in class object.common.SessionBlastObject
Boolean control, true if it is the first time we ask for the Blast interface, false if not
is_found - Variable in class object.common.Search
boolean : true when the search found at least one Gene Object, and false if not
is_found - Variable in class object.microrna.MicroCible
boolean : true when the search found at least one Gene Object, and false if not
is_gu - Variable in class object.microrna.MatchMCB
match with GU
is_gz - Variable in class object.hts.Hts_pipeline_outfile
is_gz
is_hybrid - Variable in class object.common.Order
If hybridization must be perform by platforme
is_hybrid - Variable in class object.common.User
Boolean : true if the User object is a hybridizator
is_in_replaceMode - Variable in class object.microarray.Spotting
 
is_load - Variable in class object.microarray.MicroarrayElement
Boolean true if the MicroarrayElement is load and false if not.
is_matching - Variable in class object.common.SequenceObject
Boolean : true when the Oligo associate match the sequence of this SequenceObject, false if not
is_matching - Variable in class object.hts.Hts_sample
True if a hts_result is referenced as a matching pipeline for this Hts_sample Object
is_medlab - Variable in class object.common.User
Boolean : true if the User object can connect to Medlab interface
is_micro - Variable in class object.microarray.Microarray_project_type
Is this microarray is a microarray of microRNAs
is_minseqe - Variable in class object.hts.Hts_sample
True if a hts_minseqe is referenced for this Hts_sample Object
is_mir_probe - Variable in class object.annotation.Oligo_externe
Agilent and exiqon miRNA microarrays stored as oligo_externe objects
is_normalized - Variable in class object.microarray.Microarray
True if this Microarray Object is normalized via a biostats Object
is_normalized - Variable in class object.microarray.Quantification_file
boolean to know if this object is normalized too
is_open - Variable in class object.common.Order
Boolean descibing if this Order is opened in the Project_order Object
is_open - Variable in class object.common.Project
True if this Project Object is open is the current User session
is_open - Variable in class object.microarray.Project_order
Boolean true if this Project_order object is open in the Board Object containing this Project_order Object
is_order - Variable in class object.hts.Hts_analysis
Type of Object for this Hts_analysis object is Hts_order Object
is_orderable - Variable in class object.hts.Hts_type
True if Hts_type object is orderable
is_orderable - Variable in class object.microarray.Microarray_project_type
True if the microarray_project_type is orderable
is_owner - Variable in class object.common.Project
True if User curently viewing the Project in the Web Interface is the owner, false if not
is_prod - Variable in class object.common.User
Boolean : true if the User object is a microarray productor
is_production - Variable in class object.common.Plateforme
If the Plateforme plateforme is a microarray production platforme
is_quantif - Variable in class object.hts.Hts_sample
True if hts_result Object of all type matchig, reads and analysis pipelines are referenced for this Hts_sample Object
is_quantif - Variable in class object.microarray.Microarray
True if a scan is referenced for this Microarray Object
is_reads - Variable in class object.hts.Hts_sample
True if a hts_result is referenced as a reads pipeline for this Hts_sample Object
is_real_control - Variable in class object.annotation.Oligo_control
Indicate if this Oligo_control Object is a real control ('Y') or a lost oligo ('N')
is_rmq - Variable in class object.common.User
Boolean : true if the User object is a Quality Manager
is_sample - Variable in class object.hts.Hts_analysis
Type of Object for this Hts_analysis object is Hts_sample Object
is_save - Variable in class object.common.Rstat
 
is_select - Variable in class object.annotation.Genoligo_rel
Caracteristic of the selection or not of this relation for the Gene Object.
is_spottable - Variable in class object.microarray.Microarray_project_type
True if the microarray_project_type is spottable
is_spotting_exist() - Method in class object.microarray.Spotting
 
is_superadmin - Variable in class object.common.User
Boolean : true if the User object is super-administrator of the interface
is_tiling - Variable in class object.microarray.ElementMap
if this oligo is a tiling oligo
is_tiling - Variable in class object.microarray.Feature
if this oligo is a tiling oligo
is_update - Variable in class object.common.Order
If this order has been updated
is_viewable - Variable in class object.microarray.ArrayLabo
Indicate if we can display probes sequences informations for microarray from this ArrayLabo Object
is_viewable - Variable in class object.microarray.Microarray
True if a scan and a hybridization are referenced for this Microarray Object
is_viewable - Variable in class object.microarray.Microarray_project_type
Is this microarray can be viewed in Multi_PF comparison
is_viewer - Variable in class object.common.Project
True if User curently viewing the Project in the Web Interface is a viewer, false if not
is_writer - Variable in class object.common.Project
True if User curently viewing the Project in the Web Interface is the writer, false if not
isAuthenticated(HttpServletRequest) - Method in class servlets.Proxy
 
isConnected() - Method in class JRclient.Rconnection
check connection state.
isEqual(Locale[], Locale[]) - Method in class common.beans.locale.LocaleBean
Returns true if the the specifed Locale arrays contains exactly the same locale information.
isError() - Method in class JRclient.Rpacket
check last response for RESP_ERR
isFALSE() - Method in class JRclient.RBool
 
isNA() - Method in class JRclient.RBool
 
isNotInTheVector(String) - Method in class object.common.Project
This function check if the Accession number received is not already in the vectorSequenceObject Vector
isOk() - Method in class JRclient.Rpacket
check last response for RESP_OK
isOligoMatching(String, int) - Method in class object.common.Project
This function return a boolean meaning if an Oligo match a SequenceObject
isPlate384Exists(String) - Method in class object.common.Common
This function returns a boolean informative about the existence of a Plate384
isSupportedLang(String) - Method in class common.beans.locale.LocaleBean
Returns true if the specified languge is a supported language.
isTRUE() - Method in class JRclient.RBool
 
isViewer(int, int) - Method in class object.common.Common
This function check if a user is a Viewer of a Project Object
isWriter(int, int) - Method in class object.common.Common
This function check a user is a writer of a Project Object
ITERATIONS - Static variable in class JRclient.jcrypt
 

J

jcrypt - Class in JRclient
jcrypt.java Java-based implementation of the unix crypt command Based upon C source code written by Eric Young, eay@psych.uq.oz.au
jcrypt() - Constructor for class JRclient.jcrypt
 
journal - Variable in class object.annotation.GenbankRef
Journal of this GenbankRef object
Journal - Class in object.common
Description
Journal object
Infos : KLB - IPMC - 02/2005
Journal() - Constructor for class object.common.Journal
Default constructor
Journal(int, Date, int, String, String) - Constructor for class object.common.Journal
 
journal - Variable in class object.microrna.Mirna_reference
journal
JRclient - package JRclient
 

K

key - Variable in class common.tags.generic.GetLocalTextTag
 
Key - Variable in class JRclient.Rconnection
 
key - Variable in class JRclient.RSession
 
keys() - Method in class JRclient.RList
returns all keys of the list
Keyword - Class in object.common
Description
Keyword Object concern the decription of a Project_order Object
Infos : KLB - IPMC - 02/2004
Keyword() - Constructor for class object.common.Keyword
Default constructor
Keyword(int) - Constructor for class object.common.Keyword
Constructs a Keyword object an existing Keyword ID
keyword_id - Variable in class object.common.Keyword
ID of a Keyword object
keyword_ref - Variable in class object.common.Keyword
Reference of a Keyword object

L

Labeling - Class in object.microarray
Description
A Labeling Object correspond to a channel hybridize on a microarray
Infos : KLB - IPMC - 02/2007
Labeling() - Constructor for class object.microarray.Labeling
Default constructor
Labeling(int) - Constructor for class object.microarray.Labeling
Constructs a Labeling object from an existing Labeling ID
labeling_ch1 - Variable in class object.microarray.MicroarrayElement
Labeling cy3 reference of the Microarray object corresponding to this MicroarrayElement
labeling_ch1 - Variable in class object.microarray.Scan
Labeling reference for Channel 1
labeling_ch2 - Variable in class object.microarray.MicroarrayElement
Labeling cy5 reference of the Microarray object corresponding to this MicroarrayElement
labeling_ch2 - Variable in class object.microarray.Scan
Labeling reference for Channel 2
labeling_id - Variable in class object.microarray.Labeling
ID of this Labeling object
labeling_ref - Variable in class object.microarray.Labeling
Reference of this Labeling object
labeling_type - Variable in class object.microarray.Labeling
Labeling_type Object of this Labeling object
Labeling_type - Class in object.microarray
Description
A Labeling_type belong to a Labeling Object
Infos : KLB - IPMC - 02/2004
Labeling_type() - Constructor for class object.microarray.Labeling_type
Default constructor
Labeling_type(int) - Constructor for class object.microarray.Labeling_type
Constructs a Labeling_type object from an existing Labeling_type ID
labeling_type_ch1 - Variable in class object.microarray.Scan
Labeling_type Object for Channel 1 of this Scan Object
labeling_type_ch2 - Variable in class object.microarray.Scan
Labeling_type Object for Channel 2 of this Scan Object
labeling_type_id - Variable in class object.microarray.Labeling_type
ID of this Labeling_type object
labeling_type_ref - Variable in class object.microarray.Labeling_type
Refrence of this Labeling_type object
labRefList - Variable in class object.common.ImageManager
String[] containing distinct labeling references among the Project_order Object concerned
lancer() - Method in class object.common.ExecuteCmd
Launch the execution of the list of commande to execute
language - Variable in class common.beans.locale.LocaleBean
 
lastError - Variable in class JRclient.Rconnection
last error string
lastname - Variable in class object.common.User
Lastname of the User Object
latin_name - Variable in class object.annotation.Organism
Latin name or Organism Object
launchRQuery() - Method in class object.common.Rstat
 
launchRQuery() - Method in class object.hts.Hts_RManager
 
legende - Variable in class object.common.Convert
Legende
len - Variable in class object.hts.MaMatch
 
length - Variable in class object.annotation.Chromosome
Length of this Chromosome
letter_a - Variable in class object.microarray.Plate_transfert_type
Letter_A string for Description of transfert from 96 plate
letter_b - Variable in class object.microarray.Plate_transfert_type
Letter_B string for Description of transfert from 96 plate
limma_M - Variable in class object.common.Biostats
Path to limma M normalized file
link - Variable in class object.annotation.OligoHit
First link of the OligoHit ---> details of the Oligo
Link - Class in object.common
Description
This object allow to create Link in direction of Mediante, Ensembl, Refseq, Unigene, GENBANK_GENE_ID, Gene Ontology databases
Infos : KLB - IPMC - 08/2003
Link() - Constructor for class object.common.Link
Default constructor
link2 - Variable in class object.annotation.OligoHit
Second link of the OligoHit ---> selection of the Oligo for the SequenceObject Object
list - Variable in class object.common.Xhtml
NodeList Object
listePlate384 - Variable in class object.common.Dilution
 
listing - Variable in class object.common.Attribution
Listing of microarrays or Hts_sample references in attribution
listing - Variable in class object.common.GeneCart
Listing of the symbols or oligos IDs for this GeneCart Object
load(Hashtable) - Method in class object.common.CreationPlate
This function loadParams from HTML form.
loadBcrFile(String) - Method in class object.microarray.Spotting
 
loadConfigEnv() - Method in class object.common.Xhtml
This function return a Hashtable containing all informations concerning Environmental parameters.
loadForPlateFile() - Method in class object.microarray.Spotting
 
loadGalFile(String) - Method in class object.microarray.Spotting
 
loadHashColor() - Method in class object.common.ImageManager
This function load Graph Colors for User.
loadHashMirna_target() - Method in class object.annotation.Gene
This function load a Vector containing the List of Mirna_target Objects for this Gene Object
loadHashOligoPosition() - Method in class object.microarray.Plate384
This function load the attribute hashOligoPosition from Plate Object
loadHashOligoPosition() - Method in class object.microarray.Plate96
This function load the attribute hashOligoPosition from Plate Object
loadHashOligosAffy() - Method in class object.annotation.Gene
This function load all the Oligo_affy for the Gene Object
in a Hashtable ordered in function of microarray_project_type_id of Affy Arrays
loadHashOligosExternes() - Method in class object.annotation.Gene
This function load all the Oligo_externe for the Gene Object
in a Hashtable ordered in fucntion of array_id of External Arrays
loadHashParams(Hashtable) - Method in class object.microarray.Spotting
 
loadHashSpecificity() - Method in class object.annotation.Sonde
This function initialize the hashSpecificity attribute of this Oligo Object with the 3 Specificity Object from our 3 reference databases.
loadingXmlComponent() - Method in class object.common.Xhtml
This function load the XML file and initialize the List Attribute with the CSTE_ROOT_TAG attribute TAG
loadLabRefList(int) - Method in class object.common.ImageManager
This function load attribute labRefList with distinct labbeling reference among the Project_order Object
loadMapTarget(String) - Method in class object.microrna.Mirna_mature
 
loadMapTarget(int, String, Hashtable) - Method in class object.microrna.Mttdata
 
loadOtherFiles(String, User) - Method in class object.common.Attribution
This function execute a complete attribution process from a pre-formatted file,
file which must have .medlab extension.
loadOtherFiles(String, int) - Method in class object.microarray.Spotting
 
loadPackages() - Method in class object.common.Rstat
 
loadParams(Hashtable) - Method in class object.common.Contact_client
This function loadParams from HTML form
loadParams(Hashtable, String) - Method in class object.common.Convert
This function load parameters from Html Form.
loadParams(Hashtable) - Method in class object.common.Enquete
This function loadParams from HTML form
loadParams(Hashtable) - Method in class object.common.Foq
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.common.Rstat
This function loadParams from HTML form.
loadParams(Hashtable, String) - Method in class object.common.Search
This function load parameters from Html Form.
loadParams(Hashtable) - Method in class object.common.User
 
loadParams(Hashtable) - Method in class object.hts.Hts_minseqe
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.hts.Hts_order
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.hts.Hts_result
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.hts.Hts_RManager
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.hts.Hts_run
 
loadParams(Hashtable) - Method in class object.microarray.Hybridization
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.microarray.Labeling
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.microarray.Microarray_order
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.microarray.Project_order
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.microarray.Protocol_extraction
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.microarray.Protocol_hybridization
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.microarray.Scan
This function loadParams from HTML form.
loadParams(Hashtable) - Method in class object.microarray.Spotting
 
loadParams(Hashtable) - Method in class object.microrna.MicroCible
This function load parameters from Html Form.
loadParams(Hashtable) - Method in class object.microrna.MicroSite
 
loadParams(Hashtable) - Method in class object.microrna.MicroTopTable
This function load parameters from Html Form.
loadParams(Hashtable) - Method in class object.microrna.SnipMir
This function load parameters from Html Form.
loadParams(Hashtable) - Method in class object.microrna.TargetPrediction
 
loadSequencesFile(String) - Method in class object.common.Project
This function load SequenceObject Object for this Project Object
from an upload of a file in FASTA format
loadSequencesFile(Hashtable, String, int) - Method in class object.common.SessionBlastObject
This function load Sequence for the Blast process.
loadVectorAnnotations() - Method in class object.annotation.Gene
Thhis function load a vector containing the list of GoLink Objects for this Gene Object
loadVectorCytobands() - Method in class object.annotation.Gene
This function load a vector containing the list of Cytoband Objects for this Gene Object
loadVectorExons() - Method in class object.annotation.Gene
This function load a vector containing the list of Exons Objects composing the sequence of this Gene Object
loadVectorGenbankRef() - Method in class object.annotation.Gene
This function load a vector containing the list of GenbankRef Object for this Gene Object
loadVectorOligo_adhocRelation() - Method in class object.annotation.Gene
This function load a Vector containing the List of Oligo_adhocRelation for this Gene Object
loadVectorOligos() - Method in class object.annotation.Gene
This function load a Vector containing the List of Oligos Objects for this Gene Object
loadVrkFile(String) - Method in class object.microarray.Spotting
 
loadVsmFile(String) - Method in class object.microarray.Spotting
 
locale - Variable in class common.beans.locale.LocaleBean
 
LocaleBean - Class in common.beans.locale
 
LocaleBean() - Constructor for class common.beans.locale.LocaleBean
 
logFC - Variable in class object.common.ImageManager
 
logfc - Variable in class object.microrna.MicroTopTable
logfc
logFC - Variable in class object.microrna.Mttdata
logFC
login(String, String) - Method in class JRclient.Rconnection
login using supplied user/pwd.
login - Variable in class object.common.User
Login of the User Object
logratio - Variable in class object.microarray.Feature
LogRatio of feature
longueur - Variable in class object.annotation.Gene
Length of the Gene sequence
longueur - Variable in class object.annotation.OligoHit
Longueur Of the OligoHit
lst_genes_down - Variable in class object.microrna.MicroTopTable
 
lst_genes_up - Variable in class object.microrna.MicroTopTable
 

M

MaFile - Class in object.hts
Description
MaFile Object
Infos : KLB - IPMC - 03/2010
MaFile() - Constructor for class object.hts.MaFile
Default constructor
MaFile(String) - Constructor for class object.hts.MaFile
Constructs a MaFile object from a path file
MageProtocol - Class in object.microarray
Description
External Arrays produced in others Companies
Infos : KLB - IPMC - 08/2003
MageProtocol() - Constructor for class object.microarray.MageProtocol
Default constructor
MageProtocol(String, String, String, String, String) - Constructor for class object.microarray.MageProtocol
Constructs an MageProtocol object from severals parameters
MAGEWriter - Class in object.microarray
Description: Class to write a nicely formatted MAGE-ML document with appropriate headers.
MAGEWriter() - Constructor for class object.microarray.MAGEWriter
 
MAIL_FROM - Static variable in class object.common.Common
Mail From for sending mail (mediante@ipmc.cnrs.fr)
MAIL_FROM - Static variable in class object.common.Order
Mail From for sending mail (mediante@ipmc.cnrs.fr)
MAIL_FROM - Static variable in class object.common.Project
Mail From for sending mail (mediante@ipmc.cnrs.fr)
MAIL_FROM - Static variable in class object.common.Rstat
Mail From for sending mail (mediante@ipmc.cnrs.fr)
MAIL_FROM - Static variable in class object.hts.Hts_order
Mail From for sending mail (mediante@ipmc.cnrs.fr)
MAIL_FROM - Static variable in class object.hts.Hts_RManager
Mail From for sending mail (mediante@ipmc.cnrs.fr)
MAIL_HOST - Static variable in class object.common.Common
Mail Host for sending mail (gelas.ipmc.cnrs.fr)
MAIL_HOST - Static variable in class object.common.Order
Mail Host for sending mail (gelas.ipmc.cnrs.fr)
MAIL_HOST - Static variable in class object.common.Project
Mail Host for sending mail (gelas.ipmc.cnrs.fr)
MAIL_HOST - Static variable in class object.common.Rstat
Mail Host for sending mail (gelas.ipmc.cnrs.fr)
MAIL_HOST - Static variable in class object.hts.Hts_order
Mail Host for sending mail (gelas.ipmc.cnrs.fr)
MAIL_HOST - Static variable in class object.hts.Hts_RManager
Mail Host for sending mail (gelas.ipmc.cnrs.fr)
makeBgDistribGraph() - Method in class object.common.ImageManager
 
makeBlast() - Method in class object.common.Blast
Lauch the process to run Blast program with all the parameters of this Blast object
makeBlast() - Method in class object.common.SessionBlastObject
This function launch the Blast process.
makeBlastOligo(Vector) - Method in class object.common.Project
This function lauch the Blast process beetween the Oligo Database
of the Organism of this project and the SequenceObject contained in the vectorQueryId received
makeBlastTwoSeq() - Method in class object.common.BlastTwoSeq
Launch Blast Two sequences for this object
makeChromoImage() - Method in class object.common.ImageManager
This function proceed to the creation of the image of chromosomes according to the Gene Object stored in the cart parameter.
makeClouds(String, Hashtable) - Method in class object.common.Common
This function proceed to the generation of graphe image, scatter plot style.
makeDistrib(Hashtable) - Method in class object.common.Common
This function proceed to the generation of graphe image.
makeFile(String) - Method in class object.common.RNAfold
 
makeFileForMail(String) - Method in class object.common.Project
This function create an Excel file concerning Oligo selection in this Project
makeFilesBlastTwoseq(Sequence, Sequence) - Method in class object.common.Blast
Create both files corresponding to the two Sequence received as parameters and create a Blast database with the First one.
makeFileSeq(Sequence) - Method in class object.common.Blast
Create a file from a Sequence object received as a parameter.
makeFileSeq(Vector) - Method in class object.common.Blast
Create a file from a Vector of Sequence object received as a parameter.
makeFileSequences(Vector) - Method in class object.common.Project
This function create a file containing the sequence (FASTA format) composing the vector received
makeGraphs(Hashtable, boolean) - Method in class object.common.ImageManager
This function proceed to the generation of graphe image.
makeGraphs(Hashtable, Hashtable) - Method in class object.microrna.MicroTopTable
 
makeMegaBlast() - Method in class object.common.Blast
Lauch the process to run MegaBlast program with all the parameters of this Blast object
mamap - Variable in class object.annotation.Sonde
Htmp map for Blast search
MaMatch - Class in object.hts
Description
MaMatch Object
Infos : KLB - IPMC - 03/2010
MaMatch() - Constructor for class object.hts.MaMatch
Default constructor
MaMatch(String, String, int, String, int, int) - Constructor for class object.hts.MaMatch
 
map - Variable in class object.annotation.Gene
map for image
map - Variable in class object.common.MapEST
map for image
mapEST - Variable in class object.annotation.Gene
MapEST Object of this Gene Object
mapEST - Variable in class object.annotation.Oligo
MapEST Object of this Oligo Object
MapEST - Class in object.common
Description
Describe relations between Oligos object and Ests matchs
Infos : KLB - IPMC - 07/2007
MapEST() - Constructor for class object.common.MapEST
Default constructor
MapEST(int, String) - Constructor for class object.common.MapEST
Constructs a MapEST object
mapName - Variable in class object.annotation.OligoHit
Html Map string wich separate the image in two parts : for first link (link attribute) and second link -link2 attribute
MapTarget - Class in object.microrna
Description
MapTarget
Infos : KLB - IPMC - 02/2008
MapTarget(int) - Constructor for class object.microrna.MapTarget
Default constructor
mapTargetDown - Variable in class object.microrna.Mttdata
 
mapTargetUp - Variable in class object.microrna.Mttdata
 
mark - Variable in class object.microarray.Labeling
Mark type for this Labeling Object
mask_A - Variable in class object.common.Toptable
mask_A
mask_id - Variable in class object.common.Toptable
mask_id
mask_M - Variable in class object.common.Toptable
mask_M
mask_name - Variable in class object.common.Toptable
mask_name
Match - Class in object.microrna
Description
Match
Infos : KLB - IPMC - 02/2008
Match() - Constructor for class object.microrna.Match
Default constructor
Match(double, String, String, int) - Constructor for class object.microrna.Match
Constructs a Match object
MatchMCB - Class in object.microrna
Description
Infos : KLB - IPMC - 04/2008
MatchMCB(int, boolean, String, String, String) - Constructor for class object.microrna.MatchMCB
Default constructor
mature_acc - Variable in class object.microrna.MicroTopTable
auto_mature
mature_acc - Variable in class object.microrna.Mirna_mature
ID of this Mirna_mature Object
mature_acc - Variable in class object.microrna.Mirna_target
mature_name
mature_acc - Variable in class object.microrna.Mttdata
mature_acc
mature_acc - Variable in class object.microrna.TargetPrediction
auto_mature
mature_name - Variable in class object.microrna.Mcbmatch
mature_name
mature_name - Variable in class object.microrna.Mirna_mature
Name of this Mirna_mature Object
mature_name - Variable in class object.microrna.Mirna_target
mature_name
mature_name - Variable in class object.microrna.Mttdata
accession
Mcbdata - Class in object.microrna
Description
Infos : KLB - IPMC - 04/2008
Mcbdata(String, String, String) - Constructor for class object.microrna.Mcbdata
Default constructor
Mcbmatch - Class in object.microrna
Description
Infos : KLB - IPMC - 04/2008
Mcbmatch(String, String, String) - Constructor for class object.microrna.Mcbmatch
Default constructor
medline - Variable in class object.microrna.Mirna_reference
medline
message - Variable in class object.common.Attribution
Information message displayed in JSP
message - Variable in class object.common.BlastTwoSeq
Information message
message - Variable in class object.common.Board
Message concerning this Board Object
message - Variable in class object.common.CreationPlate
Information message in case of error during the process
message - Variable in class object.common.Dilution
Information message in case of error during the process
message - Variable in class object.common.Project
Information message concerning this project (update at each step of the modifications of this project)
message - Variable in class object.common.Rstat
 
message - Variable in class object.common.Search
Information message concerning the search
message - Variable in class object.common.SessionBlastObject
Informations message concerning the Blast proceed
message - Variable in class object.hts.Hts_result
Information message in case of error during the process
message - Variable in class object.hts.Hts_RManager
 
message - Variable in class object.hts.Hts_run
Message for user information
message - Variable in class object.microarray.Scan
Information message in case of error during the process
message - Variable in class object.microarray.Spotting
 
message - Variable in class object.microrna.MicroCible
Information message concerning the search
mfe_cutoff - Variable in class object.microrna.MicroCible
 
mfe_cutoff - Variable in class object.microrna.MicroTopTable
mfe_cutoff
micro - Variable in class object.common.RNAhybrid
micro
micro - Variable in class object.microrna.MatchMCB
micro
micro_list - Variable in class object.microrna.MicroSite
micro_list
Microarray - Class in object.microarray
Description
Microarray Object
Infos : KLB - IPMC - 01/2004
Microarray() - Constructor for class object.microarray.Microarray
Default constructor
Microarray(int) - Constructor for class object.microarray.Microarray
Constructs a Microarray object from Microarray ID
Microarray(String) - Constructor for class object.microarray.Microarray
Constructs a Microarray object from Microarray slide_code
microarray - Variable in class object.microarray.MicroarrayElement
Microarray object corresponding to this MicroarrayElement
(might be not initialized most of the time)
microarray_id - Variable in class object.microarray.Control
ID of Microarray Object with which the control has been done
microarray_id - Variable in class object.microarray.Hybridization
Microarray ID asssociated to this Hybridization Object
microarray_id - Variable in class object.microarray.Microarray
ID of Microarray object
microarray_id - Variable in class object.microarray.MicroarrayElement
ID of the Microarray object corresponding to this MicroarrayElement
microarray_id - Variable in class object.microarray.Scan
ID of the Microarray Object related to this Scan object
Microarray_order - Class in object.microarray
Description
A Microarray_order Object belong to a Project_order Object
Infos : KLB - IPMC - 02/2004
Microarray_order() - Constructor for class object.microarray.Microarray_order
Default constructor
Microarray_order(int) - Constructor for class object.microarray.Microarray_order
Constructs a Microarray_order object from an existing Microarray_order ID
Microarray_order(String) - Constructor for class object.microarray.Microarray_order
Constructs a Microarray_order object from an existing Microarray_order ref
microarray_order_id - Variable in class object.microarray.Microarray
Microarray_project_type Object for this Microarray Object
microarray_order_id - Variable in class object.microarray.Microarray_project_type
Default Microarray_order ID concerning the quality control associated to the microarray_project_type
microarray_project_type - Variable in class object.annotation.Oligo_adhoc
Microarray_project_type Object owner of this Oligo_adhoc Object
microarray_project_type - Variable in class object.annotation.Oligo_externe
Microarray_project_type Object owner of this Oligo_adhoc Object
microarray_project_type - Variable in class object.common.Order
Microarray_project_type of this Microarray_order
microarray_project_type - Variable in class object.microarray.GeoSerie
microarray_project_type
microarray_project_type - Variable in class object.microarray.Microarray
Microarray_project_type Object for this Microarray Object
Microarray_project_type - Class in object.microarray
Description
Microarray_project_type Object
Infos : KLB - IPMC - 12/2005
Microarray_project_type() - Constructor for class object.microarray.Microarray_project_type
Default constructor
Microarray_project_type(int) - Constructor for class object.microarray.Microarray_project_type
Constructs a Microarray_project_type object from an existing Microarray_project_type ID
microarray_project_type - Variable in class object.microarray.Spotting
Microarray project type in spotting
microarray_project_type_id - Variable in class object.microarray.Microarray_project_type
ID of this Microarray_project_type object
microarray_project_type_ref - Variable in class object.microarray.Microarray_project_type
Reference of this Microarray_project_type object
microarray_type - Variable in class object.microarray.Microarray
Microarray_type Object for this Microarray Object
Microarray_type - Class in object.microarray
Description
MicroarrayType Object
Infos : KLB - IPMC - 01/2004
Microarray_type() - Constructor for class object.microarray.Microarray_type
Default constructor
Microarray_type(int) - Constructor for class object.microarray.Microarray_type
Constructs a Microarray_type object from Microarray_type ID
microarray_type_id - Variable in class object.microarray.Microarray_type
ID of Microarray_type object
microarray_type_ref - Variable in class object.microarray.Microarray_type
Name of the Microarray_type Object
MicroarrayElement - Class in object.microarray
Description
A light Microarray Object
Infos : KLB - IPMC - 02/2004
MicroarrayElement(int, int, String, boolean) - Constructor for class object.microarray.MicroarrayElement
Constructs a MicroarrayElement object from several parameters.
MicroCible - Class in object.microrna
Description
Infos : KLB - IPMC - 05/2007
MicroCible() - Constructor for class object.microrna.MicroCible
Default constructor
microcible - Variable in class object.microrna.SnipMir
Seed_match
MicroSite - Class in object.microrna
Description
Infos : KLB - IPMC - 05/2007
MicroSite() - Constructor for class object.microrna.MicroSite
Default constructor
MicroTopTable - Class in object.microrna
Description
Infos : KLB - IPMC - 04/2008
MicroTopTable() - Constructor for class object.microrna.MicroTopTable
Default constructor
middle - Static variable in class object.common.Link
Middle of a Http Url link (" target="_blank">)
middle_main - Static variable in class object.common.Link
 
middle_navig - Static variable in class object.common.Link
 
Mirna - Class in object.microrna
Description
Mirna objects
Infos : KLB - IPMC - 02/2008
Mirna() - Constructor for class object.microrna.Mirna
Default constructor
Mirna(int) - Constructor for class object.microrna.Mirna
Constructs a Mirna object from auto_mirna ID
mirna - Variable in class object.microrna.Mirna_mature
Mirna owner of this Mirna_mature Object
mirna_acc - Variable in class object.microrna.Mirna
Accession of this Mirna Object
Mirna_chromosome - Class in object.microrna
Description
Mirna_chromosome Objects
Infos : KLB - IPMC - 02/2008
Mirna_chromosome() - Constructor for class object.microrna.Mirna_chromosome
Default constructor
Mirna_chromosome(String, int, int, String) - Constructor for class object.microrna.Mirna_chromosome
Constructs a Mirna_chromosome object
Mirna_context - Class in object.microrna
Description
Mirna_context Objects
Infos : KLB - IPMC - 02/2008
Mirna_context() - Constructor for class object.microrna.Mirna_context
Default constructor
Mirna_context(String, String, String, String, String) - Constructor for class object.microrna.Mirna_context
Constructs a Mirna_context object
mirna_id - Variable in class object.microrna.Mirna
ID of this Mirna Object
Mirna_mature - Class in object.microrna
Description
Mirna_mature Objects
Infos : KLB - IPMC - 02/2008
Mirna_mature() - Constructor for class object.microrna.Mirna_mature
Default constructor
Mirna_mature(int) - Constructor for class object.microrna.Mirna_mature
Constructs a Mirna_mature object from auto_mature ID
Mirna_mature(String) - Constructor for class object.microrna.Mirna_mature
Constructs a Mirna_mature object from mature_name
Mirna_reference - Class in object.microrna
Description
Mirna_reference Objects
Infos : KLB - IPMC - 02/2008
Mirna_reference() - Constructor for class object.microrna.Mirna_reference
Default constructor
Mirna_reference(String, String, String, String) - Constructor for class object.microrna.Mirna_reference
Constructs a Mirna_reference object
Mirna_target - Class in object.microrna
Description
Mirna_target Objects
Infos : KLB - IPMC - 02/2008
Mirna_target() - Constructor for class object.microrna.Mirna_target
Default constructor
Mirna_target(int, String, String, int, double, String, String) - Constructor for class object.microrna.Mirna_target
Constructs a Mirna_target object
mirna_target_tool_id - Variable in class object.microrna.MapTarget
mirna_target_tool_id
mix_ref - Variable in class object.hts.Hts_result
Reference for mix sequenced
mj - Variable in class object.microarray.MAGEWriter
 
mm - Variable in class object.hts.MaMatch
 
modifySequenceObject(String, int) - Method in class object.common.Project
This function modify the attributes of a SequenceObject containing in the Project Object
mouse_quota - Variable in class object.annotation.EstTissue
 
Mstdata - Class in object.microrna
Description
Infos : KLB - IPMC - 05/2008
Mstdata(String, String, String, int, int, String, int, int) - Constructor for class object.microrna.Mstdata
Default constructor
Mttdata - Class in object.microrna
Description
Infos : KLB - IPMC - 04/2008
Mttdata(String, String) - Constructor for class object.microrna.Mttdata
Default constructor
multiplier - Variable in class object.microarray.Microarray_project_type
 
myFiles - Variable in class object.common.Rstat
String[] containing Listing of available files for this Rstat query

N

name - Variable in class common.tags.generic.GetLocalTextTag
 
name - Variable in class object.annotation.Oligo_tiling
name of Oligo_tiling Object
name - Variable in class object.annotation.Term
Gene Ontology description of the accession
name - Variable in class object.common.ToolBox
Name of the ToolBox object
name - Variable in class object.common.ToolBoxString
Name of the ToolBoxString object
name - Variable in class object.hts.Hts_analysis_parameter
name
name - Variable in class object.hts.Hts_pipeline_outfile
name
name - Variable in class object.hts.Hts_pipeline_parameter
name
name - Variable in class object.microarray.Feature
Name of Oligo object of this Feature
name - Variable in class object.microarray.MageProtocol
name of this MageProtocol Object
name - Variable in class object.microarray.SpotType
name
name - Variable in class object.microrna.Mstdata
name
nb - Variable in class object.annotation.Estoligo_rel
Number of match
nb - Variable in class object.common.Attribution
Number of arrays or hts samples to attribute to the Order Object
nb_all - Variable in class object.annotation.Histology
Pourcentage de la categorie pour human
nb_all_down - Variable in class object.microrna.MicroTopTable
 
nb_all_up - Variable in class object.microrna.MicroTopTable
 
nb_bloc - Variable in class object.common.ImageManager
Numero of the bloc to display at the screen
nb_bloc - Variable in class object.microarray.Pattern_file
Number of bloc
nb_bloc - Variable in class object.microarray.Quantification_file
Number of bloc
nb_bloc_column - Variable in class object.microarray.Pattern_file
Number of column of bloc
nb_bloc_row - Variable in class object.microarray.Pattern_file
Number of row of bloc
nb_column - Variable in class object.microarray.Pattern_file
Number of column in each bloc
nb_column - Variable in class object.microarray.Quantification_file
Number of column in each bloc
nb_est - Variable in class object.annotation.Sonde
Number of ESTs matching the Sonde Object
nb_fields - Variable in class object.common.Convert
 
nb_gene - Variable in class object.microrna.MicroTopTable
 
nb_gene_a - Variable in class object.microrna.MicroTopTable
 
nb_gene_filt - Variable in class object.microrna.MicroTopTable
 
nb_identity - Variable in class object.annotation.Spodo_hit
nb_identity
nb_lame - Variable in class object.microarray.Spotting
Number of Microarray create in this spotting session
nb_match - Variable in class object.microrna.MicroCible
Number of match between microRNAs and genes for this search
NB_MAX_RESULTS - Static variable in class object.common.Search
Number maximum of results the search can returned
nb_microarray - Variable in class object.common.Order
Number of microarrays ordered (ex :in case of 4x44k pattern = 4 x this.nb_slide) in this Microarray_order
nb_microarray - Variable in class object.microarray.GeoSerie
nb_microarray
nb_microarray_more - Variable in class object.common.Order
Number of microarrays to attribute to this Microarray_order by the IPMC production
nb_microarray_ok - Variable in class object.common.Order
Number of microarrays with informations loaded concerning the Microarray_order object related to this Order Object
nb_neoplasia - Variable in class object.annotation.Histology
Reference of Categorie Object
nb_normal - Variable in class object.annotation.Histology
ID of Categorie Object
nb_predict - Variable in class object.microrna.Mttdata
nb_predict
nb_row - Variable in class object.microarray.Pattern_file
Number of row in each bloc
nb_row - Variable in class object.microarray.Quantification_file
Number of row in each bloc
nb_sample - Variable in class object.common.Order
Number of sample in this Hts_order Object
nb_sample - Variable in class object.hts.Hts_run
Number of sample create in this hts_run Object
nb_sample_more - Variable in class object.common.Order
Number of sample in this Hts_order Object to add to close this Hts_order Object
nb_seq - Variable in class object.common.Project
 
nb_slide - Variable in class object.common.Order
Number of unique slide ordered in this Microarray_order
nb_unknown - Variable in class object.annotation.Histology
Legend of Categorie Object
nb_use - Variable in class object.microarray.Plate
Number of time this Plate object have been used for Microarray Object production
nbResultsParPAge - Static variable in class object.common.Project
Number of SeqeuenceObject displayed per page in the Oligo selection part
nbResultsParPAge - Static variable in class object.common.Search
Number of results to show in one page in the web interface
needLogin() - Method in class JRclient.Rconnection
check authentication requirement sent by server
needToConvert - Variable in class object.microarray.Spotting
 
newHdr(int, int) - Static method in class JRclient.Rtalk
creates a new header according to the type and length of the parameter
nucleic_acid_type - Variable in class object.hts.Hts_minseqe
Nucleic acid type of this Hts_minseqe object
nucleic_acid_type - Variable in class object.microarray.Labeling
Nucleic acid type of this Extraction object
Nucleic_acid_type - Class in object.microarray
Description
Nucleic_acid_type Object
Infos : KLB - IPMC - 02/2004
Nucleic_acid_type() - Constructor for class object.microarray.Nucleic_acid_type
Default constructor
Nucleic_acid_type(int) - Constructor for class object.microarray.Nucleic_acid_type
Constructs a Nucleic_acid_type object from an existing Nucleic_acid_type ID
nucleic_acid_type_id - Variable in class object.microarray.Nucleic_acid_type
ID of this Nucleic_acid_type object
nucleic_acid_type_ref - Variable in class object.microarray.Nucleic_acid_type
Reference of this Nucleic_acid_type object
number - Variable in class object.microarray.Serie
number
numberFormat - Variable in class common.beans.locale.LocaleBean
 
numberOfIdentities - Variable in class object.common.BlastHit
Number of identities

O

object.annotation - package object.annotation
 
object.common - package object.common
 
object.hts - package object.hts
 
object.microarray - package object.microarray
 
object.microrna - package object.microrna
 
Oligo - Class in object.annotation
Description
Oligo Object
Infos : KLB - IPMC - 08/2003
Oligo() - Constructor for class object.annotation.Oligo
Default constructor
Oligo(int) - Constructor for class object.annotation.Oligo
Constructs an Oligo object from an Oligo ID
Oligo_adhoc - Class in object.annotation
Description
Oligo_adhoc from ohers IPMC Arrays
Infos : KLB - IPMC - 06/2005
Oligo_adhoc() - Constructor for class object.annotation.Oligo_adhoc
Default constructor
Oligo_adhoc(int) - Constructor for class object.annotation.Oligo_adhoc
Constructs a Oligo_adhoc object from Oligo_adhoc ID
oligo_adhoc_id - Variable in class object.annotation.Oligo_adhocRelation
ID of oligo_adhoc object
oligo_adhoc_id - Variable in class object.microrna.Mttdata
oligo_adhoc_id
Oligo_adhoc_match - Class in object.annotation
Description
Oligo_adhoc_match Object belong to an Oligo_adhoc Object
Infos : KLB - IPMC - 02/2006
Oligo_adhoc_match() - Constructor for class object.annotation.Oligo_adhoc_match
Default constructor
Oligo_adhoc_match(Organism, String, String, int, int, String, String, String, String) - Constructor for class object.annotation.Oligo_adhoc_match
Constructs an Oligo_adhoc_match object
Oligo_adhocRelation - Class in object.annotation
Description
Oligo_adhocRelation Object
Infos : KLB - IPMC - 06/2005
Oligo_adhocRelation() - Constructor for class object.annotation.Oligo_adhocRelation
Default constructor
Oligo_adhocRelation(int, int, int, int, double) - Constructor for class object.annotation.Oligo_adhocRelation
Constructs an Oligo_adhocRelation object with several parameters
Oligo_affy - Class in object.annotation
Description
Oligo_affy Object
Infos : KLB - IPMC - 02/2008
Oligo_affy() - Constructor for class object.annotation.Oligo_affy
Default constructor
Oligo_affy(int) - Constructor for class object.annotation.Oligo_affy
Constructs an Oligo_affy object from an oligo_affy_id
Oligo_annotation - Class in object.annotation
Description
Oligo_annotation Object
Infos : KLB - IPMC - 02/2004
Oligo_annotation() - Constructor for class object.annotation.Oligo_annotation
Default constructor
Oligo_annotation(int) - Constructor for class object.annotation.Oligo_annotation
Constructs an Oligo_annotation object with an Oligo ID from view oligo_annotation
Oligo_annotation(String, String, String, String) - Constructor for class object.annotation.Oligo_annotation
Constructs an Oligo_annotation object with an Oligo ID from view oligo_annotation
oligo_b - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object blue
oligo_ciel - Static variable in class object.common.Spidey
Name of image corresponding to Mediante Database color code (blue)
Oligo_control - Class in object.annotation
Description
Oligo_control Object
Infos : KLB - IPMC - 08/2003
Oligo_control() - Constructor for class object.annotation.Oligo_control
Default constructor
Oligo_control(int) - Constructor for class object.annotation.Oligo_control
Constructs an Oligo_control object with an Oligo_control ID
oligo_control_id - Variable in class object.annotation.Oligo_control
ID of Oligo_control Object
oligo_ensembl - Static variable in class object.common.Spidey
Name of image corresponding to Ensembl Database color code (green)
Oligo_externe - Class in object.annotation
Description
Oligo_externe Object
Infos : KLB - IPMC - 01/2005
Oligo_externe() - Constructor for class object.annotation.Oligo_externe
Default constructor
Oligo_externe(int) - Constructor for class object.annotation.Oligo_externe
Constructs an Oligo object from an Oligo ID
oligo_g - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object grey
oligo_id - Variable in class object.annotation.Genoligo_rel
ID of an existing Oligo object
oligo_id - Variable in class object.annotation.Oligo_annotation
ID of Oligo_adhoc object associated to this relation
oligo_id - Variable in class object.annotation.Oligo_rel
ID of the Oligo, Oligo_adhoc or Oligo_control Object associated with this relation
oligo_id - Variable in class object.common.Point
ID of the Oligo Object associated with this Point Object
oligo_id - Variable in class object.common.SequenceObject
ID of an Oligo object if the SequenceObject is associate with an Oligo
oligo_id - Variable in class object.microarray.ElementMap
ID of Oligo object of this ElementMap
oligo_id - Variable in class object.microarray.Feature
ID of Oligo object of this Feature
oligo_id_str - Variable in class object.microarray.ElementMap
ID String of Oligo object of this ElementMap
oligo_id_str - Variable in class object.microarray.Feature
ID String of Oligo object of this Feature
oligo_j - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object yellow
oligo_m - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object brown
oligo_ns - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Gene Oligos View : not best oligo
oligo_ns_l - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Gene Oligos View : not best oligo but is in local set
oligo_ns_n - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Gene Oligos View : not best oligo but is in national set
oligo_ns_nl - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Gene Oligos View : not best oligo but is in national and local set
oligo_o - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object orange
oligo_ob - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection orange/blue
oligo_oj - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection orange/yellow
oligo_om - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection orange/brown
oligo_r - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object red
oligo_rb - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection red/blue
oligo_refseq - Static variable in class object.common.Spidey
Name of image corresponding to Refseq Database color code (red)
Oligo_rel - Class in object.annotation
Description
Relation between Oligo, Oligo_adhoc or Oligo_control Object and Plate Object
Infos : KLB - IPMC - 08/2003
Oligo_rel() - Constructor for class object.annotation.Oligo_rel
Default constructor
Oligo_rel(int, int, String, String, int, String, String, int) - Constructor for class object.annotation.Oligo_rel
Constructs an Oligo_rel object with all member datas
oligo_rj - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection red/yellow
oligo_rm - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection red/brown
oligo_s - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Gene Oligos View : is best oligo
oligo_s_l - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Gene Oligos View : is best oligo and is in local set
oligo_s_n - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Gene Oligos View : is best oligo and is in national set
oligo_s_nl - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Gene Oligos View : is best oligo and is in national and local set
Oligo_tiling - Class in object.annotation
Description
Oligo_tiling Object
Infos : KLB - IPMC - 08/2007
Oligo_tiling() - Constructor for class object.annotation.Oligo_tiling
Default constructor
Oligo_tiling(int) - Constructor for class object.annotation.Oligo_tiling
Constructs an Oligo_tiling object with an Oligo_control ID
oligo_tiling_id - Variable in class object.annotation.Oligo_tiling
ID of Oligo_tiling Object
oligo_v - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object green
oligo_vb - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection green/blue
oligo_vj - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection green/yellow
oligo_vm - Static variable in class object.common.Spidey
Name of image corresponding to Oligo Object in the Blast Project Selection green/brown
oligoBase - Variable in class object.annotation.Organism
Blastbase Object corresponding to the Oligo blastbase of this Organism Object
oligoGraph - Variable in class object.common.SequenceObject
Blast Graph for this sequence against our Mediante Oligo Object Database
oligoGraphMap - Variable in class object.common.SequenceObject
Blast Graph for this sequence against our Mediante Oligo Object Database
OligoHit - Class in object.annotation
Description
Visualize at the selection project page, all the Oligos matching sequences of the SequenceObject project
Infos : KLB - IPMC - 08/2003
OligoHit(int, String, String, String, String, OnMouseOver) - Constructor for class object.annotation.OligoHit
Constructs an OligoHit object from several parameters
onlyCart - Variable in class object.common.ImageManager
True if only genes in cart must be displayed on the visualization graph (directory : 'graph')
onMouseOver - Variable in class object.annotation.OligoHit
Label of the OligoHit
OnMouseOver - Class in object.common
Description
Info-bulle with fonts and background colors generate by javascript
Infos : KLB - IPMC - 08/2003
OnMouseOver() - Constructor for class object.common.OnMouseOver
Default constructor
OnMouseOver(String, String[], String[]) - Constructor for class object.common.OnMouseOver
Constructs a OnMouseOver object with title
OnMouseOver(String[], String[]) - Constructor for class object.common.OnMouseOver
Constructs a OnMouseOver object with no title
OnMouseOver(String) - Constructor for class object.common.OnMouseOver
Constructs an OnMouseOver object with no tips (only title)
open(int) - Method in class object.microarray.Project_order
Open the Microarray_order at the index 'index' of the vectorMicroarray_order of this Project_order Object
openFile(String) - Method in class JRclient.Rconnection
open a file on the Rserve for reading
openHTS(int) - Method in class object.microarray.Project_order
Open the Microarray_order at the index 'index' of the vectorMicroarray_order of this Project_order Object
options - Variable in class object.hts.Hts_analysis_parameter
options
options - Variable in class object.hts.Hts_pipeline_parameter
options
order - Variable in class object.common.Attribution
Order Object in microarray attribution
Order - Class in object.common
Description
Can be a microarray order or a hts order Objects
Infos : KLB - IPMC - 05/2009
Order() - Constructor for class object.common.Order
 
Order(int, String) - Constructor for class object.common.Order
Constructs a Order Object from an existing Order ID
Order(String, String) - Constructor for class object.common.Order
Constructs a Order Object from an existing Order ID
order_id - Variable in class object.common.Journal
ID of Order Object related to this journal Object
order_id - Variable in class object.common.Order
ID of Order Object
order_ref - Variable in class object.common.Order
Reference of this Order Object
order_stats - Variable in class object.hts.Hts_order
 
order_type - Variable in class object.common.Order
Type of order
orderedKeys - Variable in class object.common.Convert
 
ordre_id - Variable in class object.common.SequenceObject
Ordre in the Project owner if this SequenceObject
ordre_id - Variable in class object.microarray.Microarray
ordre_id of this Microarray Object in the Spotting Object
organism - Variable in class object.annotation.GenomicPosition
Organism concerning this GenomicPosition Object
organism - Variable in class object.annotation.Oligo_annotation
Organism common name string associated to this relation
organism - Variable in class object.annotation.Oligo_control
Organism common name of Oligo_control Object
Organism - Class in object.annotation
Description
Organism Object
Infos : KLB - IPMC - 08/2003
Organism() - Constructor for class object.annotation.Organism
Default constructor
Organism(int) - Constructor for class object.annotation.Organism
Constructs an Organism object from Organism ID
Organism(String) - Constructor for class object.annotation.Organism
Constructs an Organism object from an Organism common name
organism - Variable in class object.common.Project
Organism Object of this Project Object
organism - Variable in class object.common.Public_database
Organism owner of the Public_database Object
organism - Variable in class object.hts.Hts_minseqe
Organism corresponding to this Hts_minseqe object
organism - Variable in class object.microarray.Labeling
Organism corresponding to this Subject object
organism - Variable in class object.microarray.Microarray_project_type
Organism Object concerned by this Microarray_project_type object
organism - Variable in class object.microarray.Plate
Organism Object concerning this Plate object
organism - Variable in class object.microrna.MicroSite
Organism
organism - Variable in class object.microrna.TargetPrediction
Organism
organism_gene - Variable in class object.microrna.MicroCible
Organism for transcripts search
organism_id - Variable in class object.annotation.Chromosome
Organism owner of this Chromosome
organism_id - Variable in class object.annotation.Organism
ID of Organism object
organism_id - Variable in class object.annotation.Sonde
ID of Organism Object related to this Sonde Object
organism_id - Variable in class object.common.BlastBase
ID of Organism object
organism_id - Variable in class object.common.Convert
ID of the Organism concerning by the conversion operation
organism_id - Variable in class object.common.ProjectObject
ID of Organism of this Project
organism_id - Variable in class object.common.Search
ID of the Organism concerning by the search
organism_id - Variable in class object.microrna.Mcbdata
organism_id
organism_id - Variable in class object.microrna.Mirna_mature
 
organism_id - Variable in class object.microrna.Mttdata
 
organisme - Variable in class object.common.User
Organism
organizeImages() - Method in class object.microarray.Scan
 
origin - Variable in class object.microarray.Labeling
Origin of this Subject object
os - Variable in class JRclient.Rconnection
 
os - Variable in class JRclient.Rtalk
 
overlap_sense - Variable in class object.microrna.Mirna_context
overlap_sense
overlap_type - Variable in class object.microrna.Mirna_context
overlap_type
owner - Variable in class object.microarray.GeoSerie
owner of GeoSerie Object

P

p - Variable in class object.common.ExecuteCmd
Process object
packRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_common
 
packRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_hts
 
packRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_mediante
 
packRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_medlab
 
packRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_microrna
 
packRequest(HttpServletRequest, Hashtable) - Method in class servlets.Proxy_rserve
 
pair - Static variable in class object.common.Spidey
Image for pair exon
parameters - Variable in class common.beans.locale.LocaleBean
 
parameters - Variable in class object.microarray.MageProtocol
parameters of this MageProtocol Object
parent_id - Variable in class object.annotation.Oligo_adhoc
ID of parent of this Oligo_adhoc Object
parseEvalResponse(Rpacket) - Method in class JRclient.Rconnection
 
parseREXP(REXP, byte[], int) - Static method in class JRclient.REXP
parses byte buffer for binary representation of xpressions - read one xpression slot (descends recursively for aggregated xpressions such as lists, vectors etc.)
password - Variable in class object.common.User
Password of the User Object
path - Variable in class object.hts.Hts_pipeline_outfile
path
path - Variable in class object.hts.MaFile
Path of matching file reference
path_fichier - Variable in class object.common.Fichier
Relative path to file of this Fichier object
pathBiostats - Static variable in class object.common.Biostats
 
pathBlast - Static variable in class object.common.Blast
 
pathCss - Static variable in class servlets.Proxy
 
pathCss - Static variable in class servlets.Proxy_common
 
pathCss - Static variable in class servlets.Proxy_hts
 
pathCss - Static variable in class servlets.Proxy_mediante
 
pathCss - Static variable in class servlets.Proxy_medlab
 
pathCss - Static variable in class servlets.Proxy_microrna
 
pathCss - Static variable in class servlets.Proxy_rserve
 
pathDatabase - Static variable in class object.common.Blast
 
pathDB - Static variable in class servlets.Proxy
 
pathDB - Static variable in class servlets.Proxy_common
 
pathDB - Static variable in class servlets.Proxy_hts
 
pathDB - Static variable in class servlets.Proxy_mediante
 
pathDB - Static variable in class servlets.Proxy_microrna
 
pathDB - Static variable in class servlets.Proxy_rserve
 
pathDownload - Static variable in class servlets.Proxy
 
pathDownload - Static variable in class servlets.Proxy_common
 
pathDownload - Static variable in class servlets.Proxy_hts
 
pathDownload - Static variable in class servlets.Proxy_mediante
 
pathDownload - Static variable in class servlets.Proxy_microrna
 
pathDownload - Static variable in class servlets.Proxy_rserve
 
pathExecution - Variable in class object.common.ExecuteCmd
Path of the directory in which we have to launch the commandes
pathFichier - Variable in class object.common.Blast
Path of the file where the sequence to Blast are store
pathFichierOne - Variable in class object.common.BlastTwoSeq
Path of the file where the first sequence to Blast is store
pathFichierTwo - Variable in class object.common.BlastTwoSeq
Path of the file where the second sequence to Blast is store
pathFiles - Variable in class object.common.SessionBlastObject
Absolute path to the file containing the Sequences to Blast
pathFormatDB - Static variable in class object.common.Blast
 
pathFormatDB - Static variable in class object.common.Project
Path of the program formatdb on the server
pathHts_sample - Static variable in class object.hts.Hts_result
 
pathImages - Static variable in class object.common.ImageManager
 
pathImages - Static variable in class object.common.Spidey
Path of the directory containing images
pathImages - Static variable in class object.microarray.Plate
 
pathImages - Static variable in class object.microarray.Spotting
 
pathImages - Static variable in class servlets.Proxy
 
pathImages - Static variable in class servlets.Proxy_common
 
pathImages - Static variable in class servlets.Proxy_hts
 
pathImages - Static variable in class servlets.Proxy_mediante
 
pathImages - Static variable in class servlets.Proxy_medlab
 
pathImages - Static variable in class servlets.Proxy_microrna
 
pathImages - Static variable in class servlets.Proxy_rserve
 
pathImg - Static variable in class servlets.Proxy
 
pathImg - Static variable in class servlets.Proxy_common
 
pathImg - Static variable in class servlets.Proxy_hts
 
pathImg - Static variable in class servlets.Proxy_mediante
 
pathImg - Static variable in class servlets.Proxy_medlab
 
pathImg - Static variable in class servlets.Proxy_microrna
 
pathImg - Static variable in class servlets.Proxy_rserve
 
pathJs - Static variable in class servlets.Proxy
 
pathJs - Static variable in class servlets.Proxy_common
 
pathJs - Static variable in class servlets.Proxy_hts
 
pathJs - Static variable in class servlets.Proxy_mediante
 
pathJs - Static variable in class servlets.Proxy_medlab
 
pathJs - Static variable in class servlets.Proxy_microrna
 
pathJs - Static variable in class servlets.Proxy_rserve
 
pathJsp - Static variable in class servlets.Proxy
 
pathJsp - Static variable in class servlets.Proxy_common
 
pathJsp - Static variable in class servlets.Proxy_hts
 
pathJsp - Static variable in class servlets.Proxy_mediante
 
pathJsp - Static variable in class servlets.Proxy_medlab
 
pathJsp - Static variable in class servlets.Proxy_microrna
 
pathJsp - Static variable in class servlets.Proxy_rserve
 
pathJsTip - Static variable in class servlets.Proxy
 
pathMicroarray - Static variable in class object.common.ImageManager
 
pathMicroarray - Static variable in class object.microarray.Scan
 
pathPublication - Static variable in class object.microarray.Project_order
 
pathSpotting - Static variable in class object.common.ImageManager
 
pathSpotting - Static variable in class object.microarray.Spotting
 
pathTmp - Static variable in class object.common.Biostats
 
pathTmp - Static variable in class object.common.Blast
 
pathTmp - Static variable in class object.common.BlastTwoSeq
 
pathTmp - Static variable in class object.common.Convert
 
pathTmp - Static variable in class object.common.ImageManager
 
pathTmp - Static variable in class object.common.Order
path to temporary directory
pathTmp - Static variable in class object.common.Project
Path of tmp files
pathTmp - Static variable in class object.common.Rstat
path to temporary directory
pathTmp - Static variable in class object.common.SessionBlastObject
Absolute path to the temporary folder
pathTmp - Static variable in class object.common.Toptable
 
pathTmp - Static variable in class object.hts.Hts_order
path to temporary directory
pathTmp - Static variable in class object.hts.Hts_result
 
pathTmp - Static variable in class object.hts.Hts_RManager
path to temporary directory
pathTmp - Static variable in class object.microarray.Project_order
 
pathTmp - Static variable in class object.microarray.Scan
 
pathTmp - Static variable in class object.microarray.Spotting
 
pathTmp - Static variable in class servlets.Proxy
 
pathTmp - Static variable in class servlets.Proxy_common
 
pathTmp - Static variable in class servlets.Proxy_hts
 
pathTmp - Static variable in class servlets.Proxy_mediante
 
pathTmp - Static variable in class servlets.Proxy_medlab
 
pathTmp - Static variable in class servlets.Proxy_microrna
 
pathTmp - Static variable in class servlets.Proxy_rserve
 
pathToptable - Static variable in class object.common.Toptable
 
Pattern_file - Class in object.microarray
Description
A Pattern_file Object represent a file containing Pattern for a Spotting Object
Infos : KLB - IPMC - 06/2007
Pattern_file() - Constructor for class object.microarray.Pattern_file
Default constructor
Pattern_file(String) - Constructor for class object.microarray.Pattern_file
Constructs a Pattern_file object from path to file
pattern_file - Variable in class object.microarray.Spotting
 
pays - Variable in class object.common.User
Country of User object
pdf_file - Variable in class object.common.Biostats
Path of .pdf file
percentageIdentity - Variable in class object.common.BlastHit
Percentage of identity
perform() - Method in class object.hts.Hts_RManager
 
performR() - Method in class object.common.Rstat
This function perform a R query according to attributes of Rstat
PERM_OP(int, int, int, int, int[]) - Static method in class JRclient.jcrypt
 
PgsqlConnector - Class in common.sql
Description: PgsqlConnector Object allowed connexion to PostgreSQL server

Organism : IPMC
Author : K.L.B
Date : Aout 2003
PgsqlConnector() - Constructor for class common.sql.PgsqlConnector
Default constructor
PgsqlDriver - Variable in class common.sql.PgsqlConnector
Driver Object
pid_pref - Variable in class object.common.Order
Preference choice of user concerning plateforme
Plate - Class in object.microarray
Description
Plate Object
Infos : KLB - IPMC - 08/2003
Plate() - Constructor for class object.microarray.Plate
Default constructor
Plate(int) - Constructor for class object.microarray.Plate
Constructs a Plate object from an existing Plate ID
Plate(String) - Constructor for class object.microarray.Plate
Constructs a Plate object from a plate_ref
Plate384 - Class in object.microarray
Description
Plate384 Object
Infos : KLB - IPMC - 01/2004
Plate384() - Constructor for class object.microarray.Plate384
Default constructor
Plate384(int) - Constructor for class object.microarray.Plate384
Constructs a Plate384 Object from a Plate384 ID
Plate384(String) - Constructor for class object.microarray.Plate384
Constructs a Plate384 Object from a Plate384 reference
plate384Ref - Variable in class object.common.Dilution
Slide_code of the Plate384 Object in dilution
Plate96 - Class in object.microarray
Description
Plate96 Object
Infos : KLB - IPMC - 01/2004
Plate96() - Constructor for class object.microarray.Plate96
Default constructor
Plate96(int) - Constructor for class object.microarray.Plate96
Constructs a Plate96 object from a Plate96 ID
Plate96(String) - Constructor for class object.microarray.Plate96
Constructs an Plate object from Plate ref
plate96_id - Variable in class object.annotation.Oligo_rel
ID of the Plate96 if we are talking about Plate384 position
plate_A1 - Variable in class object.microarray.Plate384
ID of a Plate96 Object part of this Plate384 Object
plate_A2 - Variable in class object.microarray.Plate384
ID of a Plate96 Object part of this Plate384 Object
plate_B1 - Variable in class object.microarray.Plate384
ID of a Plate96 Object part of this Plate384 Object
plate_B2 - Variable in class object.microarray.Plate384
ID of a Plate96 Object part of this Plate384 Object
plate_id - Variable in class object.annotation.Oligo_rel
ID of Plate Object associated with this relation
plate_id - Variable in class object.microarray.Plate
ID of this Plate object
plate_ref - Variable in class object.microarray.Plate
Reference of this Plate object
plate_transfert_type - Variable in class object.microarray.Plate384
Type of transfert from plate96 Object
Plate_transfert_type - Class in object.microarray
Description
Plate_transfert_type Object
Infos : KLB - IPMC - 01/2007
Plate_transfert_type() - Constructor for class object.microarray.Plate_transfert_type
Default constructor
Plate_transfert_type(int) - Constructor for class object.microarray.Plate_transfert_type
Constructs a Plate_type object from an existing Plate_type ID
plate_transfert_type_desc - Variable in class object.microarray.Plate_transfert_type
Description of the Plate_transfert_type Object
plate_transfert_type_id - Variable in class object.microarray.Plate_transfert_type
ID of Plate_transfert_type object
plate_type - Variable in class object.microarray.Plate
Plate_type Object of this Plate object
Plate_type - Class in object.microarray
Description
Plate_type Object
Infos : KLB - IPMC - 01/2004
Plate_type() - Constructor for class object.microarray.Plate_type
Default constructor
Plate_type(int) - Constructor for class object.microarray.Plate_type
Constructs a Plate_type object from an existing Plate_type ID
plate_type_id - Variable in class object.microarray.Plate_type
ID of Plate_type object
plate_type_ref - Variable in class object.microarray.Plate_type
Reference of the Plate_type Object
plateDisplay(String[], String[]) - Method in class object.microarray.Plate
This function return a string representing the Plate according to the Plate object composition give by the this.hashOligoPosition attribute.
plateforme - Variable in class object.common.Order
Plateforme where Order is ordered
Plateforme - Class in object.common
Description
Plateforme Object for MEDIANTE DNA microarray production
Infos : KLB - IPMC - 07/2004
Plateforme() - Constructor for class object.common.Plateforme
Default constructor
Plateforme(int) - Constructor for class object.common.Plateforme
Constructs a Plateforme object from an existing Plateforme ID
plateforme - Variable in class object.common.User
If this User Object belong to a Plateforme Object
plateforme - Variable in class object.hts.Hts_type
Plateforme where Hts_type is performed
plateforme - Variable in class object.microarray.Microarray_project_type
Plateforme owner of this Microarray_project_type object
plateforme - Variable in class object.microarray.Spotting
Plateforme owner of this Spotting object
plateforme_id - Variable in class object.common.Plateforme
ID of Plateforme Object
plateforme_ref - Variable in class object.common.Plateforme
Ref of Plateforme Object
pmt_ch1 - Variable in class object.microarray.Scan
PMT used for Channel 2 mesures for this Scan object
pmt_ch2 - Variable in class object.microarray.Scan
PMT used for Channel 1 mesures for this Scan object
Point - Class in object.common
Description
Point Object concerns microarrays spots and their position and annotations on the microarray
Infos : KLB - IPMC - 01/2006
Point() - Constructor for class object.common.Point
Default constructor
Point(double, double, String, String) - Constructor for class object.common.Point
Constructs a Point object from several parameters received
popsize - Variable in class object.microrna.MapTarget
 
port - Variable in class JRclient.Rconnection
 
port - Variable in class JRclient.RSession
 
position - Variable in class object.annotation.Genoligo_rel
Start position of the Oligo Object on the sequence of the Gene Object
position - Variable in class object.annotation.Oligo_adhocRelation
Position of oligo_adhoc object sequence on the Gene object sequence
position - Variable in class object.annotation.Oligo_control
Position of Oligo_control Object on the associated gene
position - Variable in class object.annotation.Oligo_rel
Position of the oligo in the Plate Object (i.e.
position - Variable in class object.microrna.MatchMCB
position
precision - Variable in class object.common.Foq
Precision concerning the type of Foq Object
prefam_acc - Variable in class object.microrna.Mttdata
prefam_acc
prefam_id - Variable in class object.microrna.Mttdata
prefam_id
PREFIX_COMMON - Variable in class servlets.Proxy
 
PREFIX_HTS - Variable in class servlets.Proxy
 
PREFIX_MEDIANTE - Variable in class servlets.Proxy
 
PREFIX_MEDLAB - Variable in class servlets.Proxy
 
PREFIX_MICRORNA - Variable in class servlets.Proxy
 
PREFIX_RSERVE - Variable in class servlets.Proxy
 
premir - Variable in class object.microrna.Mstdata
premir
premir_end - Variable in class object.microrna.Mstdata
chr_end
premir_start - Variable in class object.microrna.Mstdata
chr_start
preSelectOligo(Vector) - Method in class object.common.Project
This function execute an oligo pre-selection for the list of
keys of SequenceObject containing in the Project Object
probe_set_id - Variable in class object.annotation.Genoligo_affy_rel
probe_set_id
probe_set_id - Variable in class object.annotation.Oligo_affy
probe_set_id of probe for this Oligo_affy Object
Probeset - Class in object.annotation
Description
Represent a Probeset cluster from Affymetrix
Infos : KLB - IPMC - 04/2008
Probeset() - Constructor for class object.annotation.Probeset
Default constructor
Probeset(String) - Constructor for class object.annotation.Probeset
Constructs a Probeset object from a Probeset ID
probeset_id - Variable in class object.annotation.Probeset
ID of the Gene object
probleme - Variable in class object.common.Foq
Problem observed
proceed() - Method in class object.common.Convert
This function proceed to the annotation conversion
proceed() - Method in class object.common.ImageManager
This function proceed to Image creation in the visualization directory 'imag'.
proceed() - Method in class object.microrna.MapTarget
 
proceedCalcul(String) - Method in class object.common.ImageManager
This function proceed to the calcul of Quality Control defined in the type parameter received.
proceedCollectSequence(Hashtable) - Method in class object.common.Project
This function collect SequenceObject Object for this Project Object,
collection from search page of MEDIANTE web interface
proceedGraphs() - Method in class object.common.ImageManager
 
proceedOligoGraph(Vector) - Method in class object.common.Project
This function proceed to the Oligo Graph by the way of a Spidey Object and the function getAlignmentBlastHits()
proceedPlate384(int) - Method in class object.common.ImageManager
This function proceed to the creation of an image reformatting the Plate384 Object from the image of the Microarray hybridization.
proceedPlate96(int) - Method in class object.common.ImageManager
This function proceed to the creation of an image reformatting the Plate96 Object from the image of the Microarray hybridization.
proceedSearch() - Method in class object.common.Search
This function proceed to the search, function of parameters initialize in the loadParams() method.
proceedSearch() - Method in class object.microrna.MicroCible
This function proceed to the search, function of parameters initialize in the loadParams() method.
proceedSearch() - Method in class object.microrna.MicroSite
 
proceedSearch() - Method in class object.microrna.MicroTopTable
This function proceed to the search.
proceedSearch() - Method in class object.microrna.TargetPrediction
 
Project - Class in object.common
Description
Project of Oligo selection in the web interface
Infos : KLB - IPMC - 08/2003
Project() - Constructor for class object.common.Project
Default constructor
Project(int) - Constructor for class object.common.Project
This function load all the parameters needed by a Project to be initialized
project - Variable in class object.common.SessionObject
Project Object
project_id - Variable in class object.common.Project
ID of Project Object
project_id - Variable in class object.common.ProjectObject
ID of Project object
project_id - Variable in class object.common.SequenceObject
ID of the Project owner if this SequenceObject
project_order - Variable in class object.common.Board
Project_order for this Board Object
project_order - Variable in class object.common.ImageManager
Project_order Object concerning this ImageManager Object
project_order - Variable in class object.hts.Hts_RManager
 
Project_order - Class in object.microarray
Description
Project_order Object for RNG-MRC Microarrays ordering
Infos : KLB - IPMC - 07/2004
Project_order() - Constructor for class object.microarray.Project_order
Default constructor
Project_order(int) - Constructor for class object.microarray.Project_order
Constructs a Project_order object from an existing Project_order ID.
project_order_id - Variable in class object.common.Biostats
ID of Project_order Object owner of this analysis
project_order_id - Variable in class object.common.Order
ID of the Project_order Object to which belong this Order object
project_order_id - Variable in class object.common.Rstat
 
project_order_id - Variable in class object.common.Toptable
ID of Project_order Object owner of this analysis
project_order_id - Variable in class object.microarray.Project_order
ID of this Project_order object
project_order_ref - Variable in class object.common.Order
Project_order_ref of Project Object related to the Microarray_order object related to this Order Object
project_order_ref - Variable in class object.microarray.Project_order
Reference of this Project_order object
ProjectObject - Class in object.common
Description
Light Project Object
Infos : KLB - IPMC - 08/2003
ProjectObject() - Constructor for class object.common.ProjectObject
Default constructor
ProjectObject(int) - Constructor for class object.common.ProjectObject
Constructs a ProjectObject object from an existing ProjectObject ID
protein_id - Variable in class object.annotation.Gene
ID from protein from NCBI genbank file
protein_id - Variable in class object.annotation.Probeset
protein_id
protocol_amplification - Variable in class object.microarray.Labeling
Protocol_amplification Object for this Extraction object
Protocol_amplification - Class in object.microarray
Description
Protocol Amplification used in microarray experiment
Infos : KLB - IPMC - 01/2004
Protocol_amplification() - Constructor for class object.microarray.Protocol_amplification
Default constructor
Protocol_amplification(int) - Constructor for class object.microarray.Protocol_amplification
Constructs a Protocol_amplification object from an existing Protocol_amplification ID
protocol_amplification_id - Variable in class object.microarray.Protocol_amplification
ID of Protocol_amplification Object
protocol_amplification_ref - Variable in class object.microarray.Protocol_amplification
Reference of Protocol_amplification Object
protocol_extraction - Variable in class object.hts.Hts_minseqe
Extraction protocol used for this Hts_minseqe object
protocol_extraction - Variable in class object.microarray.Labeling
Extraction protocol used for this Extraction object
Protocol_extraction - Class in object.microarray
Description
Protocol_extraction Object belong to Extraction Object
Infos : KLB - IPMC - 07/2004
Protocol_extraction() - Constructor for class object.microarray.Protocol_extraction
Default constructor
Protocol_extraction(int) - Constructor for class object.microarray.Protocol_extraction
Constructs a Protocol_extraction object from an existing Protocol_extraction ID.
protocol_extraction_id - Variable in class object.microarray.Protocol_extraction
ID of this Protocol_extraction object
protocol_extraction_ref - Variable in class object.microarray.Protocol_extraction
Reference of this Protocol_extraction object
protocol_hybridization - Variable in class object.microarray.Hybridization
Protocol_hybridization Object of this Hybridization Object
Protocol_hybridization - Class in object.microarray
Description
Protocol_hybridization Object belong to Hybridization Object
Infos : KLB - IPMC - 07/2004
Protocol_hybridization() - Constructor for class object.microarray.Protocol_hybridization
Default constructor
Protocol_hybridization(int) - Constructor for class object.microarray.Protocol_hybridization
Constructs a Protocol_hybridization object from an existing Protocol_hybridization ID.
protocol_hybridization_id - Variable in class object.microarray.Protocol_hybridization
ID of this Protocol_hybridization object
protocol_hybridization_ref - Variable in class object.microarray.Protocol_hybridization
Reference of this Protocol_hybridization object
protocol_labeling - Variable in class object.microarray.Labeling
Labeling protocol used for this Labeling object
Protocol_labeling - Class in object.microarray
Description
Protocol_labeling Object belong to Labeling Object
Infos : KLB - IPMC - 07/2004
Protocol_labeling() - Constructor for class object.microarray.Protocol_labeling
Default constructor
Protocol_labeling(int) - Constructor for class object.microarray.Protocol_labeling
Constructs a Protocol_labeling object from an existing Protocol_labeling ID.
protocol_labeling_id - Variable in class object.microarray.Protocol_labeling
ID of this Protocol_labeling object
protocol_labeling_ref - Variable in class object.microarray.Protocol_labeling
Reference of this Protocol_labeling object
Provider - Class in object.microarray
Description
Provider Object
Infos : KLB - IPMC - 01/2004
Provider() - Constructor for class object.microarray.Provider
Default constructor
Provider(int) - Constructor for class object.microarray.Provider
Constructs a Provider object from Provider ID
provider_id - Variable in class object.microarray.Provider
ID of Provider object
provider_ref - Variable in class object.microarray.Provider
Name of the Provider Object
Proxy - Class in servlets
Description
Servlet Controler.
Proxy() - Constructor for class servlets.Proxy
 
Proxy_common - Class in servlets
Description
Servlet Controler concerning common actions.
Proxy_common() - Constructor for class servlets.Proxy_common
 
Proxy_hts - Class in servlets
Description
Servlet Controler concerning common actions.
Proxy_hts() - Constructor for class servlets.Proxy_hts
 
Proxy_mediante - Class in servlets
Description
Servlet Controler concerning MEDIANTE actions.
Proxy_mediante() - Constructor for class servlets.Proxy_mediante
 
Proxy_medlab - Class in servlets
Description
Servlet Controler concerning MEDLAB actions.
Proxy_medlab() - Constructor for class servlets.Proxy_medlab
 
Proxy_microrna - Class in servlets
Description
Servlet Controler.
Proxy_microrna() - Constructor for class servlets.Proxy_microrna
 
Proxy_rserve - Class in servlets
Description
Servlet Controler concerning RSERVE actions.
Proxy_rserve() - Constructor for class servlets.Proxy_rserve
 
psl_coord - Variable in class object.annotation.Sonde
PSL Genome Coordinates
Public_database - Class in object.common
Description
Public_database Object is an Object corresponding to the references of an IPMC array with public databases as GEO or ArrayExpress
Infos : KLB - IPMC - 09/2004
Public_database() - Constructor for class object.common.Public_database
Default constructor
Public_database(int) - Constructor for class object.common.Public_database
Constructs a Public_database object from an existing Public_database ID
public_database_id - Variable in class object.common.Public_database
ID of Public_database Object
pubmed - Variable in class object.annotation.GenbankRef
Reference of this GenbankRef object
push(String) - Method in class object.microrna.SnipMir
 
pvalue - Variable in class object.common.RNAhybrid
pvalue
pvalue - Variable in class object.microrna.Match
pvalue
pvalue - Variable in class object.microrna.Mirna_target
pvalue
pwd - Static variable in class common.sql.PgsqlConnector
PostgreSQL database password

Q

quantif_file - Variable in class object.microarray.Quantification_file
Path to the file of this Object
quantif_file - Variable in class object.microarray.Scan
Path to quantification file for this Scan object
Quantification_file - Class in object.microarray
Description
A Quantification_file Object represent a file containing the datas of a quantifcation file for a Scan Object
Infos : KLB - IPMC - 06/2007
Quantification_file() - Constructor for class object.microarray.Quantification_file
Default constructor
Quantification_file(String, Microarray_project_type) - Constructor for class object.microarray.Quantification_file
Constructs a Quantification_file object from path to file
quantification_file - Variable in class object.microarray.Scan
 
query - Variable in class object.common.Search
Query string to search in the list of the type_recherche attribute
queryId - Variable in class object.common.BlastHit
Query id for the corresponding alignment
querySequence - Variable in class object.common.BlastHit
Query sequence
queryStartPosition - Variable in class object.common.BlastHit
Start position on the query sequence
queryStopPosition - Variable in class object.common.BlastHit
Stop position on the query sequence
question_1 - Variable in class object.common.Enquete
Question number 1
question_10 - Variable in class object.common.Enquete
Question number 10
question_2 - Variable in class object.common.Enquete
Question number 2
question_3 - Variable in class object.common.Enquete
Question number 3
question_4 - Variable in class object.common.Enquete
Question number 4
question_5 - Variable in class object.common.Enquete
Question number 5
question_6 - Variable in class object.common.Enquete
Question number 6
question_7 - Variable in class object.common.Enquete
Question number 7
question_8 - Variable in class object.common.Enquete
Question number 8
question_9 - Variable in class object.common.Enquete
Question number 9
question_9plus - Variable in class object.common.Enquete
Question number 9plus
quoteString(String) - Static method in class JRclient.REXP
 

R

r - Variable in class object.common.ExecuteCmd
Runtime object
r_script - Variable in class object.common.Biostats
Path of R script file
ratio - Variable in class object.microarray.ElementMap
Ratio Signal of the spot
ratio - Variable in class object.microarray.Feature
Ratio Signal of the spot
ratio_230 - Variable in class object.hts.Hts_minseqe
 
ratio_280 - Variable in class object.hts.Hts_minseqe
 
rayon - Variable in class object.microarray.ElementMap
rayon of the oligo on the Tiff image
rayon - Variable in class object.microarray.Feature
rayon of the oligo on the Tiff image
RBool - Class in JRclient
Implementation of tri-state logical data type in R.
RBool(boolean) - Constructor for class JRclient.RBool
 
RBool(RBool) - Constructor for class JRclient.RBool
 
RBool(int) - Constructor for class JRclient.RBool
 
Rconnection - Class in JRclient
class providing TCP/IP connection to an Rserve
Rconnection() - Constructor for class JRclient.Rconnection
make a new local connection on default port (6311)
Rconnection(String) - Constructor for class JRclient.Rconnection
make a new connection to specified host on default port (6311)
Rconnection(String, int) - Constructor for class JRclient.Rconnection
make a new connection to specified host and given port.
Rconnection(RSession) - Constructor for class JRclient.Rconnection
 
Rconnection(String, int, RSession) - Constructor for class JRclient.Rconnection
 
read() - Method in class JRclient.RFileInputStream
reads one byte from the file.
read(byte[], int, int) - Method in class JRclient.RFileInputStream
Reads specified number of bytes (or less) from the remote file.
readyToSave() - Method in class object.common.CreationPlate
This function check if the creation Plate process can be saved :
- at least one Plate384 referenced in this.hashRefGenmate
- c4 valid Plate96 Object in this.hashPlate96
ref - Variable in class object.microarray.SpotType
ref
refresh(String, String, String) - Method in class object.microarray.Project_order
 
refseq - Variable in class object.annotation.Estoligo_rel
Refseq accession number of ESTs
refseqBase - Variable in class object.annotation.Organism
Blastbase Object corresponding to the Refseq transcript blastbase of this Organism Object
region - Variable in class object.microrna.MicroCible
gene region searched
release() - Method in class common.tags.generic.GetLocalTextTag
Releases all instance variables.
release() - Method in class common.tags.generic.UseLocaleBundleTag
Releases all instance variables.
reloadHts(int) - Method in class object.common.Board
This function load the Hts_sample Object among the current Board object
reloadMic(int) - Method in class object.common.Board
This function load the Microarray Object among the current Board object
reloadOrder(int) - Method in class object.common.Board
This function load the Microarray_order Object among the current Board object
reloadScan() - Method in class object.microarray.Microarray
This function reload this.vectorScan from database.
removeFile(String) - Method in class JRclient.Rconnection
remove a file on the Rserve
removeScan(int) - Method in class object.microarray.Microarray
This function remove scan from this.vectorScan at index i received.
replaceMicroarray(Microarray) - Method in class object.microarray.Spotting
 
replaceMicroarrayAtIndex(int) - Method in class object.microarray.Spotting
 
reponse - Variable in class object.common.Contact_client
Answer done to the client
reqReturnCode - Variable in exception JRclient.RSrvException
 
request(int) - Method in class JRclient.Rtalk
sends a request with no attached parameters
request(int, byte[]) - Method in class JRclient.Rtalk
sends a request with attached parameters
request(int, byte[], byte[], int, int) - Method in class JRclient.Rtalk
sends a request with attached prefix and parameters.
request(int, String) - Method in class JRclient.Rtalk
sends a request with one string parameter attached
request(int, int) - Method in class JRclient.Rtalk
sends a request with one string parameter attached
requestLocales - Variable in class common.beans.locale.LocaleBean
 
resetBundle() - Method in class common.beans.locale.LocaleBean
Resets the ResourceBundle.
resetCart() - Method in class object.common.GeneCart
This function reset this GeneCart Object
resetCart() - Method in class object.common.ImageManager
 
resetImages() - Method in class object.common.ImageManager
This function reset images Path from the hastable this.hashImage
resetLocale() - Method in class common.beans.locale.LocaleBean
Resets all locale dependent variables.
resource - Variable in class object.common.Xhtml
Ressource to parse
responsable - Variable in class object.common.Plateforme
Production administrator of the Plateforme Object
results - Variable in class object.common.Convert
results of conversion
retoucheImage(String, String) - Method in class object.microarray.Scan
This function Modify ligth of microarray JPG images
rev_start - Variable in class object.microrna.Mstdata
rev_start
REXP - Class in JRclient
representation of R-eXpressions in Java
REXP() - Constructor for class JRclient.REXP
construct a new, empty (NULL) expression w/o attribute
REXP(int, Object) - Constructor for class JRclient.REXP
construct a new xpression of type t and content o, but no attribute
REXP(int, Object, REXP) - Constructor for class JRclient.REXP
construct a new xpression of type t, content o and attribute at
REXP(double[]) - Constructor for class JRclient.REXP
construct a new xpression of type XT_ARRAY_DOUBLE and content val
REXP(int[]) - Constructor for class JRclient.REXP
construct a new xpression of type XT_ARRAY_INT and content val
REXP(String[]) - Constructor for class JRclient.REXP
construct a new xpression of type XT_ARRAY_INT and content val
RFactor - Class in JRclient
representation of a factor variable.
RFactor() - Constructor for class JRclient.RFactor
create a new, empty factor var
RFactor(int[], String[]) - Constructor for class JRclient.RFactor
create a new factor variable, based on the supplied arrays.
RFactor(int[], Vector) - Constructor for class JRclient.RFactor
special constructor used by REXP parser to save some re-indexing and performing automatic index conversion
RFileInputStream - Class in JRclient
RFileInputStream is an InputStream to transfer files from Rserve server to the client.
RFileInputStream(Rtalk, String) - Constructor for class JRclient.RFileInputStream
tries to open file on the R server, using specified Rtalk object and filename.
RFileOutputStream - Class in JRclient
RFileOutputStream is an OutputStream to transfer files from the client to Rserve server.
RFileOutputStream(Rtalk, String) - Constructor for class JRclient.RFileOutputStream
tries to create a file on the R server, using specified Rtalk object and filename.
right - Variable in class object.common.Board
Right on this Project_order
rin - Variable in class object.hts.Hts_minseqe
 
rin_number - Variable in class object.microarray.Labeling
RNA integrity number fir this Extraction object
RList - Class in JRclient
implementation of R-lists
This is rather preliminary and may change in future since it's not really proper.
RList() - Constructor for class JRclient.RList
constructs an empty list
RList(REXP, REXP) - Constructor for class JRclient.RList
constructs an initialized list
RNAfold - Class in object.common
Description
Infos : KLB - IPMC - 05/2008
RNAfold(Sequence, int, String) - Constructor for class object.common.RNAfold
Default constructor
rnafold - Variable in class object.microrna.MatchMCB
rnafold
rnafold - Variable in class object.microrna.Mstdata
rnafold
RNAhybrid - Class in object.common
Description
Infos : KLB - IPMC - 06/2008
RNAhybrid(String, String) - Constructor for class object.common.RNAhybrid
Default constructor
rnahybrid - Variable in class object.microrna.MatchMCB
rnahybrid
rnahybrid - Variable in class object.microrna.Mstdata
rnahybrid
rng_id - Variable in class object.common.Order
RNG ID of the Microarray_order object related to this Order Object
ROUNDING_STRATEGY - Static variable in class object.common.HypDistanceCalculator
The rounding strategy for the calculations.
row - Variable in class object.annotation.Oligo_rel
Row of the oligo in the Plate Object (i.e.
row - Variable in class object.microarray.ElementMap
Row in Bloc in which the oligo is located
row - Variable in class object.microarray.Feature
Row in Bloc in which the oligo is located
row - Static variable in class object.microarray.Plate384
 
row - Static variable in class object.microarray.Plate96
 
Rpacket - Class in JRclient
small class encapsulating packets from/to Rserv
Rpacket(int, byte[]) - Constructor for class JRclient.Rpacket
construct new packet
RSession - Class in JRclient
 
RSession() - Constructor for class JRclient.RSession
 
RSession(Rconnection, Rpacket) - Constructor for class JRclient.RSession
 
RSrvException - Exception in JRclient
 
RSrvException(Rconnection, String) - Constructor for exception JRclient.RSrvException
 
RSrvException(Rconnection, String, int) - Constructor for exception JRclient.RSrvException
 
RSrvException(Rconnection, String, Rpacket) - Constructor for exception JRclient.RSrvException
 
rsrvVersion - Variable in class JRclient.Rconnection
version of the server (as reported in IDstring just after Rsrv)
rsrvVersion - Variable in class JRclient.RSession
 
rstat - Variable in class object.common.ImageManager
 
Rstat - Class in object.common
Description
A Rstat object allow to perform R queies to do microarray analysis
Infos : KLB - IPMC - 10/2008
Rstat(int, int) - Constructor for class object.common.Rstat
Default constructor
rt - Variable in class JRclient.Rconnection
 
rt - Variable in class JRclient.RFileInputStream
Rtalk class to use for communication with the Rserve
rt - Variable in class JRclient.RFileOutputStream
Rtalk class to use for communication with the Rserve
Rtalk - Class in JRclient
This class encapsulates the QAP1 protocol used by Rserv.
Rtalk(InputStream, OutputStream) - Constructor for class JRclient.Rtalk
constructor; parameters specify the streams

S

s - Variable in class JRclient.Rconnection
 
salmon - Static variable in class object.common.Spidey
Image salmon
sample_ref - Variable in class object.microarray.Labeling
Reference of this Sample object
sample_size - Variable in class object.microrna.MapTarget
 
sanger_id - Variable in class object.annotation.Oligo_adhoc_match
Sanger_id for this Oligo_adhoc_match Object
sanger_ref - Variable in class object.annotation.Oligo_adhoc_match
Sanger_ref for this Oligo_adhoc_match Object
save(User) - Method in class object.common.Attribution
This function save the attribution process concerning this Attribution Object
- update each Microarray Object
- if the microarray attribution for this Order Object is over update the Order
save() - Method in class object.common.Biostats
This function save or update this Biostats Object into database
save() - Method in class object.common.Contact_client
This function save this Contact_client Object into database Note that all attributes must be not null and not empty
save(int) - Method in class object.common.CreationPlate
This function save the creation Plate process
save(int) - Method in class object.common.Dilution
This function save the dilution process
save() - Method in class object.common.Enquete
This function save this Enquete Object into database
save() - Method in class object.common.Foq
This function save or update this Foq Object into database
NB : (user_id, date, type_foq, probleme, solution) !
save() - Method in class object.common.GeneCart
This function save or update this GeneCart Object into database
save() - Method in class object.common.Journal
This function save this Journal Object into database.
save() - Method in class object.common.Keyword
This function save or update this Keyword Object into database
NB : (keyword_ref) !
save() - Method in class object.common.Order
This function save or update this Microarray_order Object into database NB : (date_order, state, project_order_id, nb_microarray, microarray_project_type) !
save() - Method in class object.common.Project
This function save the Project and all the SequenceObject contains in the vectorSequenceObject attribute
save() - Method in class object.common.SequenceObject
This function collect SequenceObject Object for this Project Object, collection from search page of Mediante web interface
save() - Method in class object.common.Toptable
This function save or update this Biostats Object into database
save() - Method in class object.common.User
 
save() - Method in class object.hts.Hts_minseqe
This function save or update this Hts_minseqe Object into database
save() - Method in class object.hts.Hts_result
This function save or update this Hts_result Object into database
save() - Method in class object.hts.Hts_run
 
save() - Method in class object.hts.Hts_sample
This function save Hts_sample Object into database.
save() - Method in class object.microarray.Control
This function save the Control Object into the database (table slide_control)
save() - Method in class object.microarray.Hybridization
This function save or update this Hybridization Object into database
NB : (microarray_id, protocol_hybridization, amount_hyb) !
save() - Method in class object.microarray.Labeling
This function save or update Labeling Objects into database
save() - Method in class object.microarray.Microarray
This function save Microarray Object into database.
save() - Method in class object.microarray.Plate384
This function save the Plate384 Object into database
save() - Method in class object.microarray.Project_order
This function save or update this Project_order Object into database
NB : (date_project_order, project_order_ref, description, duration, user) !
save() - Method in class object.microarray.Protocol_extraction
This function save or update this Protocol_extraction Object into database
NB : (protocol_extraction_ref) !
save() - Method in class object.microarray.Protocol_hybridization
This function save or update this Protocol_hybridization Object into database NB : (tampon,duree,temperature) !
save() - Method in class object.microarray.Scan
This function save or update this Scan Object into database
save() - Method in class object.microarray.Spotting
 
saveCart(String) - Method in class object.common.ImageManager
 
saveHashColor(int) - Method in class object.common.ImageManager
This function save or update Graph Colors for User.
saveToBiostats() - Method in class object.common.Rstat
 
sc - Variable in class servlets.Proxy
 
sc - Variable in class servlets.Proxy_common
 
sc - Variable in class servlets.Proxy_hts
 
sc - Variable in class servlets.Proxy_mediante
 
sc - Variable in class servlets.Proxy_medlab
 
sc - Variable in class servlets.Proxy_microrna
 
sc - Variable in class servlets.Proxy_rserve
 
SCALE - Static variable in class object.common.HypDistanceCalculator
The number of digits after the first non-zero digit in the decimal part of a number.
Scan - Class in object.microarray
Description
Scan Object
Infos : KLB - IPMC - 02/2004
Scan() - Constructor for class object.microarray.Scan
Default constructor
Scan(int) - Constructor for class object.microarray.Scan
Constructs an Scan object from an existing Scan ID
scan_id - Variable in class object.microarray.Scan
ID of this Scan object
scan_ref - Variable in class object.microarray.Scan
Reference of this Scan object
Scanner - Class in object.microarray
Description
Scanner Object
Infos : KLB - IPMC - 02/2004
Scanner() - Constructor for class object.microarray.Scanner
Default constructor
Scanner(int) - Constructor for class object.microarray.Scanner
Constructs an Scanner object from an existing Scanner ID
scanner_id - Variable in class object.microarray.Scanner
ID of this Scanner object
scanner_ref - Variable in class object.microarray.Scanner
Reference of this Scanner object
score - Variable in class object.annotation.Oligo
not use
score - Variable in class object.annotation.Spodo_hit
score
score - Variable in class object.common.BlastHit
Score of the corresponding alignment
Search - Class in object.common
Description
Allow to Search the database for Gene like in the form in the web interface, this object can do several different search action following the parameters received from the Html Form
Infos : KLB - IPMC - 08/2003
Search() - Constructor for class object.common.Search
Default constructor
search - Variable in class object.common.SessionObject
Search Object
seed_size - Variable in class object.microrna.MicroCible
Seed size searched
seed_start - Variable in class object.microrna.MicroCible
Seed start searched
seed_stop - Variable in class object.microrna.MicroCible
Seed stop searched
sendEmail(String, String, String) - Method in class object.common.Common
 
sendEmail() - Method in class object.common.Order
This function send an e-mail to admin users to ask for action on Medlab application.
sendEmail(User) - Method in class object.common.Project
This function send an e-mail to the User Object received concerning the oligo selection in this Project Object
sendMailToAll() - Method in class object.common.Order
This function send an e-mail to all users of Mediante (used in case of mass-mailling process) - inactive most of time
sens - Variable in class object.annotation.Oligo_tiling
sens of Oligo_tiling Object
seqOne - Variable in class object.common.BlastTwoSeq
The sequence entered in the first textarea of our form
seqTwo - Variable in class object.common.BlastTwoSeq
The sequence entered in the second textarea of our form
sequence - Variable in class object.annotation.Gene
RNA sequence of this Gene object
sequence - Variable in class object.annotation.Oligo_control
Sequence of Oligo_control Object
sequence - Variable in class object.annotation.Oligo_tiling
Sequence of Oligo_tiling Object
sequence - Variable in class object.annotation.Sonde
Sequence of the Sonde Object
sequence - Variable in class object.common.RNAfold
sequence
sequence - Variable in class object.common.SequenceObject
Sequence object from Biojava API
sequence - Variable in class object.microrna.Mcbdata
sequence
sequence - Variable in class object.microrna.Mcbmatch
sequence
sequence - Variable in class object.microrna.MicroCible
sequence to search
sequence - Variable in class object.microrna.Mstdata
sequence
sequence_name - Variable in class object.common.SequenceObject
Name of the sequenceObject Object
sequenceBase - Variable in class object.annotation.Organism
Blastbase Object corresponding to the Mediante transcript blastbase of this Organism Object
SequenceObject - Class in object.common
Description
Object contained in a Project Object, it contains all we have to know about a sequence submit by user and it's association with a Mediante oligo
Infos : KLB - IPMC - 08/2003
SequenceObject() - Constructor for class object.common.SequenceObject
Default constructor
SequenceObject(Sequence) - Constructor for class object.common.SequenceObject
Construct a SequenceObject Object with a Biojava Sequence Oject
SequenceObject(int, int) - Constructor for class object.common.SequenceObject
Construct a SequenceObject Object with a Project_id and a ordre_id params
sequenceOne - Variable in class object.common.BlastTwoSeq
Sequence object for our first sequence to align
sequenceTwo - Variable in class object.common.BlastTwoSeq
Sequence object for our second sequence to align
serialVersionUID - Static variable in class JRclient.RSession
 
Serie - Class in object.microarray
Description
Serie Objects
Infos : KLB - IPMC - 10/2008
Serie(String, String, String, String) - Constructor for class object.microarray.Serie
Default constructor
serie_file - Variable in class object.common.Biostats
Path of serie file
serie_ok - Variable in class object.common.Rstat
 
serieFile - Variable in class object.common.Rstat
 
SerieFile - Class in object.microarray
Description
SerieFile Objects
Infos : KLB - IPMC - 10/2008
SerieFile() - Constructor for class object.microarray.SerieFile
Default constructor
serieToFile() - Method in class object.hts.Hts_RManager
 
service(HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy
 
service(HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_common
 
service(HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_hts
 
service(HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_mediante
 
service(HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_medlab
 
service(HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_microrna
 
service(HttpServletRequest, HttpServletResponse) - Method in class servlets.Proxy_rserve
 
servlets - package servlets
 
SessionBlastObject - Class in object.common
Description
This object allowed to launch Blast whith parameters received from an HTML form
Infos : KLB - IPMC - 12/2003
SessionBlastObject() - Constructor for class object.common.SessionBlastObject
Default constructor
SessionObject - Class in object.common
Description
Object stocked in the Browser Session, it contains several Other Objects needed during navigation in the Web interface
Infos : KLB - IPMC - 08/2003
SessionObject() - Constructor for class object.common.SessionObject
Default constructor
set(boolean) - Method in class object.microarray.ElementMap
 
set(boolean) - Method in class object.microarray.Feature
 
setAc_ref(String) - Method in class object.common.Foq
 
setAccession(String) - Method in class object.annotation.Oligo_adhoc
 
setAccession(String) - Method in class object.annotation.Oligo_affy
 
setAccession(String) - Method in class object.annotation.Oligo_control
 
setAccession(String) - Method in class object.annotation.Spodo_hit
 
setAccession(String) - Method in class object.common.SessionBlastObject
 
setAccession(String) - Method in class object.microarray.MageProtocol
 
setAccession_number(String) - Method in class object.annotation.Gene
 
setAccession_number(String) - Method in class object.annotation.Genoligo_affy_rel
 
setAccession_number(String) - Method in class object.annotation.Oligo_annotation
 
setAccession_number(String) - Method in class object.annotation.Probeset
 
setAccessionOne(String) - Method in class object.common.BlastTwoSeq
 
setAccessionTwo(String) - Method in class object.common.BlastTwoSeq
 
setAction(String) - Method in class object.common.Journal
 
setAction_corrective(boolean) - Method in class object.common.Foq
 
setAction_ok(boolean) - Method in class object.common.Foq
 
setAdd_fact(String) - Method in class object.common.User
 
setAdd_livr(String) - Method in class object.common.User
 
setAdresse(String) - Method in class object.common.Plateforme
 
setAdresse(String) - Method in class object.common.User
 
setAe_if_cy3(String) - Method in class object.microarray.Protocol_labeling
 
setAe_if_cy5(String) - Method in class object.microarray.Protocol_labeling
 
setAe_ref(String) - Method in class object.microarray.Nucleic_acid_type
 
setAe_ref(String) - Method in class object.microarray.Protocol_hybridization
 
setAgilent_design(String) - Method in class object.microarray.Microarray_project_type
 
setAlign(String) - Method in class object.microrna.MatchMCB
 
setAlignment(String) - Method in class object.common.RNAfold
 
setAlignment(String) - Method in class object.common.RNAhybrid
 
setAlignmentSize(String) - Method in class object.common.BlastHit
 
setAllOk(boolean) - Method in class object.common.Blast
 
setAmount(double) - Method in class object.hts.Hts_minseqe
 
setAmount_hyb(double) - Method in class object.microarray.Hybridization
 
setAmount_input(double) - Method in class object.microarray.Labeling
 
setAmount_output(double) - Method in class object.microarray.Labeling
 
setAmpli_amount(double) - Method in class object.microarray.Labeling
 
setAmpli_concentration(double) - Method in class object.microarray.Labeling
 
setAnnotation(String) - Method in class object.annotation.Oligo_control
 
setAppli(String) - Method in class object.common.ImageManager
 
setApv_cutoff(double) - Method in class object.microrna.MicroTopTable
 
setArray_1(int) - Method in class object.common.ImageManager
 
setArray_2(int) - Method in class object.common.ImageManager
 
setArray_labo_id(int) - Method in class object.microarray.ArrayLabo
 
setArray_labo_name(String) - Method in class object.microarray.ArrayLabo
 
setArrayexpress(String) - Method in class object.common.Public_database
 
setArrayexpress(String) - Method in class object.microarray.Labeling_type
 
setArrayexpress(String) - Method in class object.microarray.Microarray_project_type
 
setArrayLabo(ArrayLabo) - Method in class object.microarray.Microarray_project_type
 
setArrayQuality(String) - Method in class object.microarray.Microarray
 
setAuthor(String) - Method in class object.microrna.Mirna_reference
 
setAuthors(String) - Method in class object.annotation.GenbankRef
 
setAuto_mature(int) - Method in class object.microrna.Mcbmatch
 
setAuto_mature(String) - Method in class object.microrna.MicroCible
 
setAuto_mature(int) - Method in class object.microrna.Mirna_mature
 
setAuto_mature(int) - Method in class object.microrna.Mirna_target
 
setAuto_mirna(int) - Method in class object.microrna.Mirna
 
setAveExpr(double) - Method in class object.microrna.Mttdata
 
setAverage(String) - Method in class object.microarray.Feature
 
setAvgexpr(double) - Method in class object.microrna.MicroTopTable
 
setB_cutoff(double) - Method in class object.microrna.MicroTopTable
 
setBackground(String) - Method in class object.common.Biostats
 
setBackground(String) - Method in class object.common.Rstat
 
setBatchNumber(String) - Method in class object.microarray.Microarray
 
setBcr_file(String) - Method in class object.microarray.Spotting
 
setBiomaterial(String) - Method in class object.hts.Hts_minseqe
 
setBiostats_file(String) - Method in class object.common.Biostats
 
setBiostats_id(int) - Method in class object.common.Biostats
 
setBiostats_ref(String) - Method in class object.common.Biostats
 
setBlast(Blast) - Method in class object.common.BlastTwoSeq
 
setBlast(Blast) - Method in class object.common.SessionBlastObject
 
setBlastbase(BlastBase) - Method in class object.annotation.Specificity
 
setBlastbase(BlastBase) - Method in class object.common.SessionBlastObject
 
setBlastbase_id(int) - Method in class object.common.BlastBase
 
setBlastbase_name(String) - Method in class object.common.BlastBase
 
setBlastbase_type(String) - Method in class object.common.BlastBase
 
setBlastOligo(Blast) - Method in class object.common.Project
 
setBloc(String) - Method in class object.common.DisplayParams
 
setBloc(String) - Method in class object.microarray.ElementMap
 
setBloc(String) - Method in class object.microarray.Feature
 
setBundleName(String) - Method in class common.beans.locale.LocaleBean
Sets the bundle name.
setBundleName(String) - Method in class common.tags.generic.UseLocaleBundleTag
Sets the bundleName property, i.e. the base name for the ResourceBundle used for localized text.
setBvalue(double) - Method in class object.common.ImageManager
 
setCdf(double) - Method in class object.microrna.Target
 
setCdf_down(double) - Method in class object.microrna.Mttdata
 
setCdf_up(double) - Method in class object.microrna.Mttdata
 
setCell_type(String) - Method in class object.microarray.Labeling
 
setCh1(String) - Method in class object.microarray.Serie
 
setCh2(String) - Method in class object.microarray.Serie
 
setCharset(String) - Method in class common.beans.locale.LocaleBean
Sets the charset used to parse request parameters.
setChr_nb(int) - Method in class object.annotation.Organism
 
setChromosome(String) - Method in class object.annotation.GenomicPosition
 
setChromosome(String) - Method in class object.microrna.Mstdata
 
setChromosome_id(int) - Method in class object.annotation.Chromosome
 
setChromosome_id(int) - Method in class object.annotation.Cytoband
 
setChromosome_id(int) - Method in class object.annotation.GenomicPosition
 
setChromosome_id(int) - Method in class object.common.Search
 
setChromosome_name(String) - Method in class object.annotation.Chromosome
 
setClient(User) - Method in class object.common.Enquete
 
setClient_id(int) - Method in class object.common.Contact_client
 
setColor(String) - Method in class object.common.Point
 
setColor(String) - Method in class object.microarray.Labeling_type
 
setColor(String) - Method in class object.microarray.SpotType
 
setColumn(int) - Method in class object.annotation.Oligo_rel
 
setColumn(String) - Method in class object.microarray.ElementMap
 
setColumn(String) - Method in class object.microarray.Feature
 
setCommande_id(int) - Method in class object.common.Commande
 
setCommande_ref(String) - Method in class object.common.Commande
 
setComment(String) - Method in class object.common.Order
 
setComment(String) - Method in class object.microarray.Hybridization
 
setComment(String) - Method in class object.microarray.Spotting
 
setComments(String) - Method in class object.common.Journal
 
setCommon_name(String) - Method in class object.annotation.Organism
 
setCon() - Method in class common.sql.PgsqlConnector
Set Conn Object, synchronized method
setCon(Connection) - Method in class common.sql.PgsqlConnector
Set Conn Object with Connection Object
setConcentration(int) - Method in class object.microarray.Plate
 
setConcentration_bank(double) - Method in class object.hts.Hts_minseqe
 
setConcentration_sample(double) - Method in class object.hts.Hts_minseqe
 
setConnectionParam(String, String, String, String) - Method in class common.sql.PgsqlConnector
This function initialize static parameters of PgsqlConnector Objects --> connexClass, connexURL, user, pwd
setContact_client_id(int) - Method in class object.common.Contact_client
 
setContext(String) - Method in class object.annotation.Oligo_adhoc_match
 
setContig_end() - Method in class object.microrna.Mirna_chromosome
 
setContig_start(int) - Method in class object.microrna.Mirna_chromosome
 
setControl_type(Control_type) - Method in class object.microarray.Control
 
setControl_type_id(int) - Method in class object.microarray.Control_type
 
setControl_type_ref(String) - Method in class object.microarray.Control_type
 
setControlColor(String) - Method in class object.microarray.Scan
 
setCoord(String) - Method in class object.annotation.Chromosome
 
setCoord2(String) - Method in class object.annotation.Chromosome
 
setCouleur(String) - Method in class object.common.DisplayParams
 
setCount(int) - Method in class object.microrna.Target
 
setCurrentPage(int) - Method in class object.common.Project
 
setCurrentReference(String) - Method in class object.common.Attribution
 
setCy3_bruit(String) - Method in class object.microarray.ElementMap
 
setCy3_bruit(String) - Method in class object.microarray.Feature
 
setCy3_median(String) - Method in class object.microarray.ElementMap
 
setCy3_median(String) - Method in class object.microarray.Feature
 
setCy5_bruit(String) - Method in class object.microarray.ElementMap
 
setCy5_bruit(String) - Method in class object.microarray.Feature
 
setCy5_median(String) - Method in class object.microarray.ElementMap
 
setCy5_median(String) - Method in class object.microarray.Feature
 
setCy_pmol(double) - Method in class object.microarray.Labeling
 
setCytoband_id(int) - Method in class object.annotation.Cytoband
 
setCytoband_id(int) - Method in class object.common.Search
 
setCytoband_ref(String) - Method in class object.annotation.Cytoband
 
setDatabase(String) - Method in class object.common.Blast
 
setDate(Date) - Method in class object.common.Contact_client
 
setDate(Date) - Method in class object.common.CreationPlate
 
setDate(Date) - Method in class object.common.Diary
 
setDate(Date) - Method in class object.common.Foq
 
setDate(Date) - Method in class object.common.Journal
 
setDate(Date) - Method in class object.common.Project
 
setDate(Date) - Method in class object.common.ProjectObject
 
setDate(Date) - Method in class object.hts.Hts_minseqe
 
setDate(Date) - Method in class object.hts.Hts_result
 
setDate(Date) - Method in class object.hts.Hts_run
 
setDate_attribution(Date) - Method in class object.common.Attribution
 
setDate_attribution(Date) - Method in class object.hts.Hts_sample
 
setDate_attribution(Date) - Method in class object.microarray.Microarray
 
setDate_control(Date) - Method in class object.microarray.Control
 
setDate_creation(Date) - Method in class object.microarray.Plate
 
setDate_delivery(Date) - Method in class object.common.Order
 
setDate_dilution(Date) - Method in class object.microarray.Plate384
 
setDate_enquete(Date) - Method in class object.common.Enquete
 
setDate_expiration(Date) - Method in class object.microarray.Microarray
 
setDate_extraction(Date) - Method in class object.microarray.Labeling
 
setDate_hyb(Date) - Method in class object.microarray.Hybridization
 
setDate_labeling(Date) - Method in class object.microarray.Labeling
 
setDate_order(Date) - Method in class object.common.Order
 
setDate_prevision(Date) - Method in class object.common.Order
 
setDate_project_order(Date) - Method in class object.microarray.Project_order
 
setDate_sample(Date) - Method in class object.microarray.Labeling
 
setDate_scan(Date) - Method in class object.microarray.Scan
 
setDate_spotting(Date) - Method in class object.microarray.Spotting
 
setDate_subject(Date) - Method in class object.microarray.Labeling
 
setDate_wish(Date) - Method in class object.common.Order
 
setDemande(String) - Method in class object.common.Contact_client
 
setDescription(String) - Method in class object.annotation.Gene
 
setDescription(String) - Method in class object.annotation.Oligo_adhoc
 
setDescription(String) - Method in class object.annotation.Oligo_adhoc_match
 
setDescription(String) - Method in class object.annotation.Probeset
 
setDescription(String) - Method in class object.annotation.Spodo_hit
 
setDescription(String) - Method in class object.common.BlastBase
 
setDescription(String) - Method in class object.common.GeneCart
 
setDescription(String) - Method in class object.common.IdDescriptionObject
 
setDescription(String) - Method in class object.common.Project
 
setDescription(String) - Method in class object.common.ProjectObject
 
setDescription(String) - Method in class object.common.Public_database
 
setDescription(String) - Method in class object.hts.Hts_analysis
 
setDescription(String) - Method in class object.hts.Hts_analysis_parameter
 
setDescription(String) - Method in class object.hts.Hts_pipeline_outfile
 
setDescription(String) - Method in class object.hts.Hts_pipeline_parameter
 
setDescription(String) - Method in class object.hts.Hts_type
 
setDescription(String) - Method in class object.microarray.Microarray_project_type
 
setDescription(String) - Method in class object.microarray.Project_order
 
setDescription(String) - Method in class object.microrna.Mirna
 
setDiluant(String) - Method in class object.common.Dilution
 
setDiluant(String) - Method in class object.microarray.Plate384
 
setDirectory(String) - Method in class object.common.ImageManager
 
setDisease(String) - Method in class object.microarray.Labeling
 
setDisplayParams(DisplayParams) - Method in class object.common.ImageManager
 
setDuration(int) - Method in class object.microarray.Project_order
 
setDvt_stage(String) - Method in class object.microarray.Labeling
 
setDye_cy3(String) - Method in class object.microarray.Protocol_labeling
 
setDye_cy5(String) - Method in class object.microarray.Protocol_labeling
 
setEmail(String) - Method in class object.common.User
 
setEnd(int) - Method in class object.annotation.Cytoband
 
setEnd(int) - Method in class object.annotation.Exon
 
setEnd(int) - Method in class object.annotation.GenomicPosition
 
setEnergy(double) - Method in class object.common.RNAfold
 
setEnergy(double) - Method in class object.common.RNAhybrid
 
setEnquete_id(int) - Method in class object.common.Enquete
 
setEnqueteur(User) - Method in class object.common.Enquete
 
setEnrichement_down(double) - Method in class object.microrna.Mttdata
 
setEnrichement_up(double) - Method in class object.microrna.Mttdata
 
setEnsembl_id(String) - Method in class object.annotation.Probeset
 
setEnsemblBase(BlastBase) - Method in class object.annotation.Organism
 
setEnst(String) - Method in class object.microrna.Match
 
setEnst(String) - Method in class object.microrna.Mirna_target
 
setEnthalpy(String) - Method in class object.annotation.Oligo
 
setEnthalpy(String) - Method in class object.annotation.Oligo_tiling
 
setEntropy(String) - Method in class object.annotation.Oligo
 
setEntropy(String) - Method in class object.annotation.Oligo_tiling
 
setEstMatch(String) - Method in class object.annotation.Gene
 
setEstTissue_id(int) - Method in class object.annotation.EstTissue
 
setEstTissue_ref(String) - Method in class object.annotation.EstTissue
 
setEvalue(double) - Method in class object.annotation.Spodo_hit
 
setEvalue(String[]) - Method in class object.microarray.Microarray_project_type
 
setEvalue(double) - Method in class object.microrna.MicroSite
 
setEvent(String) - Method in class object.common.Diary
 
setEvents(String) - Method in class object.common.Order
 
setExcel_file(String) - Method in class object.common.Biostats
 
setExon(int) - Method in class object.annotation.Exon
 
setExon(int) - Method in class object.annotation.Oligo
 
setExpectation(String) - Method in class object.common.Blast
 
setExpectation(String) - Method in class object.common.BlastTwoSeq
 
setExpectation(String) - Method in class object.common.Project
 
setExpectation(String) - Method in class object.common.SessionBlastObject
 
setExpected_down(int) - Method in class object.microrna.Mttdata
 
setExpected_up(int) - Method in class object.microrna.Mttdata
 
setExpectValue(String) - Method in class object.common.BlastHit
 
setExt_amount(double) - Method in class object.microarray.Labeling
 
setExt_concentration(double) - Method in class object.microarray.Labeling
 
setExterne_id(String) - Method in class object.annotation.Oligo_externe
 
setExterne_name(String) - Method in class object.annotation.Oligo_externe
 
setExtraction_ref(String) - Method in class object.microarray.Labeling
 
setFax(String) - Method in class object.common.Plateforme
 
setFax(String) - Method in class object.common.User
 
setFichier_id(int) - Method in class object.common.Fichier
 
setFichier_ref(String) - Method in class object.common.Fichier
 
setFile(String) - Method in class object.common.Convert
 
setFile(String) - Method in class object.common.Search
 
setFile(String) - Method in class object.microarray.Serie
 
setFile_res(String) - Method in class object.common.Convert
 
setFirstname(String) - Method in class object.common.User
 
setFlag_norm(String) - Method in class object.microarray.Feature
 
setFlag_str(String) - Method in class object.microarray.ElementMap
 
setFlag_str(String) - Method in class object.microarray.Feature
 
setFocus(int) - Method in class object.common.CreationPlate
 
setFocusIndex(int) - Method in class object.common.CreationPlate
 
setFold(double) - Method in class object.microrna.Target
 
setFold_image(String) - Method in class object.common.RNAfold
 
setFoq_id(int) - Method in class object.common.Foq
 
setFree_energy(String) - Method in class object.annotation.Oligo
 
setFree_energy(String) - Method in class object.annotation.Oligo_tiling
 
setFValue(String) - Method in class object.common.Blast
 
setFValue(String) - Method in class object.common.BlastTwoSeq
 
setFValue(String) - Method in class object.common.SessionBlastObject
 
setGal_file(String) - Method in class object.microarray.Pattern_file
 
setGal_file(String) - Method in class object.microarray.Spotting
 
setGenbank_gene_id(int) - Method in class object.annotation.Gene
 
setGenbank_gene_id(int) - Method in class object.annotation.Probeset
 
setGenbank_gene_id(int) - Method in class object.microrna.Match
 
setGenbank_gene_id(int) - Method in class object.microrna.Mirna_target
 
setGenbank_link(String) - Method in class object.annotation.Gene
 
setGene(String) - Method in class object.annotation.Oligo_control
 
setGene_id(int) - Method in class object.annotation.Exon
 
setGene_id(int) - Method in class object.annotation.GenbankRef
 
setGene_id(int) - Method in class object.annotation.Gene
 
setGene_id(int) - Method in class object.annotation.Genoligo_affy_rel
 
setGene_id(int) - Method in class object.annotation.Genoligo_rel
 
setGene_id(int) - Method in class object.annotation.GoLink
 
setGene_id(int) - Method in class object.annotation.Oligo_adhocRelation
 
setGene_id(String) - Method in class object.annotation.Probeset
 
setGene_id(int) - Method in class object.common.MapEST
 
setGene_id(int) - Method in class object.common.SequenceObject
 
setGene_name(String) - Method in class object.microrna.MicroCible
 
setGenecart(GeneCart) - Method in class object.common.ImageManager
 
setGenecart_id(int) - Method in class object.common.GeneCart
 
setGenerif(String) - Method in class object.annotation.GenbankRef
 
setGenomicPosition(GenomicPosition) - Method in class object.annotation.Gene
 
setGenomicPosition(GenomicPosition) - Method in class object.annotation.Oligo_adhoc_match
 
setGenotype(String) - Method in class object.microarray.Labeling
 
setGeo(String) - Method in class object.common.Public_database
 
setGeo(String) - Method in class object.microarray.Microarray_project_type
 
setGeo_extract(String) - Method in class object.microarray.Labeling_type
 
setGeo_hyb(String) - Method in class object.microarray.Labeling_type
 
setGeo_id(String) - Method in class object.microarray.GeoSerie
 
setGeo_id_ref(String) - Method in class object.microarray.Feature
 
setGeo_label(String) - Method in class object.microarray.Labeling_type
 
setGeo_nucleicacid(String) - Method in class object.microarray.Labeling_type
 
setGeo_ref(String) - Method in class object.microarray.Nucleic_acid_type
 
setGi(String) - Method in class object.annotation.Estoligo_rel
 
setGo_acc(String) - Method in class object.annotation.Term
 
setGps_file(String) - Method in class object.microarray.Scan
 
setGrade(String) - Method in class object.microarray.Labeling
 
setGUwobble(boolean) - Method in class object.microrna.MicroCible
 
setHash(Hashtable) - Method in class object.common.GeneCart
 
setHashBeadToSeq(Hashtable) - Method in class object.hts.MaFile
 
setHashBlocs(Hashtable) - Method in class object.microarray.Quantification_file
 
setHashCalcul(Hashtable) - Method in class object.common.ImageManager
 
setHashColor(Hashtable) - Method in class object.common.ImageManager
 
setHashCols(Hashtable) - Method in class object.common.Biostats
 
setHashColumns(Hashtable) - Method in class object.microarray.Pattern_file
 
setHashColumns(Hashtable) - Method in class object.microarray.Quantification_file
 
setHashCoord(Hashtable) - Method in class object.microarray.Quantification_file
 
setHashData(Hashtable) - Method in class object.microrna.TargetPrediction
 
setHashDatas(Hashtable) - Method in class object.common.ImageManager
 
setHashDown(Hashtable) - Method in class object.microrna.Mttdata
 
setHashFeatures(Hashtable) - Method in class object.microarray.Quantification_file
 
setHashFile(Hashtable) - Method in class object.common.ImageManager
 
setHashFiles(Hashtable) - Method in class object.hts.Hts_RManager
 
setHashGenes(Hashtable) - Method in class object.microrna.MicroCible
 
setHashGenoligo_affy_rel(Hashtable) - Method in class object.common.Search
 
setHashGenoligo_rel(Hashtable) - Method in class object.annotation.Sonde
 
setHashGoFrequence(Hashtable) - Method in class object.microrna.MapTarget
 
setHashGroupLabel(Hashtable) - Method in class object.hts.Hts_RManager
 
setHashID(Hashtable) - Method in class object.microarray.Pattern_file
 
setHashImage(Hashtable) - Method in class object.common.ImageManager
 
setHashKeys(Hashtable) - Method in class object.microrna.MapTarget
 
setHashMaMatch(Hashtable) - Method in class object.hts.MaFile
 
setHashMap(Hashtable) - Method in class object.common.ImageManager
 
setHashMcbdata(Hashtable) - Method in class object.microrna.MicroCible
 
setHashMcbmatch(Hashtable) - Method in class object.microrna.Mcbdata
 
setHashMicros(Hashtable) - Method in class object.microrna.MicroCible
 
setHashMirna_target(Hashtable) - Method in class object.annotation.Gene
 
setHashMirna_target(Hashtable) - Method in class object.microrna.Mirna_mature
 
setHashMstdata(Hashtable) - Method in class object.microrna.MicroSite
 
setHashMttdata(Hashtable) - Method in class object.microrna.MicroTopTable
 
setHashName(Hashtable) - Method in class object.microarray.Pattern_file
 
setHashOligoPosition(Hashtable) - Method in class object.microarray.Plate
 
setHashOligosAffy(Hashtable) - Method in class object.annotation.Gene
 
setHashOligosExternes(Hashtable) - Method in class object.annotation.Gene
 
setHashOutFile(Hashtable) - Method in class object.hts.Hts_pipeline
 
setHashParameter(Hashtable) - Method in class object.hts.Hts_analysis
 
setHashParameter(Hashtable) - Method in class object.hts.Hts_pipeline
 
setHashPlate96(Hashtable) - Method in class object.common.CreationPlate
 
setHashPosition(Hashtable) - Method in class object.microarray.Spotting
 
setHashPredicted(Hashtable) - Method in class object.microrna.Mttdata
 
setHashRefGenmate(Hashtable) - Method in class object.common.CreationPlate
 
setHashScore(Hashtable) - Method in class object.microarray.Feature
 
setHashSequenceObject(Hashtable) - Method in class object.common.SessionBlastObject
 
setHashSpecificity(Hashtable) - Method in class object.annotation.Sonde
 
setHashSymbol(Hashtable) - Method in class object.microrna.Mttdata
 
setHashSymbols(Hashtable) - Method in class object.microarray.Quantification_file
 
setHashtableBlastHit(Hashtable) - Method in class object.common.Blast
 
setHashTarget(Hashtable) - Method in class object.microrna.MapTarget
 
setHashTissues(Hashtable) - Method in class object.common.MapEST
 
setHashUp(Hashtable) - Method in class object.microrna.Mttdata
 
setHdr(int, int, byte[], int) - Static method in class JRclient.Rtalk
writes cmd/resp/type byte + 3/7 bytes len into a byte buffer at specified offset.
setHeader(String) - Method in class object.microarray.SerieFile
 
setHeader(String) - Method in class object.microarray.SpotTypeFile
 
setHeaders(Vector) - Method in class object.microarray.Pattern_file
 
setHistology(String) - Method in class object.microarray.Labeling
 
setHistopathology_number(String) - Method in class object.hts.Hts_minseqe
 
setHitId(String) - Method in class object.common.BlastHit
 
setHitSequence(String) - Method in class object.common.BlastHit
 
setHitStartPosition(String) - Method in class object.common.BlastHit
 
setHitStopPosition(String) - Method in class object.common.BlastHit
 
setHowWeNormalized(String) - Method in class object.microarray.Quantification_file
 
setHts_analysis(Hts_analysis) - Method in class object.hts.Hts_RManager
 
setHts_analysis_id(int) - Method in class object.hts.Hts_analysis
 
setHts_analysis_ref(String) - Method in class object.hts.Hts_analysis
 
setHts_extraction(Hts_extraction) - Method in class object.hts.Hts_minseqe
 
setHts_extraction_id(int) - Method in class object.hts.Hts_extraction
 
setHts_extraction_ref(String) - Method in class object.hts.Hts_extraction
 
setHts_minseqe(Hts_minseqe) - Method in class object.hts.Hts_sample
 
setHts_minseqe_id(int) - Method in class object.hts.Hts_minseqe
 
setHts_minseqe_ref(String) - Method in class object.hts.Hts_minseqe
 
setHts_order_id(int) - Method in class object.hts.Hts_sample
 
setHts_pipeline(Hts_pipeline) - Method in class object.hts.Hts_result
 
setHts_pipeline_id(int) - Method in class object.hts.Hts_pipeline
 
setHts_pipeline_ref(String) - Method in class object.hts.Hts_pipeline
 
setHts_pipeline_type(String) - Method in class object.hts.Hts_pipeline
 
setHts_pipeline_type_required(String) - Method in class object.hts.Hts_analysis
 
setHts_quantification(Hts_quantification) - Method in class object.hts.Hts_minseqe
 
setHts_quantification_id(int) - Method in class object.hts.Hts_quantification
 
setHts_quantification_ref(String) - Method in class object.hts.Hts_quantification
 
setHts_result_id(int) - Method in class object.hts.Hts_result
 
setHts_result_ref(String) - Method in class object.hts.Hts_result
 
setHts_run_id(int) - Method in class object.hts.Hts_run
 
setHts_run_id(int) - Method in class object.hts.Hts_sample
 
setHts_run_ref(String) - Method in class object.hts.Hts_run
 
setHts_sample_id(int) - Method in class object.hts.Hts_minseqe
 
setHts_sample_id(int) - Method in class object.hts.Hts_result
 
setHts_sample_id(int) - Method in class object.hts.Hts_sample
 
setHts_sample_ref(String) - Method in class object.hts.Hts_sample
 
setHts_type(Hts_type) - Method in class object.common.Order
 
setHts_type(Hts_type) - Method in class object.hts.Hts_pipeline
 
setHts_type(Hts_type) - Method in class object.hts.Hts_RManager
 
setHts_type(Hts_type) - Method in class object.hts.Hts_run
 
setHts_type(Hts_type) - Method in class object.hts.Hts_sample
 
setHts_type_id(int) - Method in class object.hts.Hts_type
 
setHts_type_ref(String) - Method in class object.hts.Hts_type
 
setHuman_quota(double) - Method in class object.annotation.EstTissue
 
setHybridization(Hybridization) - Method in class object.microarray.Microarray
 
setHybridization_id(int) - Method in class object.microarray.Hybridization
 
setHybridization_id(int) - Method in class object.microarray.Labeling
 
setId(String) - Method in class common.tags.generic.UseLocaleBundleTag
Sets the id property, i.e. the name to use for the LocaleBean in the session scope.
setId(int) - Method in class object.annotation.Specificity
 
setId(String) - Method in class object.common.IdDescriptionObject
 
setId(String) - Method in class object.microarray.SpotType
 
setIdentity(double) - Method in class object.annotation.Genoligo_rel
 
setIdentity(double) - Method in class object.annotation.Oligo_adhocRelation
 
setIdentity(double) - Method in class object.annotation.Spodo_hit
 
setImage(String) - Method in class object.common.Commande
 
setImage_ch1(String) - Method in class object.microarray.Scan
 
setImage_ch2(String) - Method in class object.microarray.Scan
 
setImage_map(String) - Method in class object.common.Graph
 
setImage_path(String) - Method in class object.common.Graph
 
setImage_tosplit(String) - Method in class object.microarray.Scan
 
setImageTif(String) - Method in class object.microarray.Scan
 
setImg(String) - Method in class object.annotation.OligoHit
 
setImgA(Graph) - Method in class object.microrna.MicroTopTable
 
setImgB(Graph) - Method in class object.microrna.MicroTopTable
 
setImgDOWN(Graph) - Method in class object.microrna.MicroTopTable
 
setImgM(Graph) - Method in class object.microrna.MicroTopTable
 
setImgUP(Graph) - Method in class object.microrna.MicroTopTable
 
setInformation(String) - Method in class object.annotation.Oligo_adhoc
 
setInitialisation(boolean) - Method in class object.common.BlastTwoSeq
 
setInitialisation(boolean) - Method in class object.common.Search
 
setInitialisation(boolean) - Method in class object.common.SessionBlastObject
 
setInt(int, byte[], int) - Static method in class JRclient.Rtalk
writes bit-wise int to a byte buffer at specified position in Intel-endian form
setInterslide(String) - Method in class object.common.Biostats
 
setInterslide(String) - Method in class object.common.Rstat
 
setIntraslide(String) - Method in class object.common.Biostats
 
setIntraslide(String) - Method in class object.common.Rstat
 
setIs_384SuiteBcr_ok(boolean) - Method in class object.microarray.Spotting
 
setIs_accessionOne(boolean) - Method in class object.common.BlastTwoSeq
 
setIs_accessionTwo(boolean) - Method in class object.common.BlastTwoSeq
 
setIs_active(boolean) - Method in class object.common.Project
 
setIs_active(String) - Method in class object.common.ProjectObject
 
setIs_active(boolean) - Method in class object.hts.Hts_sample
 
setIs_active(boolean) - Method in class object.microarray.Microarray
 
setIs_active(String) - Method in class object.microarray.Plate
 
setIs_adhoc(String) - Method in class object.annotation.Oligo_rel
 
setIs_adhoc(boolean) - Method in class object.microarray.ElementMap
 
setIs_adhoc(boolean) - Method in class object.microarray.Feature
 
setIs_admin(boolean) - Method in class object.common.User
 
setIs_admin_plateforme(boolean) - Method in class object.common.Plateforme
 
setIs_affy(boolean) - Method in class object.common.Toptable
 
setIs_affy(boolean) - Method in class object.microarray.Microarray_project_type
 
setIs_analysis(boolean) - Method in class object.hts.Hts_sample
 
setIs_blast_proceeded(boolean) - Method in class object.common.SequenceObject
 
setIs_cleanup(boolean) - Method in class object.hts.Hts_minseqe
 
setIs_collaboration(boolean) - Method in class object.common.Order
 
setIs_control(String) - Method in class object.annotation.Oligo_rel
 
setIs_control(boolean) - Method in class object.microarray.ElementMap
 
setIs_control(boolean) - Method in class object.microarray.Feature
 
setIs_devis(boolean) - Method in class object.common.User
 
setIs_diluted(String) - Method in class object.microarray.Plate384
 
setIs_experiment(boolean) - Method in class object.microarray.Microarray
 
setIs_externe(boolean) - Method in class object.microarray.ElementMap
 
setIs_externe(boolean) - Method in class object.microarray.Feature
 
setIs_first(boolean) - Method in class object.common.Search
 
setIs_first(boolean) - Method in class object.common.SessionBlastObject
 
setIs_found(boolean) - Method in class object.common.Search
 
setIs_found(boolean) - Method in class object.microrna.MicroCible
 
setIs_gu(boolean) - Method in class object.microrna.MatchMCB
 
setIs_gz(boolean) - Method in class object.hts.Hts_pipeline_outfile
 
setIs_hybrid(boolean) - Method in class object.common.Order
 
setIs_hybrid(boolean) - Method in class object.common.User
 
setIs_in_replaceMode(boolean) - Method in class object.microarray.Spotting
 
setIs_load(boolean) - Method in class object.microarray.MicroarrayElement
 
setIs_matching(boolean) - Method in class object.common.SequenceObject
 
setIs_matching(boolean) - Method in class object.hts.Hts_sample
 
setIs_medlab(boolean) - Method in class object.common.User
 
setIs_micro(boolean) - Method in class object.microarray.Microarray_project_type
 
setIs_minseqe(boolean) - Method in class object.hts.Hts_sample
 
setIs_normalized(boolean) - Method in class object.microarray.Microarray
 
setIs_normalized(boolean) - Method in class object.microarray.Quantification_file
 
setIs_open(boolean) - Method in class object.common.Order
 
setIs_open(boolean) - Method in class object.common.Project
 
setIs_open(boolean) - Method in class object.microarray.Project_order
 
setIs_order(boolean) - Method in class object.hts.Hts_analysis
 
setIs_orderable(boolean) - Method in class object.hts.Hts_type
 
setIs_orderable(boolean) - Method in class object.microarray.Microarray_project_type
 
setIs_owner(boolean) - Method in class object.common.Project
 
setIs_prod(boolean) - Method in class object.common.User
 
setIs_production(boolean) - Method in class object.common.Plateforme
 
setIs_quantif(boolean) - Method in class object.hts.Hts_sample
 
setIs_quantif(boolean) - Method in class object.microarray.Microarray
 
setIs_reads(boolean) - Method in class object.hts.Hts_sample
 
setIs_real_control(String) - Method in class object.annotation.Oligo_control
 
setIs_rmq(boolean) - Method in class object.common.User
 
setIs_sample(boolean) - Method in class object.hts.Hts_analysis
 
setIs_save(boolean) - Method in class object.common.Rstat
 
setIs_select(String) - Method in class object.annotation.Genoligo_rel
 
setIs_spottable(boolean) - Method in class object.microarray.Microarray_project_type
 
setIs_superadmin(boolean) - Method in class object.common.User
 
setIs_tiling(boolean) - Method in class object.microarray.ElementMap
 
setIs_tiling(boolean) - Method in class object.microarray.Feature
 
setIs_update(boolean) - Method in class object.common.Order
 
setIs_viewable(boolean) - Method in class object.microarray.ArrayLabo
 
setIs_viewable(boolean) - Method in class object.microarray.Microarray
 
setIs_viewable(boolean) - Method in class object.microarray.Microarray_project_type
 
setIs_viewer(boolean) - Method in class object.common.Project
 
setIs_writer(boolean) - Method in class object.common.Project
 
setJournal(String) - Method in class object.annotation.GenbankRef
 
setJournal(String) - Method in class object.microrna.Mirna_reference
 
setKey(String) - Method in class common.tags.generic.GetLocalTextTag
Sets the resource key property.
setKeyword_id(int) - Method in class object.common.Keyword
 
setKeyword_ref(String) - Method in class object.common.Keyword
 
setLabeling_ch1(String) - Method in class object.microarray.MicroarrayElement
 
setLabeling_ch1(String) - Method in class object.microarray.Scan
 
setLabeling_ch2(String) - Method in class object.microarray.MicroarrayElement
 
setLabeling_ch2(String) - Method in class object.microarray.Scan
 
setLabeling_id(int) - Method in class object.microarray.Labeling
 
setLabeling_ref(String) - Method in class object.microarray.Labeling
 
setLabeling_type(Labeling_type) - Method in class object.microarray.Labeling
 
setLabeling_type_ch1(Labeling_type) - Method in class object.microarray.Scan
 
setLabeling_type_ch2(Labeling_type) - Method in class object.microarray.Scan
 
setLabeling_type_id(int) - Method in class object.microarray.Labeling_type
 
setLabeling_type_ref(String) - Method in class object.microarray.Labeling_type
 
setLabRefList(String[]) - Method in class object.common.ImageManager
 
setLanguage(String) - Method in class common.beans.locale.LocaleBean
Sets the user selected language/country code.
setLastname(String) - Method in class object.common.User
 
setLatin_name(String) - Method in class object.annotation.Organism
 
setLegende(String) - Method in class object.common.Convert
 
setLength(int) - Method in class object.annotation.Chromosome
 
setLetter_a(String) - Method in class object.microarray.Plate_transfert_type
 
setLetter_b(String) - Method in class object.microarray.Plate_transfert_type
 
setLimma_M(String) - Method in class object.common.Biostats
 
setLineWidth(int) - Method in class object.microarray.MAGEWriter
 
setLink(String) - Method in class object.annotation.OligoHit
 
setLink2(String) - Method in class object.annotation.OligoHit
 
setListePlate384(String) - Method in class object.common.Dilution
 
setListing(String) - Method in class object.common.Attribution
 
setListing(String[]) - Method in class object.common.GeneCart
 
setLogFC(double) - Method in class object.common.ImageManager
 
setLogfc(double) - Method in class object.microrna.MicroTopTable
 
setLogFC(double) - Method in class object.microrna.Mttdata
 
setLogin(String) - Method in class object.common.User
 
setLogratio(String) - Method in class object.microarray.Feature
 
setLong(long, byte[], int) - Static method in class JRclient.Rtalk
 
setLongueur(int) - Method in class object.annotation.Gene
 
setLongueur(int) - Method in class object.annotation.OligoHit
 
setLst_genes_down(String) - Method in class object.microrna.MicroTopTable
 
setLst_genes_up(String) - Method in class object.microrna.MicroTopTable
 
setMamap(String) - Method in class object.annotation.Sonde
 
setMap(String) - Method in class object.annotation.Gene
 
setMap(String) - Method in class object.common.MapEST
 
setMapEST(MapEST) - Method in class object.annotation.Gene
 
setMapEST(MapEST) - Method in class object.annotation.Oligo
 
setMapName(String) - Method in class object.annotation.OligoHit
 
setMapTargetDown(MapTarget) - Method in class object.microrna.Mttdata
 
setMapTargetUp(MapTarget) - Method in class object.microrna.Mttdata
 
setMark(String) - Method in class object.microarray.Labeling
 
setMask_A(String) - Method in class object.common.Toptable
 
setMask_id(String) - Method in class object.common.Toptable
 
setMask_M(String) - Method in class object.common.Toptable
 
setMask_name(String) - Method in class object.common.Toptable
 
setMature_acc(String) - Method in class object.microrna.MicroTopTable
 
setMature_acc(String) - Method in class object.microrna.Mirna_mature
 
setMature_acc(String) - Method in class object.microrna.Mirna_target
 
setMature_acc(String) - Method in class object.microrna.Mttdata
 
setMature_acc(String) - Method in class object.microrna.TargetPrediction
 
setMature_name(String) - Method in class object.microrna.Mcbmatch
 
setMature_name(String) - Method in class object.microrna.Mirna_mature
 
setMature_name(String) - Method in class object.microrna.Mirna_target
 
setMature_name(String) - Method in class object.microrna.Mttdata
 
setMedline(String) - Method in class object.microrna.Mirna_reference
 
setMessage(String) - Method in class object.common.Attribution
 
setMessage(String) - Method in class object.common.BlastTwoSeq
 
setMessage(String) - Method in class object.common.Board
 
setMessage(String) - Method in class object.common.CreationPlate
 
setMessage(String) - Method in class object.common.Dilution
 
setMessage(String) - Method in class object.common.Project
 
setMessage(String) - Method in class object.common.Rstat
 
setMessage(String) - Method in class object.common.Search
 
setMessage(String) - Method in class object.common.SessionBlastObject
 
setMessage(String) - Method in class object.hts.Hts_result
 
setMessage(String) - Method in class object.hts.Hts_RManager
 
setMessage(String) - Method in class object.hts.Hts_run
 
setMessage(String) - Method in class object.microarray.Scan
 
setMessage(String) - Method in class object.microarray.Spotting
 
setMessage(String) - Method in class object.microrna.MicroCible
 
setMfe_cutoff(int) - Method in class object.microrna.MicroCible
 
setMfe_cutoff(double) - Method in class object.microrna.MicroTopTable
 
setMicro(String) - Method in class object.common.RNAhybrid
 
setMicro(String) - Method in class object.microrna.MatchMCB
 
setMicro_list(String) - Method in class object.microrna.MicroSite
 
setMicroarray(Microarray) - Method in class object.microarray.MicroarrayElement
 
setMicroarray_id(int) - Method in class object.microarray.Control
 
setMicroarray_id(int) - Method in class object.microarray.Hybridization
 
setMicroarray_id(int) - Method in class object.microarray.Microarray
 
setMicroarray_id(int) - Method in class object.microarray.MicroarrayElement
 
setMicroarray_id(int) - Method in class object.microarray.Scan
 
setMicroarray_order_id(int) - Method in class object.microarray.Microarray
 
setMicroarray_order_id(int) - Method in class object.microarray.Microarray_project_type
 
setMicroarray_project_type(Microarray_project_type) - Method in class object.common.Order
 
setMicroarray_project_type(Microarray_project_type) - Method in class object.microarray.GeoSerie
 
setMicroarray_project_type(Microarray_project_type) - Method in class object.microarray.Microarray
 
setMicroarray_project_type(Microarray_project_type) - Method in class object.microarray.Spotting
 
setMicroarray_project_type_id(Microarray_project_type) - Method in class object.annotation.Oligo_adhoc
 
setMicroarray_project_type_id(Microarray_project_type) - Method in class object.annotation.Oligo_externe
 
setMicroarray_project_type_id(int) - Method in class object.microarray.Microarray_project_type
 
setMicroarray_project_type_ref(String) - Method in class object.microarray.Microarray_project_type
 
setMicroarray_type(Microarray_type) - Method in class object.microarray.Microarray
 
setMicroarray_type_id(int) - Method in class object.microarray.Microarray_type
 
setMicroarray_type_ref(String) - Method in class object.microarray.Microarray_type
 
setMicroCible(MicroCible) - Method in class object.microrna.SnipMir
 
setMirna(Mirna) - Method in class object.microrna.Mirna_mature
 
setMirna_acc(String) - Method in class object.microrna.Mirna
 
setMirna_id(String) - Method in class object.microrna.Mirna
 
setMirna_target_tool_id(int) - Method in class object.microrna.MapTarget
 
setMix_ref(String) - Method in class object.hts.Hts_result
 
setMouse_quota(double) - Method in class object.annotation.EstTissue
 
setMultiplier(int) - Method in class object.microarray.Microarray_project_type
 
setMyFiles(String[]) - Method in class object.common.Rstat
 
setName(String) - Method in class common.tags.generic.GetLocalTextTag
Sets the LocaleBean name property.
setName(String) - Method in class object.annotation.Oligo_tiling
 
setName(String) - Method in class object.annotation.Term
 
setName(String) - Method in class object.common.ToolBox
 
setName(String) - Method in class object.common.ToolBoxString
 
setName(String) - Method in class object.hts.Hts_analysis_parameter
 
setName(String) - Method in class object.hts.Hts_pipeline_outfile
 
setName(String) - Method in class object.hts.Hts_pipeline_parameter
 
setName(String) - Method in class object.microarray.Feature
 
setName(String) - Method in class object.microarray.MageProtocol
 
setName(String) - Method in class object.microarray.SpotType
 
setName(String) - Method in class object.microrna.Mstdata
 
setNb(int) - Method in class object.annotation.Estoligo_rel
 
setNb(int) - Method in class object.common.Attribution
 
setNb_all(int) - Method in class object.annotation.Histology
 
setNb_bloc(int) - Method in class object.common.ImageManager
 
setNb_bloc(int) - Method in class object.microarray.Pattern_file
 
setNb_bloc(int) - Method in class object.microarray.Quantification_file
 
setNb_bloc_column(int) - Method in class object.microarray.Pattern_file
 
setNb_bloc_row(int) - Method in class object.microarray.Pattern_file
 
setNb_column(int) - Method in class object.microarray.Pattern_file
 
setNb_column(int) - Method in class object.microarray.Quantification_file
 
setNb_est(int) - Method in class object.annotation.Sonde
 
setNb_fields(int) - Method in class object.common.Convert
 
setNb_identity(int) - Method in class object.annotation.Spodo_hit
 
setNb_lame(int) - Method in class object.microarray.Spotting
 
setNb_match(int) - Method in class object.microrna.MicroCible
 
setNb_microarray(int) - Method in class object.common.Order
 
setNb_microarray(int) - Method in class object.microarray.GeoSerie
 
setNb_microarray_more(int) - Method in class object.common.Order
 
setNb_microarray_ok(int) - Method in class object.common.Order
 
setNb_neoplasia(int) - Method in class object.annotation.Histology
 
setNb_normal(int) - Method in class object.annotation.Histology
 
setNb_predict(int) - Method in class object.microrna.Mttdata
 
setNb_row(int) - Method in class object.microarray.Pattern_file
 
setNb_row(int) - Method in class object.microarray.Quantification_file
 
setNb_sample(int) - Method in class object.common.Order
 
setNb_sample(int) - Method in class object.hts.Hts_run
 
setNb_sample_more(int) - Method in class object.common.Order
 
setNb_slide(int) - Method in class object.common.Order
 
setNb_unknown(int) - Method in class object.annotation.Histology
 
setNb_use(int) - Method in class object.microarray.Plate
 
setNeedToConvert(boolean) - Method in class object.microarray.Spotting
 
setNucleic_acid_type(Nucleic_acid_type) - Method in class object.hts.Hts_minseqe
 
setNucleic_acid_type(Nucleic_acid_type) - Method in class object.microarray.Labeling
 
setNucleic_acid_type_id(int) - Method in class object.microarray.Nucleic_acid_type
 
setNucleic_acid_type_ref(String) - Method in class object.microarray.Nucleic_acid_type
 
setNumber(String) - Method in class object.microarray.Serie
 
setNumberOfIdentities(String) - Method in class object.common.BlastHit
 
setOganism(Organism) - Method in class object.common.Project
 
setOligo_adhoc_id(int) - Method in class object.annotation.Oligo_adhocRelation
 
setOligo_adhoc_id(int) - Method in class object.microrna.Mttdata
 
setOligo_control_id(int) - Method in class object.annotation.Oligo_control
 
setOligo_id(int) - Method in class object.annotation.Genoligo_rel
 
setOligo_id(String) - Method in class object.annotation.Oligo_annotation
 
setOligo_id(int) - Method in class object.annotation.Oligo_rel
 
setOligo_id(String) - Method in class object.common.Point
 
setOligo_id(int) - Method in class object.common.SequenceObject
 
setOligo_id(int) - Method in class object.microarray.ElementMap
 
setOligo_id(int) - Method in class object.microarray.Feature
 
setOligo_id_str(String) - Method in class object.microarray.ElementMap
 
setOligo_id_str(String) - Method in class object.microarray.Feature
 
setOligo_tiling_id(int) - Method in class object.annotation.Oligo_tiling
 
setOligoBase(BlastBase) - Method in class object.annotation.Organism
 
setOligoGraph(String) - Method in class object.common.SequenceObject
 
setOligoGraphMap(String) - Method in class object.common.SequenceObject
 
setOnlyCart(boolean) - Method in class object.common.ImageManager
 
setOnMouseOver(OnMouseOver) - Method in class object.annotation.OligoHit
 
setOptions(String[]) - Method in class object.hts.Hts_analysis_parameter
 
setOptions(String[]) - Method in class object.hts.Hts_pipeline_parameter
 
setOrder(Order) - Method in class object.common.Attribution
 
setOrder_id(int) - Method in class object.common.Journal
 
setOrder_id(int) - Method in class object.common.Order
 
setOrder_ref(String) - Method in class object.common.Order
 
setOrder_stats(String) - Method in class object.hts.Hts_order
 
setOrder_type(String) - Method in class object.common.Order
 
setOrderedKeys(String[]) - Method in class object.common.Convert
 
setOrdre_id(int) - Method in class object.common.SequenceObject
 
setOrdre_id(int) - Method in class object.microarray.Microarray
 
setOrganism(Organism) - Method in class object.annotation.GenomicPosition
 
setOrganism(String) - Method in class object.annotation.Oligo_annotation
 
setOrganism(String) - Method in class object.annotation.Oligo_control
 
setOrganism(Organism) - Method in class object.common.Public_database
 
setOrganism(Organism) - Method in class object.hts.Hts_minseqe
 
setOrganism(Organism) - Method in class object.microarray.Labeling
 
setOrganism(Organism) - Method in class object.microarray.Microarray_project_type
 
setOrganism(Organism) - Method in class object.microarray.Plate
 
setOrganism(String) - Method in class object.microrna.MicroSite
 
setOrganism(Organism) - Method in class object.microrna.TargetPrediction
 
setOrganism_gene(Organism) - Method in class object.microrna.MicroCible
 
setOrganism_id(int) - Method in class object.annotation.Chromosome
 
setOrganism_id(int) - Method in class object.annotation.Organism
 
setOrganism_id(int) - Method in class object.annotation.Sonde
 
setOrganism_id(int) - Method in class object.common.BlastBase
 
setOrganism_id(int) - Method in class object.common.Convert
 
setOrganism_id(int) - Method in class object.common.ProjectObject
 
setOrganism_id(int) - Method in class object.common.Search
 
setOrganism_id(int) - Method in class object.microrna.Mcbdata
 
setOrganism_id(int) - Method in class object.microrna.Mirna_mature
 
setOrganisme(String) - Method in class object.common.User
 
setOrigin(String) - Method in class object.microarray.Labeling
 
setOverlap_sense(String) - Method in class object.microrna.Mirna_context
 
setOverlap_type(String) - Method in class object.microrna.Mirna_context
 
setOwner(String) - Method in class object.microarray.GeoSerie
 
setParameters(Hashtable) - Method in class common.beans.locale.LocaleBean
Sets the parameter list.
setParameters(String) - Method in class object.microarray.MageProtocol
 
setParent_id(int) - Method in class object.annotation.Oligo_adhoc
 
setPassword(String) - Method in class object.common.User
 
setPath(String) - Method in class object.hts.Hts_pipeline_outfile
 
setPath(String) - Method in class object.hts.MaFile
 
setPath_fichier(String) - Method in class object.common.Fichier
 
setPathFichier(String) - Method in class object.common.Blast
 
setPays(String) - Method in class object.common.User
 
setPdf_file(String) - Method in class object.common.Biostats
 
setPercentageIdentity(String) - Method in class object.common.BlastHit
 
setPid_pref(int) - Method in class object.common.Order
 
setPlate384Ref(String) - Method in class object.common.Dilution
 
setPlate96_id(int) - Method in class object.annotation.Oligo_rel
 
setPlate_A1(int) - Method in class object.microarray.Plate384
 
setPlate_A2(int) - Method in class object.microarray.Plate384
 
setPlate_B1(int) - Method in class object.microarray.Plate384
 
setPlate_B2(int) - Method in class object.microarray.Plate384
 
setPlate_id(int) - Method in class object.annotation.Oligo_rel
 
setPlate_id(int) - Method in class object.microarray.Plate
 
setPlate_ref(String) - Method in class object.microarray.Plate
 
setPlate_transfert_type(Plate_transfert_type) - Method in class object.microarray.Plate384
 
setPlate_transfert_type_desc(String) - Method in class object.microarray.Plate_transfert_type
 
setPlate_transfert_type_id(int) - Method in class object.microarray.Plate_transfert_type
 
setPlate_type(Plate_type) - Method in class object.microarray.Plate
 
setPlate_type_id(int) - Method in class object.microarray.Plate_type
 
setPlate_type_ref(String) - Method in class object.microarray.Plate_type
 
setPlateforme(Plateforme) - Method in class object.common.Order
 
setPlateforme(Plateforme) - Method in class object.common.User
 
setPlateforme(Plateforme) - Method in class object.hts.Hts_type
 
setPlateforme(Plateforme) - Method in class object.microarray.Microarray_project_type
 
setPlateforme(Plateforme) - Method in class object.microarray.Spotting
 
setPlateforme_id(int) - Method in class object.common.Plateforme
 
setPlateforme_ref(String) - Method in class object.common.Plateforme
 
setPmt_ch1(int) - Method in class object.microarray.Scan
 
setPmt_ch2(int) - Method in class object.microarray.Scan
 
setPopsize(int) - Method in class object.microrna.MapTarget
 
setPosition(int) - Method in class object.annotation.Genoligo_rel
 
setPosition(int) - Method in class object.annotation.Oligo_adhocRelation
 
setPosition(int) - Method in class object.annotation.Oligo_control
 
setPosition(String) - Method in class object.annotation.Oligo_rel
 
setPosition(int) - Method in class object.microrna.MatchMCB
 
setPostgresqlConfiguration() - Method in class object.common.Xhtml
This function load parameters to PostgreSQL connexion
setPrecision(String) - Method in class object.common.Foq
 
setPrefam_acc(String) - Method in class object.microrna.Mttdata
 
setPrefam_id(String) - Method in class object.microrna.Mttdata
 
setPremir(String) - Method in class object.microrna.Mstdata
 
setPremir_end(int) - Method in class object.microrna.Mstdata
 
setPremir_start(int) - Method in class object.microrna.Mstdata
 
setProbe_set_id(String) - Method in class object.annotation.Genoligo_affy_rel
 
setProbe_set_id(String) - Method in class object.annotation.Oligo_affy
 
setProbeset_id(String) - Method in class object.annotation.Probeset
 
setProbleme(String) - Method in class object.common.Foq
 
setProject(Project) - Method in class object.common.SessionObject
 
setProject_id(int) - Method in class object.common.Project
 
setProject_id(int) - Method in class object.common.ProjectObject
 
setProject_id(int) - Method in class object.common.SequenceObject
 
setProject_order(Project_order) - Method in class object.common.Board
 
setProject_order(Project_order) - Method in class object.common.ImageManager
 
setProject_order(Project_order) - Method in class object.hts.Hts_RManager
 
setProject_order_id(int) - Method in class object.common.Biostats
 
setProject_order_id(int) - Method in class object.common.Order
 
setProject_order_id(int) - Method in class object.common.Rstat
 
setProject_order_id(int) - Method in class object.common.Toptable
 
setProject_order_id(int) - Method in class object.microarray.Project_order
 
setProject_order_ref(String) - Method in class object.common.Order
 
setProject_order_ref(String) - Method in class object.microarray.Project_order
 
setProtein_id(String) - Method in class object.annotation.Gene
 
setProtein_id(String) - Method in class object.annotation.Probeset
 
setProtocol_amplification(Protocol_amplification) - Method in class object.microarray.Labeling
 
setProtocol_amplification_id(int) - Method in class object.microarray.Protocol_amplification
 
setProtocol_amplification_ref(String) - Method in class object.microarray.Protocol_amplification
 
setProtocol_extraction(Protocol_extraction) - Method in class object.hts.Hts_minseqe
 
setProtocol_extraction(Protocol_extraction) - Method in class object.microarray.Labeling
 
setProtocol_extraction_id(int) - Method in class object.microarray.Protocol_extraction
 
setProtocol_extraction_ref(String) - Method in class object.microarray.Protocol_extraction
 
setProtocol_hybridization(Protocol_hybridization) - Method in class object.microarray.Hybridization
 
setProtocol_hybridization_id(int) - Method in class object.microarray.Protocol_hybridization
 
setProtocol_hybridization_ref(String) - Method in class object.microarray.Protocol_hybridization
 
setProtocol_labeling(Protocol_labeling) - Method in class object.microarray.Labeling
 
setProtocol_labeling_id(int) - Method in class object.microarray.Protocol_labeling
 
setProtocol_labeling_ref(String) - Method in class object.microarray.Protocol_labeling
 
setProvider_id(int) - Method in class object.microarray.Provider
 
setProvider_ref(String) - Method in class object.microarray.Provider
 
setPsl_coord(String) - Method in class object.annotation.Sonde
 
setPublic_database_id(int) - Method in class object.common.Public_database
 
setPubmed(int) - Method in class object.annotation.GenbankRef
 
setPvalue(double) - Method in class object.common.RNAhybrid
 
setPvalue(double) - Method in class object.microrna.Match
 
setPvalue(double) - Method in class object.microrna.Mirna_target
 
setQuantif_file(String) - Method in class object.microarray.Quantification_file
 
setQuantif_file(String) - Method in class object.microarray.Scan
 
setQuantification_file(Quantification_file) - Method in class object.microarray.Scan
 
setQuery(String) - Method in class object.common.Search
 
setQueryId(String) - Method in class object.common.BlastHit
 
setQuerySequence(String) - Method in class object.common.BlastHit
 
setQueryStartPosition(String) - Method in class object.common.BlastHit
 
setQueryStopPosition(String) - Method in class object.common.BlastHit
 
setQuestion_1(int) - Method in class object.common.Enquete
 
setQuestion_10(String) - Method in class object.common.Enquete
 
setQuestion_2(String) - Method in class object.common.Enquete
 
setQuestion_3(int) - Method in class object.common.Enquete
 
setQuestion_4(int) - Method in class object.common.Enquete
 
setQuestion_5(int) - Method in class object.common.Enquete
 
setQuestion_6(int) - Method in class object.common.Enquete
 
setQuestion_7(String) - Method in class object.common.Enquete
 
setQuestion_8(int) - Method in class object.common.Enquete
 
setQuestion_9(String) - Method in class object.common.Enquete
 
setQuestion_9plus(String) - Method in class object.common.Enquete
 
setR_script(String) - Method in class object.common.Biostats
 
setRatio(String) - Method in class object.microarray.ElementMap
 
setRatio(String) - Method in class object.microarray.Feature
 
setRatio_230(double) - Method in class object.hts.Hts_minseqe
 
setRatio_280(double) - Method in class object.hts.Hts_minseqe
 
setRayon(int) - Method in class object.microarray.ElementMap
 
setRayon(int) - Method in class object.microarray.Feature
 
setReadImageCMD() - Method in class object.common.Rstat
 
setRef(String) - Method in class object.microarray.SpotType
 
setRefseq(String) - Method in class object.annotation.Estoligo_rel
 
setRefseqBase(BlastBase) - Method in class object.annotation.Organism
 
setRegion(String) - Method in class object.microrna.MicroCible
 
setReponse(String) - Method in class object.common.Contact_client
 
setRequestLocales(Locale[]) - Method in class common.beans.locale.LocaleBean
Sets the set of locales received with the request, and resets the currently selected locale if the new set is different from the current set.
setResponsable(String) - Method in class object.common.Plateforme
 
setResults(Hashtable) - Method in class object.common.Convert
 
setRev_start(int) - Method in class object.microrna.Mstdata
 
setRight(boolean) - Method in class object.common.Board
 
setRin(double) - Method in class object.hts.Hts_minseqe
 
setRin_number(int) - Method in class object.microarray.Labeling
 
setRnafold(RNAfold) - Method in class object.microrna.MatchMCB
 
setRnafold(RNAfold) - Method in class object.microrna.Mstdata
 
setRnahybrid(RNAhybrid) - Method in class object.microrna.MatchMCB
 
setRnahybrid(RNAhybrid) - Method in class object.microrna.Mstdata
 
setRng_id(int) - Method in class object.common.Order
 
setRow(String) - Method in class object.annotation.Oligo_rel
 
setRow(String) - Method in class object.microarray.ElementMap
 
setRow(String) - Method in class object.microarray.Feature
 
setRstat(Rstat) - Method in class object.common.ImageManager
 
setSample_ref(String) - Method in class object.microarray.Labeling
 
setSanger_id(String) - Method in class object.annotation.Oligo_adhoc_match
 
setSanger_ref(String) - Method in class object.annotation.Oligo_adhoc_match
 
setScan_id(int) - Method in class object.microarray.Scan
 
setScan_ref(String) - Method in class object.microarray.Scan
 
setScanner_id(int) - Method in class object.microarray.Scanner
 
setScanner_ref(String) - Method in class object.microarray.Scanner
 
setScore(double) - Method in class object.annotation.Oligo
 
setScore(double) - Method in class object.annotation.Spodo_hit
 
setScore(String) - Method in class object.common.BlastHit
 
setSearch(Search) - Method in class object.common.SessionObject
 
setSeed_size(int) - Method in class object.microrna.MicroCible
 
setSeed_start(int) - Method in class object.microrna.MicroCible
 
setSeed_stop(int) - Method in class object.microrna.MicroCible
 
setSendBufferSize(long) - Method in class JRclient.Rconnection
Sets send buffer size of the Rserve (in bytes) for the current connection.
setSens(String) - Method in class object.annotation.Oligo_tiling
 
setSeqOne(String) - Method in class object.common.BlastTwoSeq
 
setSeqTwo(String) - Method in class object.common.BlastTwoSeq
 
setSequence(String) - Method in class object.annotation.Gene
 
setSequence(String) - Method in class object.annotation.Oligo_control
 
setSequence(String) - Method in class object.annotation.Oligo_tiling
 
setSequence(String) - Method in class object.annotation.Sonde
 
setSequence(Sequence) - Method in class object.common.RNAfold
 
setSequence(Sequence) - Method in class object.common.SequenceObject
 
setSequence(String) - Method in class object.microrna.Mcbdata
 
setSequence(String) - Method in class object.microrna.Mcbmatch
 
setSequence(String) - Method in class object.microrna.MicroCible
 
setSequence(String) - Method in class object.microrna.Mstdata
 
setSequence_name(String) - Method in class object.common.SequenceObject
 
setSequenceBase(BlastBase) - Method in class object.annotation.Organism
 
setSequenceOne(Sequence) - Method in class object.common.BlastTwoSeq
 
setSequenceTwo(Sequence) - Method in class object.common.BlastTwoSeq
 
setSerie_file(String) - Method in class object.common.Biostats
 
setSerie_ok(boolean) - Method in class object.common.Rstat
 
setSerieFile(SerieFile) - Method in class object.common.Rstat
 
setShort_accession(String) - Method in class object.annotation.Oligo_adhoc
 
setShort_slide_code(String) - Method in class object.microarray.Microarray
 
setShortName(String) - Method in class object.microarray.Feature
 
setShortref(String) - Method in class object.annotation.Genoligo_affy_rel
 
setShortref(String) - Method in class object.annotation.Probeset
 
setShortRef(String) - Method in class object.hts.Hts_type
 
setShortRef(String) - Method in class object.microarray.Microarray_project_type
 
setSize(int) - Method in class object.annotation.Genoligo_rel
 
setSize(int) - Method in class object.annotation.Oligo_adhocRelation
 
setSize_spot(int) - Method in class object.common.ImageManager
 
setSlide_code(String) - Method in class object.microarray.Microarray
 
setSlide_code(String) - Method in class object.microarray.MicroarrayElement
 
setSnip_sequence(String) - Method in class object.microrna.SnipMir
 
setSoftware_id(int) - Method in class object.microrna.MicroTopTable
 
setSolution(String) - Method in class object.common.Foq
 
setSolvant(String) - Method in class object.microarray.Plate
 
setSonde_id(int) - Method in class object.annotation.Sonde
 
setSonde_type(String) - Method in class object.microrna.MicroSite
 
setSonde_type_id(int) - Method in class object.annotation.Sonde
 
setSpecificity(String) - Method in class object.annotation.Specificity
 
setSpo_ref(String) - Method in class object.microarray.Microarray_project_type
 
setSpotter(Spotter) - Method in class object.microarray.Spotting
 
setSpotter_id(int) - Method in class object.microarray.Spotter
 
setSpotter_ref(String) - Method in class object.microarray.Spotter
 
setSpotting_id(int) - Method in class object.microarray.Control
 
setSpotting_id(int) - Method in class object.microarray.Microarray
 
setSpotting_id(int) - Method in class object.microarray.MicroarrayElement
 
setSpotting_id(int) - Method in class object.microarray.Spotting
 
setSpotting_ref(String) - Method in class object.microarray.Spotting
 
setSpottype_file(String) - Method in class object.common.Biostats
 
setSpotTypeFile(SpotTypeFile) - Method in class object.common.Rstat
 
setStade(String) - Method in class object.microarray.Labeling
 
setStart(int) - Method in class object.annotation.Cytoband
 
setStart(int) - Method in class object.annotation.Exon
 
setStart(int) - Method in class object.annotation.GenomicPosition
 
setStart(int) - Method in class object.microrna.Mstdata
 
setState(String) - Method in class object.common.Order
 
setStaticParams(Hashtable) - Method in class object.common.Biostats
Initialize static parameters from the configuration file
- pathTmp
- pathBiostats
setStaticParams(Hashtable, Hashtable, Hashtable) - Method in class object.common.Blast
Initialize static parameters from the configuration file
- ext_tmp
- ext_blast
- ext_bl2seq
- pathBlast
- pathFormatDB
- pathDatabase
- pathTmp
setStaticParams(Hashtable, Hashtable) - Method in class object.common.BlastTwoSeq
Initialize static parameters from the configuration file
- ext_seq
- ext_bl2seq
- pathTmp
setStaticParams(Hashtable) - Method in class object.common.Common
Initialize static parameters from the configuration file - MAIL_HOST - MAIL_FROM
setStaticParams(Hashtable) - Method in class object.common.Convert
This function initialize static parameters of Search Objects --> see : nbResultsParPAge and NB_MAX_RESULTS
setStaticParams(Hashtable) - Method in class object.common.ImageManager
Initialize static parameters from the configuration file
- pathMicroarray
- pathSpotting
- pathImages
- pathTmp
setStaticParams(Hashtable) - Method in class object.common.OnMouseOver
Initialization function for the backgrouds and fonts for the OnMouseOver Objects
setStaticParams(Hashtable, Hashtable) - Method in class object.common.Order
Initialize static parameters from the configuration file - MAIL_HOST - MAIL_FROM
setStaticParams(Hashtable, Hashtable, Hashtable, Hashtable) - Method in class object.common.Project
Initialize static parameters from the configuration file :
- ext_seq
- ext_tmp
- ext_oli
- pathTmp
- pathFormatDB
- nbResultsParPAge
- MAIL_HOST
- MAIL_FROM
setStaticParams(Hashtable, Hashtable) - Method in class object.common.Rstat
Initialize static parameters from the configuration file - MAIL_HOST - MAIL_FROM
setStaticParams(Hashtable) - Method in class object.common.Search
This function initialize static parameters of Search Objects --> see : nbResultsParPAge and NB_MAX_RESULTS
setStaticParams(Hashtable, Hashtable) - Method in class object.common.SessionBlastObject
Initialize static parameters from the configuration file
- ext_seq
- ext_tmp
- pathTmp
setStaticParams(Hashtable, Hashtable) - Method in class object.common.Spidey
This function initialize static parameters of Spidey Objects All the names of images Static parameters of this class are initialized with informations containing in the application config file.
setStaticParams(Hashtable) - Method in class object.common.Toptable
Initialize static parameters from the configuration file - pathTmp - pathBiostats
setStaticParams(Hashtable) - Method in class object.hts.Hts_result
Initialize static parameters from the configuration file - pathMicroarray - pathTmp
setStaticParams(Hashtable, Hashtable) - Method in class object.hts.Hts_RManager
Initialize static parameters from the configuration file - MAIL_HOST - MAIL_FROM
setStaticParams(Hashtable) - Method in class object.microarray.Plate
 
setStaticParams(Hashtable) - Method in class object.microarray.Project_order
Initialize static parameters from the configuration file
- pathTmp
- pathPublication
setStaticParams(Hashtable) - Method in class object.microarray.Scan
Initialize static parameters from the configuration file - pathMicroarray - pathTmp
setStaticParams(Hashtable) - Method in class object.microarray.Spotting
Initialize static parameters from the MEDLAB configuration file
setStepFourDone(boolean) - Method in class object.microarray.Spotting
 
setStepOneDone(boolean) - Method in class object.common.Attribution
 
setStepOneDone(boolean) - Method in class object.microarray.Spotting
 
setStepThreeDone(boolean) - Method in class object.microarray.Spotting
 
setStorage(Storage) - Method in class object.microarray.Plate
 
setStorage_id(int) - Method in class object.microarray.Storage
 
setStorage_ref(String) - Method in class object.microarray.Storage
 
setStrand(String) - Method in class object.annotation.GenomicPosition
 
setStrand(String) - Method in class object.microrna.Mirna_chromosome
 
setSubject_ref(String) - Method in class object.microarray.Labeling
 
setSupportedLangs(String) - Method in class common.beans.locale.LocaleBean
Sets the set of supported languages, provided as a comma separated list of country/language codes.
setSupportedLangs(String) - Method in class common.tags.generic.UseLocaleBundleTag
Sets the supportedLangs property, i.e. a comma separated list of language/country codes.
setSValue(String) - Method in class object.common.Blast
 
setSValue(String) - Method in class object.common.BlastTwoSeq
 
setSValue(String) - Method in class object.common.SessionBlastObject
 
setSymbol(String) - Method in class object.annotation.Gene
 
setSymbol(String) - Method in class object.annotation.Genoligo_affy_rel
 
setSymbol(String) - Method in class object.annotation.Oligo_annotation
 
setSymbol(String) - Method in class object.annotation.Probeset
 
setSymbol(String) - Method in class object.common.Point
 
setSymbol(String) - Method in class object.microarray.ElementMap
 
setSymbol(String) - Method in class object.microrna.Match
 
setSymbol(String) - Method in class object.microrna.Mcbdata
 
setSymbol(String) - Method in class object.microrna.Mirna_target
 
setSymbol(String) - Method in class object.microrna.TargetPrediction
 
setSymbolSearch(String[]) - Method in class object.common.DisplayParams
 
setSynonym(String) - Method in class object.annotation.Gene
 
setTaille(int) - Method in class object.annotation.Sonde
 
setTarget(String) - Method in class object.common.RNAhybrid
 
setTarget(String) - Method in class object.microrna.MatchMCB
 
setTaxonomy_id(int) - Method in class object.annotation.Organism
 
setTelephone(String) - Method in class object.common.Plateforme
 
setTelephone(String) - Method in class object.common.User
 
setTemperature(int) - Method in class object.microarray.Hybridization
 
setTemps(int) - Method in class object.microarray.Hybridization
 
setTemps_creation(String) - Method in class object.common.CreationPlate
 
setTemps_creation(String) - Method in class object.microarray.Plate384
 
setTerm(Term) - Method in class object.annotation.GoLink
 
setTerm(Term) - Method in class object.microrna.Target
 
setText(String) - Method in class object.microarray.MageProtocol
 
setTissue(String) - Method in class object.hts.Hts_minseqe
 
setTissue(String) - Method in class object.microarray.Labeling
 
setTissue_id(int) - Method in class object.annotation.Tissue
 
setTissue_ref(String) - Method in class object.annotation.Tissue
 
setTitle(String) - Method in class object.microarray.GeoSerie
 
setTitre(String) - Method in class object.annotation.GenbankRef
 
setTm(double) - Method in class object.annotation.Oligo_tiling
 
setTm(double) - Method in class object.annotation.Sonde
 
setTmpDir(String) - Method in class object.common.Biostats
 
setToptable(String) - Method in class object.common.ImageManager
 
setToptable_file(String) - Method in class object.common.Toptable
 
setToptable_gene(Toptable) - Method in class object.microrna.MicroTopTable
 
setToptable_id(int) - Method in class object.common.Toptable
 
setToptable_image(String) - Method in class object.common.Toptable
 
setToptable_micro(Toptable) - Method in class object.microrna.MicroTopTable
 
setToptable_ref(String) - Method in class object.common.Toptable
 
setTranscript_id(String) - Method in class object.microrna.Mirna_context
 
setTranscript_name(String) - Method in class object.microrna.Mirna_context
 
setTranscript_source(String) - Method in class object.microrna.Mirna_context
 
setTreatment(String) - Method in class object.hts.Hts_minseqe
 
setTwoMuch(boolean) - Method in class object.common.Search
 
setTwoMuch(boolean) - Method in class object.microrna.MicroCible
 
setTxt_file(String) - Method in class object.microarray.Spotting
 
setType(String) - Method in class object.annotation.Term
 
setType(String) - Method in class object.common.Biostats
 
setType(String) - Method in class object.hts.Hts_analysis_parameter
 
setType(String) - Method in class object.hts.Hts_pipeline_parameter
 
setType(String) - Method in class object.microarray.MageProtocol
 
setType(String) - Method in class object.microarray.Scan
 
setType_contact(String) - Method in class object.common.Contact_client
 
setType_convert(String) - Method in class object.common.Convert
 
setType_fichier(String) - Method in class object.common.Fichier
 
setType_file(String) - Method in class object.microarray.Quantification_file
 
setType_foq(String) - Method in class object.common.Foq
 
setType_graphe(String) - Method in class object.common.ImageManager
 
setType_recherche(String) - Method in class object.common.Search
 
setUnigene_id(String) - Method in class object.annotation.Gene
 
setUnite(String) - Method in class object.common.User
 
setUnreleased(boolean) - Method in class object.microarray.GeoSerie
 
setUser(User) - Method in class object.common.Board
 
setUser(User) - Method in class object.common.Board_user
 
setUser(User) - Method in class object.common.GeneCart
 
setUser(User) - Method in class object.common.Keyword
 
setUser(User) - Method in class object.common.Order
 
setUser(User) - Method in class object.common.SessionObject
 
setUser(User) - Method in class object.hts.Hts_sample
 
setUser(User) - Method in class object.microarray.Microarray
 
setUser(User) - Method in class object.microarray.Plate
 
setUser(User) - Method in class object.microarray.Project_order
 
setUser(User) - Method in class object.microarray.Spotting
 
setUser_dest_id(int) - Method in class object.common.Foq
 
setUser_dilution(User) - Method in class object.microarray.Plate384
 
setUser_hybrid(int) - Method in class object.common.Order
 
setUser_id(int) - Method in class object.common.Contact_client
 
setUser_id(int) - Method in class object.common.Convert
 
setUser_id(int) - Method in class object.common.Foq
 
setUser_id(int) - Method in class object.common.ImageManager
 
setUser_id(int) - Method in class object.common.Journal
 
setUser_id(int) - Method in class object.common.Rstat
 
setUser_id(int) - Method in class object.common.User
 
setUser_id(int) - Method in class object.hts.Hts_RManager
 
setUser_owner(int) - Method in class object.common.Project
 
setUser_owner(int) - Method in class object.common.ProjectObject
 
setUser_viewer(String) - Method in class object.common.Project
 
setUser_writer(int) - Method in class object.common.Project
 
setUser_writer(int) - Method in class object.common.ProjectObject
 
setValue(int) - Method in class object.common.ToolBox
 
setValue(String) - Method in class object.common.ToolBoxString
 
setValue(String) - Method in class object.hts.Hts_analysis_parameter
 
setValue(String) - Method in class object.hts.Hts_pipeline_parameter
 
setVectorAnnotations(Vector) - Method in class object.annotation.Gene
 
setVectorBiostats(Vector) - Method in class object.microarray.Project_order
 
setVectorCMD(Vector) - Method in class object.common.Rstat
 
setVectorCMD(Vector) - Method in class object.hts.Hts_RManager
 
setVectorCommande(Vector) - Method in class object.annotation.Oligo
 
setVectorCytobands(Vector) - Method in class object.annotation.Gene
 
setVectOrderedNames(Vector) - Method in class object.hts.Hts_pipeline
 
setVectorExons(Vector) - Method in class object.annotation.Gene
 
setVectorGenbankRef(Vector) - Method in class object.annotation.Gene
 
setVectorGenes(Vector) - Method in class object.common.Search
 
setVectorGenoligo_rel(Vector) - Method in class object.annotation.Sonde
 
setVectorHitOrdre(Vector) - Method in class object.common.Blast
 
setVectorHts_order(Vector) - Method in class object.hts.Hts_RManager
 
setVectorHts_order(Vector) - Method in class object.microarray.Project_order
 
setVectorHts_result(Vector) - Method in class object.hts.Hts_sample
 
setVectorHts_sample(Vector) - Method in class object.common.Attribution
 
setVectorHts_sample(Vector) - Method in class object.hts.Hts_order
 
setVectorHts_sample(Vector) - Method in class object.hts.Hts_RManager
 
setVectorHts_sample(Vector) - Method in class object.hts.Hts_run
 
setVectorJournal(Vector) - Method in class object.common.Order
 
setVectorKeys(Vector) - Method in class object.microrna.MapTarget
 
setVectorKeys(Vector) - Method in class object.microrna.MicroCible
 
setVectorKeys(Vector) - Method in class object.microrna.MicroSite
 
setVectorKeys(Vector) - Method in class object.microrna.MicroTopTable
 
setVectorKeys(Vector) - Method in class object.microrna.TargetPrediction
 
setVectorKeyword(Vector) - Method in class object.microarray.Project_order
 
setVectorLabeling(Vector) - Method in class object.microarray.Hybridization
 
setVectorMatch(Vector) - Method in class object.microrna.Mttdata
 
setVectorMatch(Vector) - Method in class object.microrna.Target
 
setVectorMatchMCB(Vector) - Method in class object.microrna.Mcbmatch
 
setVectorMicroarray(Vector) - Method in class object.common.Attribution
 
setVectorMicroarray(Vector) - Method in class object.common.Rstat
 
setVectorMicroarray(Vector) - Method in class object.microarray.Microarray_order
 
setVectorMicroarray(Vector) - Method in class object.microarray.Spotting
 
setVectorMicroarray_order(Vector) - Method in class object.microarray.Project_order
 
setVectorMicroarrays(Vector) - Method in class object.common.ImageManager
 
setVectorMirna_chromosome(Vector) - Method in class object.microrna.Mirna
 
setVectorMirna_context(Vector) - Method in class object.microrna.Mirna
 
setVectorMirna_mature(Vector) - Method in class object.annotation.Oligo_adhoc
 
setVectorMirna_reference(Vector) - Method in class object.microrna.Mirna
 
setVectorMirna_target(Vector) - Method in class object.microrna.MapTarget
 
setVectorOligo_adhocRelation(Vector) - Method in class object.annotation.Gene
 
setVectorOligos(Vector) - Method in class object.annotation.Gene
 
setVectorOrdered(Vector) - Method in class object.microrna.TargetPrediction
 
setVectorPlate(Vector) - Method in class object.microarray.Spotting
 
setVectorPlate384(Vector) - Method in class object.common.Dilution
 
setVectorPlate384(Vector) - Method in class object.microarray.Spotting
 
setVectorProject_order(Vector) - Method in class object.common.Board_user
 
setVectorScan(Vector) - Method in class object.microarray.Microarray
 
setVectorSequence(Vector) - Method in class object.microrna.MicroSite
 
setVectorSequenceObject(Vector) - Method in class object.common.Project
 
setVectorSequenceOrdre(Vector) - Method in class object.common.SessionBlastObject
 
setVectorSerie(Vector) - Method in class object.microarray.SerieFile
 
setVectorSondes(Vector) - Method in class object.common.Search
 
setVectorSpodo_hits(Vector) - Method in class object.annotation.Oligo_adhoc
 
setVectorSpotType(Vector) - Method in class object.microarray.SpotTypeFile
 
setVectorToptable(Vector) - Method in class object.microarray.Project_order
 
setVille(String) - Method in class object.common.User
 
setVille_fact(String) - Method in class object.common.User
 
setVille_livr(String) - Method in class object.common.User
 
setVolume(int) - Method in class object.common.CreationPlate
 
setVolume(int) - Method in class object.common.Dilution
 
setVolume(int) - Method in class object.microarray.Plate
 
setVrk_file(String) - Method in class object.microarray.Spotting
 
setVsm_file(String) - Method in class object.microarray.Spotting
 
setWavelength(String) - Method in class object.microarray.Labeling_type
 
setWhatIsValue(String) - Method in class object.microarray.Quantification_file
 
setWorkingDIR(String) - Method in class object.common.Rstat
 
setWorkingDIR(String) - Method in class object.hts.Hts_RManager
 
setWValue(String) - Method in class object.common.Blast
 
setWValue(String) - Method in class object.common.BlastTwoSeq
 
setWValue(String) - Method in class object.common.SessionBlastObject
 
setX(double) - Method in class object.common.Point
 
setX_coord(int) - Method in class object.microarray.ElementMap
 
setX_coord(int) - Method in class object.microarray.Feature
 
setX_pos(int) - Method in class object.annotation.EstTissue
 
setXhybrid(double) - Method in class object.annotation.Specificity
 
setXhybrid_max(double) - Method in class object.annotation.Sonde
 
setXhybridMatch(String) - Method in class object.annotation.Gene
 
setXsome(String) - Method in class object.microrna.Mirna_chromosome
 
setY(double) - Method in class object.common.Point
 
setY_coord(int) - Method in class object.microarray.ElementMap
 
setY_coord(int) - Method in class object.microarray.Feature
 
setY_pos(int) - Method in class object.annotation.EstTissue
 
setYitle(String) - Method in class object.microrna.Mirna_reference
 
setZipcode(String) - Method in class object.common.User
 
setZipcode_fact(String) - Method in class object.common.User
 
setZipcode_livr(String) - Method in class object.common.User
 
shifts2 - Static variable in class JRclient.jcrypt
 
short_accession - Variable in class object.annotation.Oligo_adhoc
Accession of this Oligo_adhoc Object
short_slide_code - Variable in class object.microarray.Microarray
Short slide code of the Microarray Object
shortName - Variable in class object.microarray.Feature
shortName of Oligo object of this Feature
shortref - Variable in class object.annotation.Genoligo_affy_rel
shortref
shortref - Variable in class object.annotation.Probeset
shortref of microarray_project_type
shortRef - Variable in class object.hts.Hts_type
ShortRef of this Hts_type object
shortRef - Variable in class object.microarray.Microarray_project_type
ShortRef of this Microarray_project_type object
shutdown() - Method in class JRclient.Rconnection
shutdown remote Rserv.
size() - Method in class JRclient.RFactor
returns the number of caes
size - Variable in class object.annotation.Genoligo_rel
Size of the Oligo Object on the sequence of the Gene Object
size - Variable in class object.annotation.Oligo_adhocRelation
Size of match of the oligo_adhoc on the Gene
size - Variable in class object.common.Spidey
Size of graphs
size_of_support - Variable in class object.common.Attribution
 
size_spot - Variable in class object.common.ImageManager
 
skb - Static variable in class JRclient.jcrypt
 
slide_code - Variable in class object.microarray.Microarray
Code of the Microarray Object
slide_code - Variable in class object.microarray.MicroarrayElement
Slide_code of the Microarray object corresponding to this MicroarrayElement
snip_sequence - Variable in class object.microrna.SnipMir
snp_sequence
SnipMir - Class in object.microrna
Description
Infos : KLB - IPMC - 10/2008
SnipMir() - Constructor for class object.microrna.SnipMir
Default constructor
software_id - Variable in class object.microrna.MicroTopTable
software
solution - Variable in class object.common.Foq
Action anwser to the problem observed
solvant - Variable in class object.microarray.Plate
Solvant use for this Plate object
Sonde - Class in object.annotation
Description
Sonde Object can be Oligo Object, Oligo_adhoc Object or Oligo_control Object
Infos : KLB - IPMC - 08/2005
Sonde(int, int) - Constructor for class object.annotation.Sonde
Constructs a Sonde Object from an existing Sonde ID
sonde_id - Variable in class object.annotation.Sonde
ID of Sonde Object
sonde_type - Variable in class object.microrna.MicroSite
sonde_type
sonde_type_id - Variable in class object.annotation.Sonde
ID of Sonde type
sortMyKeys() - Method in class object.microrna.MapTarget
 
sortMyVector(String) - Method in class object.microrna.MicroCible
 
sortMyVector(String) - Method in class object.microrna.MicroSite
 
sortMyVector(String) - Method in class object.microrna.MicroTopTable
 
sortMyVector(Hashtable) - Method in class object.microrna.TargetPrediction
 
Specificity - Class in object.annotation
Description
Contains all informations concernng specificity of a Sonde Object with a BlastBase Object
Infos : KLB - IPMC - 08/2003
Specificity() - Constructor for class object.annotation.Specificity
Default constructor
Specificity(int, BlastBase, String, double) - Constructor for class object.annotation.Specificity
Construct a Specificity Object with several parameters
specificity - Variable in class object.annotation.Specificity
String describing this Specificity Object
Spidey - Class in object.common
Description
Spidey is the class which do all graph in the application
Infos : KLB - IPMC - 08/2003
Spidey() - Constructor for class object.common.Spidey
Default constructor
spo_ref - Variable in class object.microarray.Microarray_project_type
EvryRef of this Microarray_project_type object
Spodo_hit - Class in object.annotation
Description
Spodo_hit object
Infos : KLB - IPMC - 02/2009
Spodo_hit(String, double, double, double, int, String) - Constructor for class object.annotation.Spodo_hit
Default constructor
Spotter - Class in object.microarray
Description
Spotter Object
Infos : KLB - IPMC - 01/2004
Spotter() - Constructor for class object.microarray.Spotter
Default constructor
Spotter(int) - Constructor for class object.microarray.Spotter
Constructs a Spotter Object from an existing Spotter ID
spotter - Variable in class object.microarray.Spotting
Spotter Object
spotter_id - Variable in class object.microarray.Spotter
ID of Spotter object
spotter_ref - Variable in class object.microarray.Spotter
Reference of Spotter Object
Spotting - Class in object.microarray
Description
Spotting Object
Infos : KLB - IPMC - 01/2004
Spotting() - Constructor for class object.microarray.Spotting
Default constructor
Spotting(int) - Constructor for class object.microarray.Spotting
Constructs a Spotting object from Spotting ID
spotting_id - Variable in class object.microarray.Control
ID of Spotting Object for which the control has been done
spotting_id - Variable in class object.microarray.Microarray
Spotting Object for this Microarray Object
spotting_id - Variable in class object.microarray.MicroarrayElement
ID of the Spotting Object parent of the Microarray object corresponding to this MicroarrayElement
spotting_id - Variable in class object.microarray.Spotting
ID of Spotting object
spotting_ref - Variable in class object.microarray.Spotting
Reference of Spotting object
SpotType - Class in object.microarray
Description
SpotType Objects
Infos : KLB - IPMC - 10/2008
SpotType(String, String, String, String) - Constructor for class object.microarray.SpotType
Default constructor
spottype_file - Variable in class object.common.Biostats
Path of spottype file
spotTypeFile - Variable in class object.common.Rstat
 
SpotTypeFile - Class in object.microarray
Description
SpotTypeFile Objects
Infos : KLB - IPMC - 10/2008
SpotTypeFile() - Constructor for class object.microarray.SpotTypeFile
Default constructor
SPtrans - Static variable in class JRclient.jcrypt
 
stade - Variable in class object.microarray.Labeling
Cancer stade of this Subject object
start - Variable in class object.annotation.Cytoband
Start of this Cytoband
start - Variable in class object.annotation.Exon
Start of the exon on the Chromosome corresponding for the Gene object
start - Variable in class object.annotation.GenomicPosition
Start position on the Chromosome
start - Variable in class object.hts.MaMatch
 
start - Variable in class object.microrna.Mstdata
start
state - Variable in class object.common.Order
State of this Order, it can be 'send', 'biostat', 'hybrid', 'prod', 'devis', 'reject', 'cancel' or 'wait'
stepFourDone - Variable in class object.microarray.Spotting
 
stepOneDone - Variable in class object.common.Attribution
Flag set to true when step one is done
stepOneDone - Variable in class object.microarray.Spotting
 
stepThreeDone - Variable in class object.microarray.Spotting
 
stopper() - Method in class object.common.ExecuteCmd
Stop the execution of the list of commande
storage - Variable in class object.microarray.Plate
Strorage used for this Plate object
Storage - Class in object.microarray
Description
Storage Object
Infos : KLB - IPMC - 01/2004
Storage() - Constructor for class object.microarray.Storage
Default constructor
Storage(int) - Constructor for class object.microarray.Storage
Constructs a Storage Object from Storage ID
storage_id - Variable in class object.microarray.Storage
ID of Storage object
storage_ref - Variable in class object.microarray.Storage
Name of the Storage Object
strand - Variable in class object.annotation.GenomicPosition
Strand for this GenomicPosition Object
strand - Variable in class object.hts.MaMatch
 
strand - Variable in class object.microrna.Mirna_chromosome
strand
subject_ref - Variable in class object.microarray.Labeling
Reference of this Subject object
supportedLangs - Variable in class common.beans.locale.LocaleBean
 
supportedLangs - Variable in class common.tags.generic.UseLocaleBundleTag
 
SValue - Variable in class object.common.Blast
Value of S value for executing Blast program
SValue - Variable in class object.common.BlastTwoSeq
Value of S value for executing Blast program
SValue - Variable in class object.common.SessionBlastObject
S value for the Blast ( '1' is single strain (direct), '2' for single strain (indirect), '3' for both)
switchState() - Method in class object.hts.Hts_sample
This function switch is_active boolean state of this Hts_sample Object into database.
switchState() - Method in class object.microarray.Microarray
This function switch is_active boolean state of this Microarray Object into database.
symbol - Variable in class object.annotation.Gene
Gene symbol (name)
symbol - Variable in class object.annotation.Genoligo_affy_rel
symbol
symbol - Variable in class object.annotation.Oligo_annotation
Gene symbol associated to this relation
symbol - Variable in class object.annotation.Probeset
Gene symbol (name)
symbol - Variable in class object.common.Point
Gene symbol associated with this Point Object
symbol - Variable in class object.microarray.ElementMap
Symbol of Oligo object of this ElementMap
symbol - Variable in class object.microrna.Match
symbol
symbol - Variable in class object.microrna.Mcbdata
symbol
symbol - Variable in class object.microrna.Mirna_target
symbol
symbol - Variable in class object.microrna.TargetPrediction
symbol
symbolSearch - Variable in class object.common.DisplayParams
List of string symbol asked for image display, without internal modifications
synonym - Variable in class object.annotation.Gene
Gene symbol (synonyms)

T

tag - Variable in class JRclient.RList
xpressions containing head and body.
taille - Variable in class object.annotation.Sonde
Length of the sequence of the Sonde Object
target - Variable in class object.common.RNAhybrid
target
target - Variable in class object.microrna.MatchMCB
target
Target - Class in object.microrna
Description
Target
Infos : KLB - IPMC - 02/2008
Target() - Constructor for class object.microrna.Target
Default constructor
Target(Term) - Constructor for class object.microrna.Target
Constructs a Target object
TargetPrediction - Class in object.microrna
Description
Infos : KLB - IPMC - 09/2008
TargetPrediction() - Constructor for class object.microrna.TargetPrediction
Default constructor
taxonomy_id - Variable in class object.annotation.Organism
Taxonomy ID from external database (9606 from Homo Sapiens and 10090 for Mus musculus)
telephone - Variable in class object.common.Plateforme
Phone number of Plateforme Object
telephone - Variable in class object.common.User
Phone number of the User Object
temperature - Variable in class object.microarray.Hybridization
Temperature for this Hybridization
temps - Variable in class object.microarray.Hybridization
Duration for this Hybridization
temps_creation - Variable in class object.common.CreationPlate
Time of creation plate (not use)
temps_creation - Variable in class object.microarray.Plate384
Creation time for the Plate384 creation process
term - Variable in class object.annotation.GoLink
Term describing the Gene Ontology link with the gene
Term - Class in object.annotation
Description
Gene Ontology Term
Infos : KLB - IPMC - 08/2003
Term() - Constructor for class object.annotation.Term
Default constructor
Term(String) - Constructor for class object.annotation.Term
Construct a Term Object with a Gene Ontology accession
Term(String, String, String) - Constructor for class object.annotation.Term
Construct a Term Object with a Gene Ontology accession
term - Variable in class object.microrna.Target
Term of this Target Object
text - Variable in class object.microarray.MageProtocol
text of this MageProtocol Object
tf - Variable in class object.microrna.MicroTopTable
 
tiffInfo(String) - Method in class object.microarray.Scan
This function return a string concerning informations about tiff image path received
TIP_BG - Static variable in class object.common.OnMouseOver
Background color of Tips
TIP_FONT - Static variable in class object.common.OnMouseOver
Font of Tips
Tissue - Class in object.annotation
Description
Tissue
Infos : KLB - IPMC - 05/2007
Tissue() - Constructor for class object.annotation.Tissue
Default constructor
Tissue(int) - Constructor for class object.annotation.Tissue
Construct a Tissue Object with a Tissue ID
tissue - Variable in class object.hts.Hts_minseqe
Tissue from which this Hts_minseqe object come from
tissue - Variable in class object.microarray.Labeling
Tissue Object from which this Sample object come from
tissue_id - Variable in class object.annotation.Tissue
Tissue ID
tissue_ref - Variable in class object.annotation.Tissue
Tissue ref
title - Variable in class object.common.OnMouseOver
Title of OnMouseOver Object
title - Variable in class object.microarray.GeoSerie
title of GeoSerie Object
title - Variable in class object.microrna.Mirna_reference
title
TITLE_BG - Static variable in class object.common.OnMouseOver
Background color of Title
TITLE_FONT - Static variable in class object.common.OnMouseOver
Font of Title
title_graph - Variable in class object.common.ImageManager
Title of graph
titre - Variable in class object.annotation.GenbankRef
Title of this GenbankRef object
tm - Variable in class object.annotation.Oligo_tiling
tm of Oligo_tiling Object
tm - Variable in class object.annotation.Sonde
Melting temperature of the Sonde Object
tmpDir - Variable in class object.common.Biostats
 
toArray(Enumeration) - Method in class common.tags.generic.UseLocaleBundleTag
Converts an Enumeration of Locale objects to a Locale array.
toFile(String) - Method in class object.microarray.SerieFile
 
toFile(String) - Method in class object.microarray.SpotTypeFile
 
toLanguage(Locale) - Method in class common.beans.locale.LocaleBean
Returns the language/country code for the specified Locale.
toLocale(String) - Method in class common.beans.locale.LocaleBean
Returns a Locale for the specifed language/country code.
ToolBox - Class in object.common
Description
ToolBox object are used to display informations in Select Html Box
Infos : KLB - IPMC - 01/2004
ToolBox() - Constructor for class object.common.ToolBox
Default constructor
ToolBox(int, String) - Constructor for class object.common.ToolBox
Constructs a ToolBox object from value and name
ToolBoxString - Class in object.common
Description
ToolBoxString object are used to display informations in Select Html Box
Infos : KLB - IPMC - 12/2008
ToolBoxString() - Constructor for class object.common.ToolBoxString
Default constructor
ToolBoxString(String, String) - Constructor for class object.common.ToolBoxString
Constructs a ToolBoxString object from value and name
toptable - Variable in class object.common.ImageManager
 
Toptable - Class in object.common
Description
TopTable Objects : Top Table of a statistical analysis for an experimental condition
Infos : KLB - IPMC - 10/2007
Toptable() - Constructor for class object.common.Toptable
Default constructor
Toptable(int) - Constructor for class object.common.Toptable
Constructs a Toptable object from a Toptable ID
Toptable(String) - Constructor for class object.common.Toptable
Constructs a Toptable object from a Toptable file
toptable_file - Variable in class object.common.Toptable
Path of Toptable file
toptable_gene - Variable in class object.microrna.MicroTopTable
toptable_gene
toptable_id - Variable in class object.common.Toptable
ID of Toptable Object
toptable_image - Variable in class object.common.Toptable
Path of Toptable image
toptable_micro - Variable in class object.microrna.MicroTopTable
toptable_micro
toptable_ref - Variable in class object.common.Toptable
reference of Toptable Object
toString() - Method in class JRclient.RBool
 
toString() - Method in class JRclient.REXP
displayable contents of the expression.
toString() - Method in class JRclient.RFactor
displayable representation of the factor variable
toString() - Method in class JRclient.Rpacket
 
toString() - Method in class object.microarray.Serie
 
toString() - Method in class object.microarray.SpotType
 
tr - Static variable in class object.common.Spidey
Image empty
transcript_id - Variable in class object.microrna.Mirna_context
transcript_id
transcript_name - Variable in class object.microrna.Mirna_context
transcript_name
transcript_source - Variable in class object.microrna.Mirna_context
transcript_source
transferCharset - Static variable in class JRclient.Rconnection
This static variable specifies the character set used to encode string for transfer.
treatment - Variable in class object.hts.Hts_minseqe
 
twoarraygraph - Variable in class object.common.ImageManager
 
twoMuch - Variable in class object.common.Search
boolean : true when the search found two much Gene Objects ( limit is attribute : NB_MAX_RESULTS)
twoMuch - Variable in class object.microrna.MicroCible
boolean : true when the search found two much Gene Objects ( limit is attribute : NB_MAX_RESULTS)
txt_file - Variable in class object.microarray.Spotting
.TXT File describing this Spotting Object
type - Variable in class object.annotation.Sonde
 
type - Variable in class object.annotation.Term
Type of this Gene Ontology term
type - Variable in class object.common.Biostats
Type of normalized files
type - Variable in class object.hts.Hts_analysis_parameter
type
type - Variable in class object.hts.Hts_pipeline_parameter
type
type - Variable in class object.microarray.MageProtocol
type of this MageProtocol Object
type - Variable in class object.microarray.Scan
Type of Scan Object
type_contact - Variable in class object.common.Contact_client
Type contact (mail or phone)
type_convert - Variable in class object.common.Convert
Type of conversion
type_fichier - Variable in class object.common.Fichier
Type of this Fichier object
type_file - Variable in class object.microarray.Quantification_file
Type of the file (Agilent or Genepix)
type_foq - Variable in class object.common.Foq
Type of the Foq Object
type_graphe - Variable in class object.common.ImageManager
Type of graph for visualization (directory : 'graph')
type_recherche - Variable in class object.common.Search
Type of search to proceed (can be : id_reference, keyword, geneOntology or cytoband)

U

unigene_id - Variable in class object.annotation.Gene
Unigene reference for this Gene Object - Unigene Database
unite - Variable in class object.common.User
Unite
unreleased - Variable in class object.microarray.GeoSerie
 
update(String) - Method in class object.common.ImageManager
This function update the list of Microarrays in the attribute this.vectorMicroarrays
update() - Method in class object.common.SequenceObject
This function collect SequenceObject Object for this Project Object, collection from search page of Mediante web interface
update() - Method in class object.hts.Hts_sample
This function update Hts_sample Object into database.
update() - Method in class object.microarray.Microarray
This function update Microarray Object into database.
update() - Method in class object.microarray.Plate384
This function update the Plate384 Object into database
update() - Method in class object.microarray.Plate96
This function save the Plate96 Object into database
update(Hashtable) - Method in class object.microarray.SerieFile
 
update(Hashtable) - Method in class object.microarray.SpotTypeFile
 
update_rights() - Method in class object.common.User
This function update this User Object into database
updateColleague(String, String, String, String) - Method in class object.common.User
This function manage all action concerning colleague for this User Object
updateFiles(Hashtable) - Method in class object.common.Rstat
 
updateFocusIndex() - Method in class object.common.CreationPlate
This function update the this.focus int following submission steps focus = {8,6,7,9,0,1,3,4,5} in the case of IPMC creation plate process
updateMIAME(Hashtable) - Method in class object.common.Common
 
updateVec() - Method in class JRclient.RList
internal function that updates cached vectors
updateVolumeAndUse(int) - Method in class object.microarray.Plate96
 
UseLocaleBundleTag - Class in common.tags.generic
 
UseLocaleBundleTag() - Constructor for class common.tags.generic.UseLocaleBundleTag
 
UseLocaleBundleTagExtraInfo - Class in common.tags.generic
 
UseLocaleBundleTagExtraInfo() - Constructor for class common.tags.generic.UseLocaleBundleTagExtraInfo
 
user - Static variable in class common.sql.PgsqlConnector
PostgreSQL database user name
user - Variable in class object.common.Board
User owner of this Board Object
user - Variable in class object.common.Board_user
 
user - Variable in class object.common.GeneCart
User owner of this GeneCart Object
user - Variable in class object.common.Keyword
User owner of this Keyword Object
user - Variable in class object.common.Order
User owner of the Microarray_order object related to this Order Object
user - Variable in class object.common.SessionObject
User object, user curently browsing the web Interface
User - Class in object.common
Description
User Object
Infos : KLB - IPMC - 08/2003
User() - Constructor for class object.common.User
Default constructor
User(String, String) - Constructor for class object.common.User
Construct a User Object with login and password attributes
User(int) - Constructor for class object.common.User
Construct a User Object with ID of an existing User Object
user - Variable in class object.hts.Hts_sample
User owner of this Hts_sample Object
user - Variable in class object.microarray.Microarray
User owner of this Microarray Object
user - Variable in class object.microarray.Plate
User who have created this Plate object
user - Variable in class object.microarray.Project_order
User owner of this Project_order object
user - Variable in class object.microarray.Spotting
User of this Spotting
user_dest_id - Variable in class object.common.Foq
ID of User Object for which the Foq Object is destinate
user_dilution - Variable in class object.microarray.Plate384
User that have been proceeded to the dilution process
user_hybrid - Variable in class object.common.Order
ID of user going to hybridize the microarrays for this order
user_id - Variable in class object.common.Contact_client
ID of User object who get the contatc whith the client
user_id - Variable in class object.common.Convert
ID of the User processing the request
user_id - Variable in class object.common.Foq
ID of User Object who describe the Foq Object
user_id - Variable in class object.common.ImageManager
ID of User owning this ImageManager Object
user_id - Variable in class object.common.Journal
ID of User owner of this journal Object
user_id - Variable in class object.common.Rstat
 
user_id - Variable in class object.common.User
ID of User object
user_id - Variable in class object.hts.Hts_RManager
ID of Users performing R queries
user_owner - Variable in class object.common.Project
ID of User Object owner of this Project Object
user_owner - Variable in class object.common.ProjectObject
ID of the User owner of this Project
user_viewer - Variable in class object.common.Project
String of IDs of User curently viewer of this Project Object
user_writer - Variable in class object.common.Project
ID of User Object curently the only writer for this Project Object
user_writer - Variable in class object.common.ProjectObject
ID of the User currently writer of this Project

V

val - Variable in class JRclient.RBool
 
val - Variable in class JRclient.RFactor
values (content: String), ergo category names
value - Variable in class object.common.ToolBox
value of the ToolBox object
value - Variable in class object.common.ToolBoxString
value of the ToolBoxString object
value - Variable in class object.hts.Hts_analysis_parameter
value
value - Variable in class object.hts.Hts_pipeline_parameter
value
vectorAnnotations - Variable in class object.annotation.Gene
Vector of GoLink Object for this Gene object
vectorBiostats - Variable in class object.microarray.Project_order
Vector of Biostats object associated in this Project_order object
vectorCMD - Variable in class object.common.Rstat
Vector containing Command to R
vectorCMD - Variable in class object.hts.Hts_RManager
Vector containing Command to R
vectorCommande - Variable in class object.annotation.Oligo
Vector of Commande Object in which this Oligo have been ordered
vectorControl - Variable in class object.microarray.Spotting
Vector of Control Object in this Spotting Object
vectorCytobands - Variable in class object.annotation.Gene
Vector of Cytoband Object for this Gene object
vectOrderedNames - Variable in class object.hts.Hts_pipeline
 
vectorExons - Variable in class object.annotation.Gene
Vector of Exons Object which composed this Gene object
vectorGenbankRef - Variable in class object.annotation.Gene
Vector of GenbankRef Object for this Gene object
vectorGenes - Variable in class object.common.Search
Vector of Gene Objects found with this search
vectorGenoligo_rel - Variable in class object.annotation.Sonde
Vector containing relation with Gene Object concerning this Sonde Object
vectorHitOrdre - Variable in class object.common.Blast
Vector containing the order of the sequence in which the Blast program proceed
vectorHts_order - Variable in class object.hts.Hts_RManager
Vector containing Hts_order Objects
vectorHts_order - Variable in class object.microarray.Project_order
Vector of Hts_order object associated in this Project_order object
vectorHts_result - Variable in class object.hts.Hts_sample
Hts_result Vector for this Hts_sample Object
vectorHts_sample - Variable in class object.common.Attribution
Vector of Hts_sample Object in attribution
vectorHts_sample - Variable in class object.hts.Hts_order
Vector containing Hts_sample Objects corresponding this Hts_order Object
vectorHts_sample - Variable in class object.hts.Hts_RManager
Vector containing Hts_sample Objects
vectorHts_sample - Variable in class object.hts.Hts_run
Vector of Hts_sample Object creating by this Hts_run Object
vectorJournal - Variable in class object.common.Order
Vector containing journal actions event for this order Object
vectorKeys - Variable in class object.microrna.MapTarget
vectorKeys
vectorKeys - Variable in class object.microrna.MicroCible
Vector of keys ordered
vectorKeys - Variable in class object.microrna.MicroSite
Vector of keys ordered
vectorKeys - Variable in class object.microrna.MicroTopTable
 
vectorKeys - Variable in class object.microrna.TargetPrediction
Vector of genes ordered
vectorKeyword - Variable in class object.microarray.Project_order
Vector of Keyword object associated in this Project_order object
vectorLabeling - Variable in class object.microarray.Hybridization
Vector of Labeling used for this Hybridization Object
vectorMatch - Variable in class object.microrna.Mttdata
 
vectorMatch - Variable in class object.microrna.Target
Term of this Target Object
vectorMatchMCB - Variable in class object.microrna.Mcbmatch
vectorMatch
vectorMature - Variable in class object.microrna.Mirna
Vector of Mature microRNA
vectorMicroarray - Variable in class object.common.Attribution
Vector of Microarray Object in attribution
vectorMicroarray - Variable in class object.common.Rstat
Vector containing Microarrays Objects corresponding this Rstat
vectorMicroarray - Variable in class object.microarray.Microarray_order
Vector containing Microarrays Objects corresponding this Microarray_order
vectorMicroarray - Variable in class object.microarray.Spotting
Vector of Microarray Object creating by this Spotting Object
vectorMicroarray_order - Variable in class object.microarray.Project_order
Vector of Microarray_order object associated in this Project_order object
vectorMicroarrays - Variable in class object.common.ImageManager
Vector containing Microarray Objects selected for visualization
vectorMirna_chromosome - Variable in class object.microrna.Mirna
Vector of Contig Position
vectorMirna_context - Variable in class object.microrna.Mirna
Vector of Context
vectorMirna_mature - Variable in class object.annotation.Oligo_adhoc
Vector of Mirna_mature objects matched by this Oligo_adhoc Object
vectorMirna_reference - Variable in class object.microrna.Mirna
Vector of Literrature reference
vectorMirna_target - Variable in class object.microrna.MapTarget
vectorMirna_target
vectorOligo_adhocRelation - Variable in class object.annotation.Gene
Vector of Oligo_adhocRelation Object for this Gene object
vectorOligos - Variable in class object.annotation.Gene
Vector of Oligo Object matching this Gene object
vectorOrdered - Variable in class object.microrna.TargetPrediction
Vector of names ordered
vectorPlate - Variable in class object.microarray.Spotting
 
vectorPlate384 - Variable in class object.common.Dilution
Vector of Plate384 Object concerning by this dilution process
vectorPlate384 - Variable in class object.microarray.Spotting
Vector of Plate384 Object concerning this Spotting Object
vectorProject_order - Variable in class object.common.Board_user
Project_order for this Board Object
vectorScan - Variable in class object.microarray.Microarray
Scan(s) Vector for this Microarray Object
vectorScore - Variable in class object.microarray.Quantification_file
 
vectorSequence - Variable in class object.microrna.MicroSite
Vector of sequence
vectorSequence - Variable in class object.microrna.SnipMir
 
vectorSequenceObject - Variable in class object.common.Project
Vector containing the order of SequenceObject composing this Project Object in which we have to display the SequenceObject in the web interface
vectorSequenceOrdre - Variable in class object.common.SessionBlastObject
Vector of Sequences needed to blast in the order of the user
vectorSerie - Variable in class object.microarray.SerieFile
Vector of targets of SerieFile Object
vectorSondes - Variable in class object.common.Search
Vector of Sondes Objects found with this search
vectorSpodo_hits - Variable in class object.annotation.Oligo_adhoc
Vector of Spodo_hits objects owned by this Oligo_adhoc Object
vectorSpotType - Variable in class object.microarray.SpotTypeFile
Vector of spotType of SpotTypeFile Object
vectorToptable - Variable in class object.microarray.Project_order
Vector of Toptable object associated in this Project_order object
ville - Variable in class object.common.User
Town of User object
ville_fact - Variable in class object.common.User
Billing town of User object
ville_livr - Variable in class object.common.User
Sending town of User object
voidEval(String) - Method in class JRclient.Rconnection
evaluates the given command, but does not fetch the result (useful for assignment operations)
voidEvalDetach(String) - Method in class JRclient.Rconnection
evaluates the given command, detaches the session (see @link{detach()}) and closes connection while the command is being evaluted (requires Rserve 0.4+).
volume - Variable in class object.common.CreationPlate
Volume from Plate 96 to Plate 384
volume - Variable in class object.common.Dilution
Volume of the dilution
volume - Variable in class object.microarray.Plate
Volume of oligo in this Plate object
vrk_file - Variable in class object.microarray.Spotting
.VRK File describing this Spotting Object
vsm_file - Variable in class object.microarray.Spotting
.VSM File describing this Spotting Object

W

wavelength - Variable in class object.microarray.Labeling_type
wavelength default of this Labeling_type object
whatIsValue - Variable in class object.microarray.Quantification_file
 
workingDIR - Variable in class object.common.Rstat
 
workingDIR - Variable in class object.hts.Hts_RManager
 
write(int) - Method in class JRclient.RFileOutputStream
writes one byte to the file.
write(byte[]) - Method in class JRclient.RFileOutputStream
writes the content of b into the file.
write(byte[], int, int) - Method in class JRclient.RFileOutputStream
Writes specified number of bytes to the remote file.
write(Writer, MAGEJava) - Method in class object.microarray.MAGEWriter
 
WValue - Variable in class object.common.Blast
Value of W value for executing Blast program
WValue - Variable in class object.common.BlastTwoSeq
Value of W value for executing Blast program
WValue - Variable in class object.common.SessionBlastObject
W value for the Blast (length of minmal identical word to find)

X

x - Variable in class object.common.Point
X coord on the microarray for this Point Object
x_coord - Variable in class object.microarray.ElementMap
X_coord of the oligo on the Tiff image
x_coord - Variable in class object.microarray.Feature
X_coord of the oligo on the Tiff image
x_pos - Variable in class object.annotation.EstTissue
 
Xhtml - Class in object.common
Description
This object is the main key to parse XML config files of the applications
Infos : KLB - IPMC - 08/2003
Xhtml() - Constructor for class object.common.Xhtml
Constructeur Xhtml sans fichier passe en parametre.
Xhtml(String) - Constructor for class object.common.Xhtml
Constructeur Xhtml avec fichier passe en parametre; parsing automatique du fichier
xhybrid - Variable in class object.annotation.Specificity
X_hybridation concerning this Specificity Object
xhybrid_max - Variable in class object.annotation.Sonde
H_HYBRID value for this Sonde Object
xhybridMatch - Variable in class object.annotation.Gene
list of Xhybrid match along the transcript
XMLFile - Variable in class object.common.Xhtml
XML Document to parse ( MEDIANTE_CONFIG file )
xmlFormat - Variable in class object.microarray.MAGEWriter
 
xsome - Variable in class object.microrna.Mirna_chromosome
xsome
Xt - Variable in class JRclient.REXP
xpression type
XT_ARRAY_BOOL - Static variable in class JRclient.REXP
xpression type: RBool[]
XT_ARRAY_BOOL_UA - Static variable in class JRclient.REXP
internal use only!
XT_ARRAY_DOUBLE - Static variable in class JRclient.REXP
xpression type: double[]
XT_ARRAY_INT - Static variable in class JRclient.REXP
xpression type: int[]
XT_ARRAY_STR - Static variable in class JRclient.REXP
xpression type: String[] (currently not used, Vector is used instead)
XT_BOOL - Static variable in class JRclient.REXP
xpression type: RBool
XT_CLOS - Static variable in class JRclient.REXP
xpression type: closure (there is no java class for that type (yet?).
XT_DOUBLE - Static variable in class JRclient.REXP
xpression type: double
XT_FACTOR - Static variable in class JRclient.REXP
xpression type: RFactor; this XT is internally generated (ergo is does not come from Rsrv.h) to support RFactor class which is built from XT_ARRAY_INT
XT_INT - Static variable in class JRclient.REXP
xpression type: integer
XT_LANG - Static variable in class JRclient.REXP
xpression type: language construct (currently content is same as list)
XT_LIST - Static variable in class JRclient.REXP
xpression type: RList
XT_NULL - Static variable in class JRclient.REXP
xpression type: NULL
XT_STR - Static variable in class JRclient.REXP
xpression type: String
XT_SYM - Static variable in class JRclient.REXP
xpression type: symbol (content is symbol name: String)
XT_UNKNOWN - Static variable in class JRclient.REXP
xpression type: unknown; no assumptions can be made about the content
XT_VECTOR - Static variable in class JRclient.REXP
xpression type: Vector
xtName(int) - Static method in class JRclient.REXP
returns human-readable name of the xpression type as string.

Y

y - Variable in class object.common.Point
Y coord on the microarray for this Point Object
y_coord - Variable in class object.microarray.ElementMap
Y_coord of the oligo on the Tiff image
y_coord - Variable in class object.microarray.Feature
Y_coord of the oligo on the Tiff image
y_pos - Variable in class object.annotation.EstTissue
 

Z

zipcode - Variable in class object.common.User
Zipcode of User object
zipcode_fact - Variable in class object.common.User
Billing Zipcode of User object
zipcode_livr - Variable in class object.common.User
Sending Zipcode of User object

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z