object.microrna
Class MicroCible

java.lang.Object
  object.microrna.MicroCible

All Implemented Interfaces:

java.io.Serializable

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

Description
Infos : KLB - IPMC - 05/2007

See Also:

Serialized Form

Field Summary

private java.lang.String	auto_mature micro_name searched
private java.lang.String	gene_name gene_name searched
private boolean	GUwobble true if search concerns GU wobble match
private java.util.Hashtable	hashGenes
private java.util.Hashtable	hashMcbdata Results for this search
private java.util.Hashtable	hashMicros
private java.util.Hashtable	hashStarts
private boolean	is_found boolean : true when the search found at least one Gene Object, and false if not
private java.lang.String	message Information message concerning the search
private int	mfe_cutoff
private int	nb_match Number of match between microRNAs and genes for this search
private Organism	organism_gene Organism for transcripts search
private java.lang.String	region gene region searched
private int	seed_size Seed size searched
private int	seed_start Seed start searched
private int	seed_stop Seed stop searched
private java.lang.String	sequence sequence to search
private boolean	twoMuch boolean : true when the search found two much Gene Objects ( limit is attribute : NB_MAX_RESULTS)
private java.util.Vector	vectorKeys Vector of keys ordered

Constructor Summary

MicroCible()
Default constructor

Method Summary

void	doRNAhybrid()
java.lang.String	getAuto_mature() micro_name searched
java.lang.String	getGene_name() gene_name searched
boolean	getGUwobble() GUwobble
java.util.Hashtable	getHashGenes() Hash containing genes
java.util.Hashtable	getHashMcbdata() Results for this search
java.util.Hashtable	getHashMicros() Hash containing microRNAs
boolean	getIs_found() boolean : true when the search found at least one Gene Object, and false if not
java.lang.String	getMessage() Information message concerning the search
int	getMfe_cutoff() mfe_cutoff
int	getNb_match() Number of match between microRNAs and genes for this search
Organism	getOrganism_gene() Organism for transcripts search
java.lang.String	getReal_micro_seq(java.lang.String micro_seq)
java.lang.String	getRegion() gene region searched
java.lang.String	getReverse(java.lang.String seq)
int	getSeed_size() Seed size searched
int	getSeed_start() Seed start searched
int	getSeed_stop() Seed stop searched
java.util.Vector	getSeedsWobble(java.lang.String seed)
java.lang.String	getSeqToFold(java.lang.String micro_seq, java.lang.String tr_seq)
java.lang.String	getSequence() sequence
java.lang.String	getSonde(java.lang.String premir, int mature_from, int mature_to)
boolean	getTwoMuch() boolean : true when the search found two much Gene Objects ( limit is attribute : NB_MAX_RESULTS)
java.util.Vector	getVectorKeys() Vector of keys ordered
void	initGenes()
void	initMicros()
void	loadParams(java.util.Hashtable params) This function load parameters from Html Form.
void	proceedSearch() This function proceed to the search, function of parameters initialize in the loadParams() method.
void	setAuto_mature(java.lang.String auto_mature)
void	setGene_name(java.lang.String gene_name)
void	setGUwobble(boolean GUwobble)
void	setHashGenes(java.util.Hashtable hashGenes)
void	setHashMcbdata(java.util.Hashtable hashMcbdata)
void	setHashMicros(java.util.Hashtable hashMicros)
void	setIs_found(boolean is_found)
void	setMessage(java.lang.String message)
void	setMfe_cutoff(int mfe_cutoff)
void	setNb_match(int nb_match)
void	setOrganism_gene(Organism organism_gene)
void	setRegion(java.lang.String region)
void	setSeed_size(int seed_size)
void	setSeed_start(int seed_start)
void	setSeed_stop(int seed_stop)
void	setSequence(java.lang.String sequence)
void	setTwoMuch(boolean twoMuch)
void	setVectorKeys(java.util.Vector vectorKeys)
void	sortMyVector(java.lang.String type)

Methods inherited from class java.lang.Object

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

Field Detail

seed_start

private int seed_start

Seed start searched

seed_stop

private int seed_stop

Seed stop searched

seed_size

private int seed_size

Seed size searched

organism_gene

private Organism organism_gene

Organism for transcripts search

gene_name

private java.lang.String gene_name

gene_name searched

sequence

private java.lang.String sequence

sequence to search

auto_mature

private java.lang.String auto_mature

micro_name searched

region

private java.lang.String region

gene region searched

message

private java.lang.String message

Information message concerning the search

is_found

private boolean is_found

boolean : true when the search found at least one Gene Object, and false if not

twoMuch

private boolean twoMuch

boolean : true when the search found two much Gene Objects ( limit is attribute : NB_MAX_RESULTS)

nb_match

private int nb_match

Number of match between microRNAs and genes for this search

GUwobble

private boolean GUwobble

true if search concerns GU wobble match

mfe_cutoff

private int mfe_cutoff

hashMcbdata

private java.util.Hashtable hashMcbdata

Results for this search

vectorKeys

private java.util.Vector vectorKeys

Vector of keys ordered

hashMicros

private java.util.Hashtable hashMicros

hashGenes

private java.util.Hashtable hashGenes

hashStarts

private java.util.Hashtable hashStarts

Constructor Detail

MicroCible

public MicroCible()

Default constructor

Method Detail

getSeed_start

public int getSeed_start()

Seed start searched

setSeed_start

public void setSeed_start(int seed_start)

getSeed_stop

public int getSeed_stop()

Seed stop searched

setSeed_stop

public void setSeed_stop(int seed_stop)

getSeed_size

public int getSeed_size()

Seed size searched

setSeed_size

public void setSeed_size(int seed_size)

getOrganism_gene

public Organism getOrganism_gene()

Organism for transcripts search

setOrganism_gene

public void setOrganism_gene(Organism organism_gene)

getGene_name

public java.lang.String getGene_name()

gene_name searched

setGene_name

public void setGene_name(java.lang.String gene_name)

getSequence

public java.lang.String getSequence()

sequence

setSequence

public void setSequence(java.lang.String sequence)

getAuto_mature

public java.lang.String getAuto_mature()

micro_name searched

setAuto_mature

public void setAuto_mature(java.lang.String auto_mature)

getRegion

public java.lang.String getRegion()

gene region searched

setRegion

public void setRegion(java.lang.String region)

getMessage

public java.lang.String getMessage()

Information message concerning the search

setMessage

public void setMessage(java.lang.String message)

getHashMcbdata

public java.util.Hashtable getHashMcbdata()

Results for this search

setHashMcbdata

public void setHashMcbdata(java.util.Hashtable hashMcbdata)

getVectorKeys

public java.util.Vector getVectorKeys()

Vector of keys ordered

setVectorKeys

public void setVectorKeys(java.util.Vector vectorKeys)

getIs_found

public boolean getIs_found()

boolean : true when the search found at least one Gene Object, and false if not

setIs_found

public void setIs_found(boolean is_found)

getTwoMuch

public boolean getTwoMuch()

boolean : true when the search found two much Gene Objects ( limit is attribute : NB_MAX_RESULTS)

setTwoMuch

public void setTwoMuch(boolean twoMuch)

getNb_match

public int getNb_match()

Number of match between microRNAs and genes for this search

setNb_match

public void setNb_match(int nb_match)

getGUwobble

public boolean getGUwobble()

GUwobble

setGUwobble

public void setGUwobble(boolean GUwobble)

getMfe_cutoff

public int getMfe_cutoff()

mfe_cutoff

setMfe_cutoff

public void setMfe_cutoff(int mfe_cutoff)

getHashMicros

public java.util.Hashtable getHashMicros()

Hash containing microRNAs

setHashMicros

public void setHashMicros(java.util.Hashtable hashMicros)

getHashGenes

public java.util.Hashtable getHashGenes()

Hash containing genes

setHashGenes

public void setHashGenes(java.util.Hashtable hashGenes)

loadParams

public void loadParams(java.util.Hashtable params)

This function load parameters from Html Form. If everything ok it calls proceedSearch() medthod.

Parameters:

params - Hashtable containing all the parameters needed to initialize the Search Object
- key 'organism' : ID of an existing Organism Object
- key 'chromosome' : ID of an existing Chromosome Object
- key 'type_recherche' : Type of Search to proceed (can be : 'id_reference', 'keyword', 'geneOntology' or 'cytoband')
- key 'cytoband' : ID of an existing Cytoband Object
- key 'query' : Query string to search
- key 'file' : name of the file uploaded

See Also:

proceedSearch()

proceedSearch

public void proceedSearch()

This function proceed to the search, function of parameters initialize in the loadParams() method.
It fills the vectorGenes attribute. The queries launch are :
- type_recherche = 'id_reference' : search table gene_description (ensembl_id, genbank_gene_id, accession_number,symbol,refseq_transcript,refseq_gene_id,unigene_id and cluster_gene_id)
- type_recherche = 'keyword' : search table gene_description (description)
- type_recherche = 'geneOntology' : search the query string in table term and next the relation with Gene in the go_link table.
- type_recherche = 'oligo_adhoc' :
- type_recherche = 'cytoband' : search relation with Gene in cytoband_rel table

See Also:

Gene, Gene.Gene(int)

initMicros

public void initMicros()

initGenes

public void initGenes()

getSonde

public java.lang.String getSonde(java.lang.String premir,
                                 int mature_from,
                                 int mature_to)

getReal_micro_seq

public java.lang.String getReal_micro_seq(java.lang.String micro_seq)

getSeqToFold

public java.lang.String getSeqToFold(java.lang.String micro_seq,
                                     java.lang.String tr_seq)

getReverse

public java.lang.String getReverse(java.lang.String seq)

sortMyVector

public void sortMyVector(java.lang.String type)

doRNAhybrid

public void doRNAhybrid()

getSeedsWobble

public java.util.Vector getSeedsWobble(java.lang.String seed)