object.common
Class Common

java.lang.Object
  object.common.Common

All Implemented Interfaces:

java.io.Serializable

public class Common
extends java.lang.Object
implements java.io.Serializable

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

See Also:

Serialized Form

Field Summary

static java.lang.String	MAIL_FROM Mail From for sending mail (mediante@ipmc.cnrs.fr)
static java.lang.String	MAIL_HOST Mail Host for sending mail (gelas.ipmc.cnrs.fr)

Constructor Summary

Common()
Default constructor

Method Summary

boolean	checkExtensionFile(java.lang.String type, java.lang.String fileName) This function check if the received match the type file received
boolean	checkUserIsOwner(int user_id, int microarray_id) This function returns a boolean according to correspondance between user_id received and User owner of the microarray_id received
java.util.Vector	getAllAddress() This function return a Vector containing email String of all Users Object.
java.util.Vector	getAllChromosome(int organism_id) This function returns a Vector containing all the Chromosome Object for the Organism received
java.util.Vector	getAllClient() This function returns a Vector containing ToolBox Object concerning User Object
java.util.Vector	getAllDiary() This function returns a Vector containing all the Diary Object
java.util.Vector	getAllEnquete() This function returns a Vector containing ToolBox Object concerning Enquete Object
java.util.Vector	getAllEstTissue() This function return a Vector containing all EstTissue object define in database.
java.util.Vector	getAllFoq() This function returns a Vector containing Foq Object
java.util.Vector	getAllGeoSerie()
java.util.Vector	getAllGOterm()
java.util.Vector	getAllMicroarray_project_type(int organism_id) Allowed to return all Microarray_project_type in the Database concerning an Organism ID
java.util.Vector	getAllMirna_mature() This function returns a Vector containing ToolBox Object concerning all Mirna_mature Objects
java.util.Vector	getAllMirna()
java.util.Vector	getAllMoIDForUser(int user_id) This function returns a vector containing ToolBox Object containing informations concerning Microarray_order Objects belonging to the User Object received.
java.util.Vector	getAllOrders() This function return a Vector containing Order Objects concerning all the Microarray_order stored in Database, ordered by state and date_attribution
java.util.Vector	getAllOrders(int plateforme_id, java.lang.String type)
java.util.Vector	getAllPlateforme() This function returns a vector containing all Plateforme Objects stored in database.
java.util.Vector	getAllProject_orderForPF(int plateforme_id) This function returns a vector containing ToolBox Object concerning Project_order Objects belonging to the Plateforme Object received.
java.lang.String	getAllRefPlaques384_ForDilution() This function returns a String of all the 384 Plate wich are not diluted
java.util.Vector	getAllUserColleague(int user_id) This function allowed to get all the Colleagues of a User
java.util.Vector	getAllUserForPF(int plateforme_id) This function returns a vector containing ToolBox Object concerning User Objects belonging to the Plateforme Object received.
java.util.Vector	getAllUsers() This function returns a vector containing all User Objects stored in database.
java.lang.String	getANForGID(int gene_id) This function returns the accession number for the gene_id received
int	getAuto_matureForMature_acc(java.lang.String mature_acc)
java.lang.String	getBlastParameters(java.lang.String kind) This function returns a select box for an HTML form describing the parameters for the execution of a Blast
java.lang.String	getContact(java.lang.String lastname, java.lang.String firstname, java.lang.String title, java.lang.String email, java.lang.String telephone)
java.util.Vector	getContactClient(int client_id) This function returns a Vector containing Contact_client Object concerning client_id received (user_id).
int	getCT_idForMID(int microarray_id) This function returns a control_type_id for the microarray_id received, in case of this Microarray Object is a Control Object.
IdDescriptionObject	getENSG(java.lang.String enst) This function returns the ensg and description from an enst reference
java.lang.String	getEvents(java.util.Vector vectorJournal)
java.lang.String	getFileName(java.lang.String path) This function returns the name of the file of the path reveiced
java.lang.String	getFileNameNoExt(java.lang.String path) This function returns the name of the file of the path reveiced
Gene	getFirstGeneForOID(int oligo_id) This function return the first Gene Object matching the Oligo Object from the oligo_id received
java.lang.String	getGal_fileFromMID(int microarray_id) This function return the gal file a the Spotting Object of the Microarray Object ID received
IdDescriptionObject	getGenbank_gene_id(java.lang.String refseq) This function returns the genbank_gene_id and description from a refseq reference
java.util.Vector	getGeneCartForUser(int user_id) This function returns a vector containing ToolBox Object of GeneCart Object owned by the User received.
int	getGIDForAN(java.lang.String accession_number) This function returns the gene ID for the accession_number received
int	getGIDForSymbol(java.lang.String symbol, java.lang.String organism_id) This function returns the Mediante gene ID for the symbol and organism ID received
java.lang.String	getGiFromRefseq(java.lang.String refseq) This function returns the gi number for the refseq reference received
java.util.Hashtable	getGoFrequence(int organism_id)
java.util.Hashtable	getHashAdhoc() This function return a Hashtable containing Oligo_annotation Objects.
java.util.Hashtable	getHashIDtoAcc(Microarray_project_type microarray_project_type) This function return a Hashtable containing the symbol of gene symbol.
java.util.Hashtable	getHashMap_toID(Microarray_project_type microarray_project_type) 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.
java.util.Hashtable	getHashOIDForControl() 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.
java.util.Hashtable	getHashOligo_annotation(boolean is_affy) This function return a Hashtable containing Oligo_annotation Objects.
java.util.Hashtable	getHtsInfos(java.lang.String type_user, java.lang.String annee, java.lang.String support) This function return a Hashtable containing informations concerning the production of Hts samples among the different plateforms.
int	getId(java.lang.String probe_ref)
boolean	getIs_allowed(int user_id, int project_order_id) This function returns a boolean concerning the possibility to see a Project_order for a User Object.
boolean	getIs_best_oligo(int oligo_id) This function returns a boolean corresponding to the fact that the oligo received is a "best" oligo
boolean	getIs_local_ordered(int oligo_id) This function returns a boolean corresponding to the existence of an oligo in the Local set ordered
boolean	getIs_national_ordered(int oligo_id) This function returns a boolean corresponding to the existence of an oligo in the National set ordered
boolean	getIs_selected(int oligo_id) This function returns a boolean corresponding to the existence of an oligo in the Local set ordered
java.util.Hashtable	getMainEstTissue() This function return a Hashtable containing the main est_tissue_id for the EstTissue which are not main EstTissue.
java.lang.String	getMega(int size) This function make the conversion beetween sequence base size and MegaBase size
java.lang.String	getMicroarray_orderLabel(int microarray_order_id) This function returns a description string of the Microarray_order Objects ID received.
java.util.Hashtable	getMicroarrayInfos(java.lang.String type_user, java.lang.String annee, java.lang.String support) This function return a Hashtable containing informations concerning the production of Microarrays among the different plateforms.
int	getMPTForRefAndPF(java.lang.String ref, int plateforme_id) This function returns the ID of the Microarray_project_type Object identified by both parameters.
java.lang.String	getOrder_ref(int order_id, java.lang.String type) This function return the mo_ref parameter of the Microarray_order Object received.
java.lang.String	getOrder_type(int order_id) Return the Order_type for an Order Object
java.util.Vector	getOrderForPlateforme() This function return a Vector containing Order Objects concerning all the Microarray_order waiting for plateforme attribution
int	getPO_IDForMO_ID(int microarray_order_id) This function return the project_order_id parameter of the Project_order Object owning the Microarray_order received.
int	getPopSize(int organism_id)
java.util.Vector	getProjectForUser(int user_id) This function returns a vector containing ToolBox Object of Project Object owned by the User received.
double	getRounded(double x)
double	getRounded2(double x)
double	getRounded4(double x)
Scan	getScanForMicroarray_id(int microarray_id) This function returns a Scan Object according to the microarray_id received
java.lang.String	getSelectBoxColor(java.lang.String name, java.lang.String selected)
java.lang.String	getSEQForAN(java.lang.String accession_number) This function returns the sequence for the accession number received
java.lang.String	getSEQForGID(int gene_id) This function returns the sequence for the gene_id received
java.lang.String	getSEQForOligo_adhoc_id(java.lang.String accession) This function returns the sequence for the sonde reference received
int	getSid_for_mid(int microarray_id)
java.lang.String	getSlide_code(java.lang.String quantif_file, int microarray_order_id) This function returns the slide code of the Microarray ID from which we received
java.lang.String	getSlide_codeForMicroarray_id(int microarray_id) This function returns the slide code of the Microarray ID received
java.lang.String	getSymbolForGeneList(java.lang.String project_id_str) This function returns a String containing distinct gene symbol from Gene Object belonging to the Project Object with the ID received as a String.
java.lang.String	getSymbolForGO(int organism_id, java.lang.String go_acc) This function returns a String containing distinct gene symbol for gene Ontology term
java.lang.String	getSymbolForMirna_mature(java.lang.String mature_acc) 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).
java.lang.String	getSymbolForOAID(int oligo_adhoc_id) This function returns the annotation for the oligo_adhoc_id received
java.util.Hashtable	getTestHash() This function return a Hashtable containing the ID and REF of Plate Object from plate SQL table.
java.lang.String	getTexteEmail(java.lang.String email)
java.util.Vector	getToolBoxHts_analysis(int hts_type_id)
java.util.Vector	getToolBoxHts_pipeline(int hts_type_id)
java.util.Vector	getToolBoxHts_run(int plateforme_id)
java.util.Vector	getToolBoxMicroarray(java.lang.String type, int id) This function returns a Vector containing ToolBox Object concerning all the Spotting Object not yet Cross linked
java.util.Vector	getToolBoxSpotting(int plateforme_id, boolean local_only) This function returns a Vector containing ToolBox Object concerning all the Spotting Object associated to the ID of Plateforme Object received
java.util.Vector	getToptableForUser(User user)
int	getUser_idForMPT_id(int microarray_project_type_id) 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.
int	getUser_idForProject_order_id(int project_order_id) This function returns the User Object ID owner of the Project_order Object ID received.
java.lang.String	getValidPathFile(java.lang.String file)
java.util.Vector	getVectorKeywords(User user) This function returns a Vector containing Keyword Objects for User Object received
java.util.Vector	getVectorMicroarray_project_type()
java.util.Vector	getVectorMicroarrayForPlateforme(Plateforme plateforme) This function returns a Vector containing ToolBox Object concerning microarray Object produced by Plateforme Object received
java.util.Vector	getVectorMPTForPF(java.lang.String type, Plateforme plateforme) This function returns a Vector containing ToolBox Object concerning type Object received for the Plateforme Object received.
java.util.Vector	getVectorPO_view(User user) This function returns a Vector containing toolBox Object of Project_order visualisable by the User Object received order by date_project_order
java.util.Vector	getVectorPO(User user) This function returns a Vector containing toolBox Object of Project_order owned by the User Object received order by date_project_order
java.util.Vector	getVectorPOForUser(int user_id) This function return a Vector containing ToolBox Object of Project_order Objects (project_order_id, project_order_ref) owning by the user received
java.util.Vector	getVectorSlideList(java.lang.String label_search, ImageManager imageManager) 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.
java.util.Vector	getVectorToolBox(java.lang.String type) This function returns a Vector containing ToolBox Object concerning type Object received.
boolean	isPlate384Exists(java.lang.String plate_ref) This function returns a boolean informative about the existence of a Plate384
boolean	isViewer(int project_id, int user_id) This function check if a user is a Viewer of a Project Object
boolean	isWriter(int project_id, int user_id) This function check a user is a writer of a Project Object
Graph	makeClouds(java.lang.String type, java.util.Hashtable hashMttdata) This function proceed to the generation of graphe image, scatter plot style.
Graph	makeDistrib(java.util.Hashtable hashPoints) This function proceed to the generation of graphe image.
java.lang.String	sendEmail(java.lang.String email, java.lang.String subject, java.lang.String texte)
void	setStaticParams(java.util.Hashtable hashMailConfiguration) Initialize static parameters from the configuration file - MAIL_HOST - MAIL_FROM
void	updateMIAME(java.util.Hashtable hashParams)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAIL_HOST

public static java.lang.String MAIL_HOST

Mail Host for sending mail (gelas.ipmc.cnrs.fr)

MAIL_FROM

public static java.lang.String MAIL_FROM

Mail From for sending mail (mediante@ipmc.cnrs.fr)

Constructor Detail

Common

public Common()

Default constructor

Method Detail

setStaticParams

public void setStaticParams(java.util.Hashtable hashMailConfiguration)

Initialize static parameters from the configuration file - MAIL_HOST - MAIL_FROM

getAllUserColleague

public java.util.Vector getAllUserColleague(int user_id)

This function allowed to get all the Colleagues of a User

Parameters:

user_id - ID of an existing User

Returns:

Vector of Users objects colleague of the User

See Also:

ToolBox, ToolBox.ToolBox(int,String)

getAllMicroarray_project_type

public java.util.Vector getAllMicroarray_project_type(int organism_id)

Allowed to return all Microarray_project_type in the Database concerning an Organism ID

Parameters:

organism_id - ID of an Organism Object

Returns:

Vector of all Microarray_project_type in the Database concerning the Organism received

See Also:

Microarray_project_type, Microarray_project_type.Microarray_project_type(int)

getENSG

public IdDescriptionObject getENSG(java.lang.String enst)

This function returns the ensg and description from an enst reference

Parameters:

enst - represent a refernce to an Enst (ENSEMBL transcript)

Returns:

IdDescriptionObject object

See Also:

IdDescriptionObject

getGenbank_gene_id

public IdDescriptionObject getGenbank_gene_id(java.lang.String refseq)

This function returns the genbank_gene_id and description from a refseq reference

Parameters:

refseq - represent a reference to refseq sequence (REFSEQ transcript)

Returns:

IdDescriptionObject object containing genbank_gene_id and description

See Also:

IdDescriptionObject

getGiFromRefseq

public java.lang.String getGiFromRefseq(java.lang.String refseq)

This function returns the gi number for the refseq reference received

Parameters:

refseq - represent a reference to refseq sequence (REFSEQ transcript)

Returns:

gi genbank reference corresponding to the refseq reference

getSymbolForOAID

public java.lang.String getSymbolForOAID(int oligo_adhoc_id)

This function returns the annotation for the oligo_adhoc_id received

Parameters:

oligo_adhoc_id - ID of an existing oligo_adhoc Object

Returns:

symbol

See Also:

Oligo_adhoc, Gene

getANForGID

public java.lang.String getANForGID(int gene_id)

This function returns the accession number for the gene_id received

Parameters:

gene_id - ID of an existing Gene Object

Returns:

accession_number refseq reference for the Gene id received

See Also:

Gene

getGIDForSymbol

public int getGIDForSymbol(java.lang.String symbol,
                           java.lang.String organism_id)

This function returns the Mediante gene ID for the symbol and organism ID received

Parameters:

symbol - Symbol of an existing Gene Object

organism_id - ID of an Organism Object

Returns:

accession_number refseq reference for the Gene id received

See Also:

Gene

getSEQForGID

public java.lang.String getSEQForGID(int gene_id)

This function returns the sequence for the gene_id received

Parameters:

gene_id - ID of an existing Gene Object

Returns:

sequence RNA sequence for the gene_id received

See Also:

Gene

getSEQForAN

public java.lang.String getSEQForAN(java.lang.String accession_number)

This function returns the sequence for the accession number received

Parameters:

accession_number - accession_number of an existing Gene Object

Returns:

sequence RNA sequence for the accession_number received

See Also:

Gene

getSEQForOligo_adhoc_id

public java.lang.String getSEQForOligo_adhoc_id(java.lang.String accession)

This function returns the sequence for the sonde reference received

Parameters:

accession - sonde from an existing Oligo_adhoc Object

Returns:

sequence RNA sequence for the sonde received

See Also:

Oligo_adhoc

getGIDForAN

public int getGIDForAN(java.lang.String accession_number)

This function returns the gene ID for the accession_number received

Parameters:

accession_number - Attribute accession_number of an existing Gene Object

Returns:

gene_id ID of the Gene object corresponding to the accession_number received

See Also:

Gene

getBlastParameters

public java.lang.String getBlastParameters(java.lang.String kind)

This function returns a select box for an HTML form describing the parameters for the execution of a Blast

Parameters:

kind - Kind of blast we are going to launch :
if kind = 'blast' --> evalue : 10,1e-1,1e-10,1e-20,1e-50,1e-100
if kind = 'bl2seq' --> evalue : 10,1e-10,1e-100

Returns:

str String for select box in the form

getAllChromosome

public java.util.Vector getAllChromosome(int organism_id)

This function returns a Vector containing all the Chromosome Object for the Organism received

Parameters:

organism_id - ID of an existing Organism Object

Returns:

allChromosome Vector containing all the Chromosome Object for the Organism received

See Also:

Chromosome, Chromosome.Chromosome(int)

getMega

public java.lang.String getMega(int size)

This function make the conversion beetween sequence base size and MegaBase size

Parameters:

size - length of a RNA sequence in bases

Returns:

size length of a RNA sequence in MedgaBases

getAllRefPlaques384_ForDilution

public java.lang.String getAllRefPlaques384_ForDilution()

This function returns a String of all the 384 Plate wich are not diluted

Returns:

str containing the list of Plate_ref of Plate384 Object separate with ','

See Also:

Plate384

isPlate384Exists

public boolean isPlate384Exists(java.lang.String plate_ref)

This function returns a boolean informative about the existence of a Plate384

Parameters:

plate_ref - Attribute plate_ref of a Plate384 Object

Returns:

bool true if the plate_ref exists and false if not exists

See Also:

Plate384

getToolBoxMicroarray

public java.util.Vector getToolBoxMicroarray(java.lang.String type,
                                             int id)

This function returns a Vector containing ToolBox Object concerning all the Spotting Object not yet Cross linked

Returns:

allToolBoxUser Vector containing Toolbox containing spotting_id and date_spotting of all the Spotting Object wich are not yet Cross Linked

See Also:

Spotting, ToolBox, ToolBox.ToolBox(int,String)

getToolBoxSpotting

public java.util.Vector getToolBoxSpotting(int plateforme_id,
                                           boolean local_only)

This function returns a Vector containing ToolBox Object concerning all the Spotting Object associated to the ID of Plateforme Object received

Returns:

allToolBoxUser Vector containing Toolbox containing spotting_id and spotting_ref of all the Spotting Object associated to the ID of Plateforme Object received

See Also:

Spotting, ToolBox, ToolBox.ToolBox(int,String)

getVectorToolBox

public java.util.Vector getVectorToolBox(java.lang.String type)

This function returns a Vector containing ToolBox Object concerning type Object received.

Parameters:

type - Type of Object we want get in ToolBox Objects, type can be :
- blastbase,
- est_tissue,
- labeling_type,
- microarray,
- microarray_type,
- microarray_project_type,
- nucleic_acid_type,
- organism,
- plate384,
- plate96,
- plateforme,
- protocol_amplification,
- protocol_hybridization,
- protocol_extraction,
- protocol_labeling,
- scanner,
- spotter,
- storage,
- toptable,
- mirna_target_tool,
- user,

Returns:

allToolBox Vector containg Toolbox containing id and ref concerning type Object received

See Also:

ToolBox, ToolBox.ToolBox(int,String)

getVectorMPTForPF

public java.util.Vector getVectorMPTForPF(java.lang.String type,
                                          Plateforme plateforme)

This function returns a Vector containing ToolBox Object concerning type Object received for the Plateforme Object received.

Parameters:

type - Type of Object we want get in ToolBox Objects, type can be :
- spottable --> mean flag is_spottable=true,
- orderable --> mean flag is_orderable=true,
- externe --> mean flag is_extern or is_tilling or is_affy = true,

Returns:

allToolBox Vector containg Toolbox containing id and ref concerning type Object received

See Also:

Microarray_project_type, ToolBox, ToolBox.ToolBox(int,String)

getVectorKeywords

public java.util.Vector getVectorKeywords(User user)

This function returns a Vector containing Keyword Objects for User Object received

Parameters:

user - User Object

Returns:

vectorKeywords Vector containing Keywords Objects for the user

See Also:

User, Keyword, Keyword.Keyword(int)

getVectorMicroarrayForPlateforme

public java.util.Vector getVectorMicroarrayForPlateforme(Plateforme plateforme)

This function returns a Vector containing ToolBox Object concerning microarray Object produced by Plateforme Object received

Parameters:

plateforme - Plateforme Object

Returns:

allToolBox Vector containg Toolbox containing id and ref concerning microarray Object

See Also:

Plateforme, Microarray, ToolBox, ToolBox.ToolBox(int,String)

getIs_national_ordered

public boolean getIs_national_ordered(int oligo_id)

This function returns a boolean corresponding to the existence of an oligo in the National set ordered

Parameters:

oligo_id - ID of an existing Oligo Object

Returns:

bool true if ordered in the National Set and false if not

See Also:

Oligo

getIs_local_ordered

public boolean getIs_local_ordered(int oligo_id)

This function returns a boolean corresponding to the existence of an oligo in the Local set ordered

Parameters:

oligo_id - ID of an existing Oligo Object

Returns:

bool true if ordered in the Local Set and false if not

See Also:

Oligo

getIs_selected

public boolean getIs_selected(int oligo_id)

This function returns a boolean corresponding to the existence of an oligo in the Local set ordered

Parameters:

oligo_id - ID of an existing Oligo Object

Returns:

bool true if ordered in the Local Set and false if not

See Also:

Oligo

getIs_best_oligo

public boolean getIs_best_oligo(int oligo_id)

This function returns a boolean corresponding to the fact that the oligo received is a "best" oligo

Parameters:

oligo_id - ID of an existing Oligo Object

Returns:

bool true if the oligo is a "best" and false if not

See Also:

Oligo

getSlide_codeForMicroarray_id

public java.lang.String getSlide_codeForMicroarray_id(int microarray_id)

This function returns the slide code of the Microarray ID received

Parameters:

microarray_id - ID of an existing Microarray Object

Returns:

slide_code Slide code of the microarray object concerned

See Also:

Microarray

getFileName

public java.lang.String getFileName(java.lang.String path)

This function returns the name of the file of the path reveiced

Parameters:

path - Absolute path of a file

Returns:

file_name name of the file from the absolute path received

getFileNameNoExt

public java.lang.String getFileNameNoExt(java.lang.String path)

This function returns the name of the file of the path reveiced

Parameters:

path - Absolute path of a file

Returns:

file_name name of the file from the absolute path received

checkExtensionFile

public boolean checkExtensionFile(java.lang.String type,
                                  java.lang.String fileName)

This function check if the received match the type file received

Parameters:

type - Type of file we want, could be :
- 'gal'
- 'dat'
- 'cel'
- 'xls'
- 'r'
- 'medlab'
- 'txt_xls'
- 'vsm'
- 'bcr'
- 'vrk'
- 'tif'
- 'jpg'
- 'gps'
- 'tif_jpg'
- 'gpr_txt_xls'
- 'pdf'

fileName - name of the file to check

Returns:

boolean true if fileName extension match the type we specified

checkUserIsOwner

public boolean checkUserIsOwner(int user_id,
                                int microarray_id)

This function returns a boolean according to correspondance between user_id received
and User owner of the microarray_id received

Parameters:

user_id - ID of an existing User Object

microarray_id - ID of an existing Microarray Object

Returns:

bool true if true

See Also:

Microarray

getScanForMicroarray_id

public Scan getScanForMicroarray_id(int microarray_id)

This function returns a Scan Object according to the microarray_id received

Parameters:

microarray_id - ID of an existing Microarray Object

Returns:

scan Scan Object for the Microarray Object received.

See Also:

Microarray, Scan

getFirstGeneForOID

public Gene getFirstGeneForOID(int oligo_id)

This function return the first Gene Object matching the Oligo Object from the oligo_id received

Parameters:

oligo_id - ID of an existing Oligo Object

Returns:

gene Gene object

See Also:

Oligo, Gene

getGal_fileFromMID

public java.lang.String getGal_fileFromMID(int microarray_id)

This function return the gal file a the Spotting Object of the Microarray Object ID received

Returns:

gal Path to gal_file file from Spotting Object owner of the Microarray Object

See Also:

Microarray, Spotting

getMicroarrayInfos

public java.util.Hashtable getMicroarrayInfos(java.lang.String type_user,
                                              java.lang.String annee,
                                              java.lang.String support)

This function return a Hashtable containing informations concerning
the production of Microarrays among the different plateforms.

Returns:

hash Hashtable containing informations concerning the production of Microarrays among the different plateforms.

See Also:

Plateforme

getHtsInfos

public java.util.Hashtable getHtsInfos(java.lang.String type_user,
                                       java.lang.String annee,
                                       java.lang.String support)

This function return a Hashtable containing informations concerning
the production of Hts samples among the different plateforms.

Returns:

hash Hashtable containing informations concerning the production of Hts samples among the different plateforms.

See Also:

Plateforme

getTestHash

public java.util.Hashtable getTestHash()

This function return a Hashtable containing the ID and REF of Plate Object from plate SQL table.

Returns:

hash Hashtable containing plate_id as the key and the plate_ref as the values.

See Also:

Plate

getVectorSlideList

public java.util.Vector getVectorSlideList(java.lang.String label_search,
                                           ImageManager imageManager)

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.
Note : no microarray from Affymetrix can be viewed (microarray_project_type_id in (33,34)).

Should be modifyed !!!

Parameters:

label_search - String of label search into the ImageManager Object.

imageManager - ImageManager Object concerned.

Returns:

hash Hashtable containing slide_codes of Microarrays contained in the Project_order of the ImageManager Object and not selected in the vectorMicroarrays parameter of the ImageManager Object.

See Also:

Microarray, ImageManager

getAllAddress

public java.util.Vector getAllAddress()

This function return a Vector containing email String of all Users Object.

Returns:

vectorAddress Vector containing email String of all Users Object.

See Also:

User

getOrder_ref

public java.lang.String getOrder_ref(int order_id,
                                     java.lang.String type)

This function return the mo_ref parameter of the Microarray_order Object received.

Parameters:

order_id - ID of an existing Order Object (Microarray_order or Hts_order).

type - Type of the Order Object (Microarray_order or Hts_order).

Returns:

order_ref Order reference for the order ID received (Microarray_order ref or Hts_order re?)

See Also:

Order, Microarray_order, Hts_order

getPO_IDForMO_ID

public int getPO_IDForMO_ID(int microarray_order_id)

This function return the project_order_id parameter of the Project_order Object owning the Microarray_order received.

Parameters:

microarray_order_id - ID of an existing Microarray_order Object.

Returns:

project_order_id project_order_id parameter of the Project_order Object.

See Also:

Microarray_order, Project_order

getUser_idForMPT_id

public int getUser_idForMPT_id(int microarray_project_type_id)

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.

Parameters:

microarray_project_type_id - ID of an existing Microarray_project_type Object.

Returns:

project_order_id project_order_id parameter of the Project_order Object.

See Also:

Microarray_project_type, Microarray_order, User

getMPTForRefAndPF

public int getMPTForRefAndPF(java.lang.String ref,
                             int plateforme_id)

This function returns the ID of the Microarray_project_type Object identified by both parameters.

Parameters:

ref - Spotting reference (spo_ref) of the Microarray_project_type Object.

plateforme_id - ID of the Plateforme Object owner of the Spotting Object in save.

Returns:

microarray_project_type_id ID of the Microarray_project_type Object identified by both parameters.

See Also:

Microarray_project_type, Spotting, Plateforme

getContactClient

public java.util.Vector getContactClient(int client_id)

This function returns a Vector containing Contact_client Object concerning client_id received (user_id).

Parameters:

client_id - ID of User Object corresponding to this client

Returns:

vectorContactClient

See Also:

User, Contact_client, Contact_client.Contact_client(int)

getAllClient

public java.util.Vector getAllClient()

This function returns a Vector containing ToolBox Object concerning User Object

Returns:

vectorToolBox Vector containg Toolbox containing id and ref concerning User Object

See Also:

User, ToolBox, ToolBox.ToolBox(int,String)

getAllFoq

public java.util.Vector getAllFoq()

This function returns a Vector containing Foq Object

Returns:

vectorFoqClient

See Also:

Foq, Foq.Foq(int)

getAllEnquete

public java.util.Vector getAllEnquete()

This function returns a Vector containing ToolBox Object concerning Enquete Object

Returns:

allToolBox Vector containg Toolbox containing id and ref concerning Enquete Object

See Also:

ToolBox, ToolBox.ToolBox(int,String)

getSymbolForGO

public java.lang.String getSymbolForGO(int organism_id,
                                       java.lang.String go_acc)

This function returns a String containing distinct gene symbol for gene Ontology term

Parameters:

organism_id - ID of Organism Object

go_acc - Gene Ontology accession number

Returns:

String allSymbol

getSymbolForGeneList

public java.lang.String getSymbolForGeneList(java.lang.String project_id_str)

This function returns a String containing distinct gene symbol from Gene Object
belonging to the Project Object with the ID received as a String.

Parameters:

project_id_str - String of an ID of Project Object stored in database.

Returns:

symbols List of gene symbol from Gene Object concerned by the Project Object received.

See Also:

Gene, Project

getProjectForUser

public java.util.Vector getProjectForUser(int user_id)

This function returns a vector containing ToolBox Object of Project Object owned by the User received.

Parameters:

user_id - ID of an existing User Object

Returns:

vectorToolBox Vector containing ToolBox Object of Project Object owned by the User received.

See Also:

User, Project, ToolBox, ToolBox.ToolBox(int, String)

getGeneCartForUser

public java.util.Vector getGeneCartForUser(int user_id)

This function returns a vector containing ToolBox Object of GeneCart Object owned by the User received.

Parameters:

user_id - ID of an existing User Object

Returns:

vectorToolBox Vector containing ToolBox Object of GeneCart Object owned by the User received.

See Also:

User, GeneCart, ToolBox, ToolBox.ToolBox(int, String)

getAllUserForPF

public java.util.Vector getAllUserForPF(int plateforme_id)

This function returns a vector containing ToolBox Object concerning User Objects belonging to the Plateforme Object received.

Parameters:

plateforme_id - ID of an existing Plateforme Object

Returns:

vectorToolBox Vector containing ToolBox Object concerning User Objects belonging to the Plateforme Object received

See Also:

Plateforme, User, ToolBox, ToolBox.ToolBox(int, String)

getCT_idForMID

public int getCT_idForMID(int microarray_id)

This function returns a control_type_id for the microarray_id received,
in case of this Microarray Object is a Control Object.

Returns:

control_type_id

See Also:

Microarray, Control_type, Control

getIs_allowed

public boolean getIs_allowed(int user_id,
                             int project_order_id)

This function returns a boolean concerning the possibility to see a Project_order for a User Object.

Parameters:

user_id - ID of an existing User Object

project_order_id - ID of an existing Project_order Object

Returns:

bool true if the User can see the Oroject_order or false if not.

See Also:

Project_order, User

getAllUsers

public java.util.Vector getAllUsers()

This function returns a vector containing all User Objects stored in database.

Returns:

vectorAllUsers Vector containing all User Objects stored in database.

See Also:

User

getAllPlateforme

public java.util.Vector getAllPlateforme()

This function returns a vector containing all Plateforme Objects stored in database.

Returns:

vectorAllPlateforme Vector containing all Plateforme Objects stored in database.

See Also:

Plateforme

getAllMoIDForUser

public java.util.Vector getAllMoIDForUser(int user_id)

This function returns a vector containing ToolBox Object containing informations concerning Microarray_order
Objects belonging to the User Object received.

Parameters:

user_id - ID of user concerned

Returns:

vectorToolBox Vector containing ToolBox Object containing informations (microarray_order_id / mo_ref + nb_lame) concerning Microarray_order Objects belonging to the User Object received.

See Also:

User, Microarray_order, ToolBox, ToolBox.ToolBox(int, String)

isViewer

public boolean isViewer(int project_id,
                        int user_id)

This function check if a user is a Viewer of a Project Object

Parameters:

project_id - ID of an existing Project Object

user_id - ID of an existing User Object

Returns:

bool, true if user is viewer, false if not

isWriter

public boolean isWriter(int project_id,
                        int user_id)

This function check a user is a writer of a Project Object

Parameters:

project_id - ID of an existing Project Object

user_id - ID of an existing User Object

Returns:

bool, true if user is writer, false if not

getVectorPOForUser

public java.util.Vector getVectorPOForUser(int user_id)

This function return a Vector containing ToolBox Object of Project_order Objects (project_order_id, project_order_ref) owning by the user received

Parameters:

user_id - ID of an existing User Object.

Returns:

vectorToolBox

See Also:

Project_order

getSlide_code

public java.lang.String getSlide_code(java.lang.String quantif_file,
                                      int microarray_order_id)

This function returns the slide code of the Microarray ID from which we received

Parameters:

microarray_order_id - ID of an existing Microarray_order Object

quantif_file - Quantification_file for the microarray search

Returns:

slide_code Slide code of the microarray object concerned

See Also:

Microarray

getAllProject_orderForPF

public java.util.Vector getAllProject_orderForPF(int plateforme_id)

This function returns a vector containing ToolBox Object concerning Project_order Objects belonging to the Plateforme Object received.

Parameters:

plateforme_id - ID of an existing Plateforme Object

getMicroarray_orderLabel

public java.lang.String getMicroarray_orderLabel(int microarray_order_id)

This function returns a description string of the Microarray_order Objects ID received.

Parameters:

microarray_order_id - ID of an existing Microarray_order Object

getAllEstTissue

public java.util.Vector getAllEstTissue()

This function return a Vector containing all EstTissue object define in database.

Returns:

vector containing all EstTissue Object

See Also:

EstTissue

getMainEstTissue

public java.util.Hashtable getMainEstTissue()

This function return a Hashtable containing the main est_tissue_id for the EstTissue which are not main EstTissue.

Returns:

Hashtable containing est_tissue_id as key and main_tissue (= the main est_tissue_id) as val

See Also:

EstTissue

getAllMirna_mature

public java.util.Vector getAllMirna_mature()

This function returns a Vector containing ToolBox Object concerning all Mirna_mature Objects

Returns:

toolBox Vector containing Toolbox containing auto_mature as key and unique mature_name as val.

See Also:

Mirna_mature, ToolBox, ToolBox.ToolBox(int,String)

getSymbolForMirna_mature

public java.lang.String getSymbolForMirna_mature(java.lang.String mature_acc)

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).

Parameters:

mature_acc - mature_acc attribute of a Mirna_mature Object

Returns:

symbols list of Symbols of Genes Objects predicted as target (Microcible 1to8) of the Mirna_mature received.

getVectorPO

public java.util.Vector getVectorPO(User user)

This function returns a Vector containing toolBox Object of Project_order owned by the User Object received order by date_project_order

Parameters:

user - User Object concerned

Returns:

vectorToolBox Vector containing toolBox Object owned by the User Object received order by date_project_order

See Also:

ToolBox, ToolBox.ToolBox(int,String)

getVectorPO_view

public java.util.Vector getVectorPO_view(User user)

This function returns a Vector containing toolBox Object of Project_order visualisable by the User Object received order by date_project_order

Parameters:

user - User Object concerned

Returns:

Vector containing toolBox Object of Project_order visualisable by the User Object received order by date_project_order

See Also:

ToolBox, ToolBox.ToolBox(int,String)

getUser_idForProject_order_id

public int getUser_idForProject_order_id(int project_order_id)

This function returns the User Object ID owner of the Project_order Object ID received.

Parameters:

project_order_id - ID of the Porject_order concerned

Returns:

user_id ID of User owner of the Project_order Object ID received

See Also:

Project_order

getHashOligo_annotation

public java.util.Hashtable getHashOligo_annotation(boolean is_affy)

This function return a Hashtable containing Oligo_annotation Objects.

Parameters:

is_affy - boolean concerning the SQL view to select : oligo_annotation or oligo_affy_annotation if true

Returns:

hash Oligo_annotation Objects with oligo_id or probe_set_id as the Key

See Also:

Oligo_annotation

getHashAdhoc

public java.util.Hashtable getHashAdhoc()

This function return a Hashtable containing Oligo_annotation Objects.

Returns:

hash Oligo_annotation Objects with oligo_id or oligo_externe_id as the Key

See Also:

Oligo_annotation, Oligo, Oligo_externe

getHashIDtoAcc

public java.util.Hashtable getHashIDtoAcc(Microarray_project_type microarray_project_type)

This function return a Hashtable containing the symbol of gene symbol.

Parameters:

microarray_project_type - microarray_project_type concerned

Returns:

hash Hashtable containing oligo_id or oligo_externe_id as the Key and the gene symbol as the valule

See Also:

Oligo, Oligo_externe

getHashMap_toID

public java.util.Hashtable getHashMap_toID(Microarray_project_type microarray_project_type)

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.

Parameters:

microarray_project_type - Type of Microarray_project_type Object

Returns:

hash Hashtable containing ref as the key and oligo_id or oligo_externe_id as the value

See Also:

Microarray_project_type, Oligo_externe

getHashOIDForControl

public java.util.Hashtable getHashOIDForControl()

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.

Returns:

hash Hashtable containing ref as the key and oligo_id or oligo_externe_id as the value

See Also:

Microarray_project_type, Oligo_externe

getId

public int getId(java.lang.String probe_ref)

getAllDiary

public java.util.Vector getAllDiary()

This function returns a Vector containing all the Diary Object

Returns:

allChromosome a Vector containing all the Diary Object

See Also:

Diary, Diary.Diary(java.util.Date, String)

getSid_for_mid

public int getSid_for_mid(int microarray_id)

getEvents

public java.lang.String getEvents(java.util.Vector vectorJournal)

getAllMirna

public java.util.Vector getAllMirna()

getAuto_matureForMature_acc

public int getAuto_matureForMature_acc(java.lang.String mature_acc)

getContact

public java.lang.String getContact(java.lang.String lastname,
                                   java.lang.String firstname,
                                   java.lang.String title,
                                   java.lang.String email,
                                   java.lang.String telephone)

makeDistrib

public Graph makeDistrib(java.util.Hashtable hashPoints)
                  throws java.lang.Exception

This function proceed to the generation of graphe image.

Parameters:

hashPoints - Hashtable of Point Object concerned by this graph.

Throws:

java.lang.Exception

See Also:

Point

makeClouds

public Graph makeClouds(java.lang.String type,
                        java.util.Hashtable hashMttdata)
                 throws java.lang.Exception

This function proceed to the generation of graphe image, scatter plot style.

Parameters:

hashMttdata - Hashtable of Mttdata drawned of the graph.

type - Stringcan be 'DOWN' or 'UP' to select for each Mttdata Object which one are plotted

Throws:

java.lang.Exception

See Also:

Mttdata

getRounded

public double getRounded(double x)

getRounded2

public double getRounded2(double x)

getRounded4

public double getRounded4(double x)

getToptableForUser

public java.util.Vector getToptableForUser(User user)

getPopSize

public int getPopSize(int organism_id)

getGoFrequence

public java.util.Hashtable getGoFrequence(int organism_id)

getVectorMicroarray_project_type

public java.util.Vector getVectorMicroarray_project_type()

getValidPathFile

public java.lang.String getValidPathFile(java.lang.String file)

getSelectBoxColor

public java.lang.String getSelectBoxColor(java.lang.String name,
                                          java.lang.String selected)

getAllGeoSerie

public java.util.Vector getAllGeoSerie()

updateMIAME

public void updateMIAME(java.util.Hashtable hashParams)

getAllGOterm

public java.util.Vector getAllGOterm()

getTexteEmail

public java.lang.String getTexteEmail(java.lang.String email)

sendEmail

public java.lang.String sendEmail(java.lang.String email,
                                  java.lang.String subject,
                                  java.lang.String texte)

getAllOrders

public java.util.Vector getAllOrders()

This function return a Vector containing Order Objects concerning all the Microarray_order stored in Database, ordered by state and date_attribution

Returns:

Vector containing Order Objects concerning all the Microarray_order stored in Database

getOrderForPlateforme

public java.util.Vector getOrderForPlateforme()

This function return a Vector containing Order Objects concerning all the Microarray_order waiting for plateforme attribution

Returns:

Vector containing Order Objects concerning all the Microarray_order waiting for plateforme attribution

getAllOrders

public java.util.Vector getAllOrders(int plateforme_id,
                                     java.lang.String type)

getOrder_type

public java.lang.String getOrder_type(int order_id)

Return the Order_type for an Order Object

getToolBoxHts_pipeline

public java.util.Vector getToolBoxHts_pipeline(int hts_type_id)

getToolBoxHts_run

public java.util.Vector getToolBoxHts_run(int plateforme_id)

getToolBoxHts_analysis

public java.util.Vector getToolBoxHts_analysis(int hts_type_id)