object.annotation
Class Gene

java.lang.Object
  object.annotation.Gene

All Implemented Interfaces:

java.io.Serializable

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

Description
In fact represent more a Transcript than a Gene
Infos : KLB - IPMC - 08/2003

See Also:

Organism, Oligo, Oligo_adhoc, Exon, Cytoband, Oligo_externe, GoLink, Serialized Form

Field Summary

private java.lang.String	accession_number Accession number of the Gene Object - refernce to a Bio Database like Refseq
private java.lang.String	description Description of the Gene object in the bio-litterature
private java.lang.String	estMatch list of number of match EST along the transcript
private int	genbank_gene_id genbank gene id of the Gene Object - reference to genbank_gene_id database
private java.lang.String	genbank_link ID link from NCBI genbank file to database MIM, MGI, RGD
private int	gene_id ID of the Gene object
private GenomicPosition	genomicPosition GenomicPosition Object concerning this Gene Object
private java.util.Hashtable	hashMirna_target Hash of Target with key is the tool of target prediction
private java.util.Hashtable	hashOligosAffy Hashtable of Oligo_affy Object matching this Gene object
private java.util.Hashtable	hashOligosExternes Hashtable of Oligo_externe Object matching this Gene object
private int	longueur Length of the Gene sequence
private java.lang.String	map map for image
private MapEST	mapEST MapEST Object of this Gene Object
private java.lang.String	protein_id ID from protein from NCBI genbank file
private java.lang.String	sequence RNA sequence of this Gene object
private java.lang.String	symbol Gene symbol (name)
private java.lang.String	synonym Gene symbol (synonyms)
private java.lang.String	unigene_id Unigene reference for this Gene Object - Unigene Database
private java.util.Vector	vectorAnnotations Vector of GoLink Object for this Gene object
private java.util.Vector	vectorCytobands Vector of Cytoband Object for this Gene object
private java.util.Vector	vectorExons Vector of Exons Object which composed this Gene object
private java.util.Vector	vectorGenbankRef Vector of GenbankRef Object for this Gene object
private java.util.Vector	vectorOligo_adhocRelation Vector of Oligo_adhocRelation Object for this Gene object
private java.util.Vector	vectorOligos Vector of Oligo Object matching this Gene object
private java.lang.String	xhybridMatch list of Xhybrid match along the transcript

Constructor Summary

Gene()
Default constructor

Gene(int gene_id)
Constructs a Gene object from a Gene ID
NB : the constructor does not load all Vectors of the Gene Object.

Gene(java.lang.String accession_number)
Constructs a Gene object from Accession number reference
NB : the constructor does not load all Vectors of the Gene Object.

Method Summary

java.lang.String	displayOligos() 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
java.lang.String	getAccession_number() Accession number of the Gene Object - refernce to a Bio Database like Refseq
java.lang.String	getDescription() Description of the Gene object in the bio-litterature
java.lang.String	getEstMatch() list of number of match EST along the transcript
int	getGenbank_gene_id() genbank_gene id of the Gene Object - reference to genbank_gene_id database
java.lang.String	getGenbank_link() ID link from NCBI genbank file to database MIM, MGI, RGD
int	getGene_id() ID of the Gene object
GenomicPosition	getGenomicPosition() GenomicPosition Object concerning this Gene Object
java.util.Hashtable	getHashMirna_target() Hashtable of Mirna_target for this Gene object
java.util.Hashtable	getHashOligosAffy() Hashtable of Oligo_affy Object matching this Gene object
java.util.Hashtable	getHashOligosExternes() Hashtable of Oligo_externe Object matching this Gene object
int	getLongueur() Length of the Gene sequence
java.lang.String	getMap() map for images
MapEST	getMapEST() MapEST Object of this Gene Object
java.lang.String	getProtein_id() ID from protein from NCBI genbank file
java.lang.String	getSequence() RNA sequence of this Gene object
java.lang.String	getSymbol() Gene symbol (name)
java.lang.String	getSynonym() Gene symbol (synonyms)
java.lang.String	getUnigene_id() Unigene reference for this Gene Object - Unigene Database
java.util.Vector	getVectorAnnotations() Vector of GoLink Object for this Gene object
java.util.Vector	getVectorCytobands() Vector of Cytoband Object for this Gene object
java.util.Vector	getVectorExons() Vector of Exons Object which composed this Gene object
java.util.Vector	getVectorGenbankRef() Vector of GenbankRef Object for this Gene object
java.util.Vector	getVectorOligo_adhocRelation() Vector of PcrRelation Object for this Gene object
java.util.Vector	getVectorOligos() Vector of Oligo Object matching this Gene object
java.lang.String	getXhybridMatch() list of Xhybrid match along the transcript
void	loadHashMirna_target() This function load a Vector containing the List of Mirna_target Objects for this Gene Object
void	loadHashOligosAffy() 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
void	loadHashOligosExternes() This function load all the Oligo_externe for the Gene Object in a Hashtable ordered in fucntion of array_id of External Arrays
void	loadVectorAnnotations() Thhis function load a vector containing the list of GoLink Objects for this Gene Object
void	loadVectorCytobands() This function load a vector containing the list of Cytoband Objects for this Gene Object
void	loadVectorExons() This function load a vector containing the list of Exons Objects composing the sequence of this Gene Object
void	loadVectorGenbankRef() This function load a vector containing the list of GenbankRef Object for this Gene Object
void	loadVectorOligo_adhocRelation() This function load a Vector containing the List of Oligo_adhocRelation for this Gene Object
void	loadVectorOligos() This function load a Vector containing the List of Oligos Objects for this Gene Object
void	setAccession_number(java.lang.String accession_number)
void	setDescription(java.lang.String description)
void	setEstMatch(java.lang.String estMatch)
void	setGenbank_gene_id(int genbank_gene_id)
void	setGenbank_link(java.lang.String genbank_link)
void	setGene_id(int gene_id)
void	setGenomicPosition(GenomicPosition genomicPosition)
void	setHashMirna_target(java.util.Hashtable hashMirna_target)
void	setHashOligosAffy(java.util.Hashtable hashOligosAffy)
void	setHashOligosExternes(java.util.Hashtable hashOligosExternes)
void	setLongueur(int longueur)
void	setMap(java.lang.String map)
void	setMapEST(MapEST mapEST)
void	setProtein_id(java.lang.String protein_id)
void	setSequence(java.lang.String sequence)
void	setSymbol(java.lang.String symbol)
void	setSynonym(java.lang.String synonym)
void	setUnigene_id(java.lang.String unigene_id)
void	setVectorAnnotations(java.util.Vector vectorAnnotations)
void	setVectorCytobands(java.util.Vector vectorCytobands)
void	setVectorExons(java.util.Vector vectorExons)
void	setVectorGenbankRef(java.util.Vector vectorGenbankRef)
void	setVectorOligo_adhocRelation(java.util.Vector vectorOligo_adhocRelation)
void	setVectorOligos(java.util.Vector vectorOligos)
void	setXhybridMatch(java.lang.String xhybridMatch)

Methods inherited from class java.lang.Object

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

Field Detail

gene_id

private int gene_id

ID of the Gene object

longueur

private int longueur

Length of the Gene sequence

description

private java.lang.String description

Description of the Gene object in the bio-litterature

accession_number

private java.lang.String accession_number

Accession number of the Gene Object - refernce to a Bio Database like Refseq

genbank_gene_id

private int genbank_gene_id

genbank gene id of the Gene Object - reference to genbank_gene_id database

symbol

private java.lang.String symbol

Gene symbol (name)

synonym

private java.lang.String synonym

Gene symbol (synonyms)

unigene_id

private java.lang.String unigene_id

Unigene reference for this Gene Object - Unigene Database

sequence

private java.lang.String sequence

RNA sequence of this Gene object

vectorOligos

private java.util.Vector vectorOligos

Vector of Oligo Object matching this Gene object

vectorOligo_adhocRelation

private java.util.Vector vectorOligo_adhocRelation

Vector of Oligo_adhocRelation Object for this Gene object

vectorExons

private java.util.Vector vectorExons

Vector of Exons Object which composed this Gene object

vectorAnnotations

private java.util.Vector vectorAnnotations

Vector of GoLink Object for this Gene object

vectorCytobands

private java.util.Vector vectorCytobands

Vector of Cytoband Object for this Gene object

hashOligosExternes

private java.util.Hashtable hashOligosExternes

Hashtable of Oligo_externe Object matching this Gene object

hashOligosAffy

private java.util.Hashtable hashOligosAffy

Hashtable of Oligo_affy Object matching this Gene object

vectorGenbankRef

private java.util.Vector vectorGenbankRef

Vector of GenbankRef Object for this Gene object

hashMirna_target

private java.util.Hashtable hashMirna_target

Hash of Target with key is the tool of target prediction

protein_id

private java.lang.String protein_id

ID from protein from NCBI genbank file

genbank_link

private java.lang.String genbank_link

ID link from NCBI genbank file to database MIM, MGI, RGD

genomicPosition

private GenomicPosition genomicPosition

GenomicPosition Object concerning this Gene Object

estMatch

private java.lang.String estMatch

list of number of match EST along the transcript

xhybridMatch

private java.lang.String xhybridMatch

list of Xhybrid match along the transcript

map

private java.lang.String map

map for image

mapEST

private MapEST mapEST

MapEST Object of this Gene Object

Constructor Detail

Gene

public Gene()

Default constructor

Gene

public Gene(int gene_id)

Constructs a Gene object from a Gene ID
NB : the constructor does not load all Vectors of the Gene Object.

Parameters:

gene_id - ID of an existing Gene Object

See Also:

GenomicPosition

Gene

public Gene(java.lang.String accession_number)

Constructs a Gene object from Accession number reference
NB : the constructor does not load all Vectors of the Gene Object.

Parameters:

accession_number - Accession number of an existing Gene Object

See Also:

GenomicPosition

Method Detail

getGene_id

public int getGene_id()

ID of the Gene object

setGene_id

public void setGene_id(int gene_id)

getLongueur

public int getLongueur()

Length of the Gene sequence

setLongueur

public void setLongueur(int longueur)

getDescription

public java.lang.String getDescription()

Description of the Gene object in the bio-litterature

setDescription

public void setDescription(java.lang.String description)

getAccession_number

public java.lang.String getAccession_number()

Accession number of the Gene Object - refernce to a Bio Database like Refseq

setAccession_number

public void setAccession_number(java.lang.String accession_number)

getGenbank_gene_id

public int getGenbank_gene_id()

genbank_gene id of the Gene Object - reference to genbank_gene_id database

setGenbank_gene_id

public void setGenbank_gene_id(int genbank_gene_id)

getSynonym

public java.lang.String getSynonym()

Gene symbol (synonyms)

setSynonym

public void setSynonym(java.lang.String synonym)

getSymbol

public java.lang.String getSymbol()

Gene symbol (name)

setSymbol

public void setSymbol(java.lang.String symbol)

getUnigene_id

public java.lang.String getUnigene_id()

Unigene reference for this Gene Object - Unigene Database

setUnigene_id

public void setUnigene_id(java.lang.String unigene_id)

getSequence

public java.lang.String getSequence()

RNA sequence of this Gene object

setSequence

public void setSequence(java.lang.String sequence)

getVectorOligos

public java.util.Vector getVectorOligos()

Vector of Oligo Object matching this Gene object

setVectorOligos

public void setVectorOligos(java.util.Vector vectorOligos)

getVectorOligo_adhocRelation

public java.util.Vector getVectorOligo_adhocRelation()

Vector of PcrRelation Object for this Gene object

setVectorOligo_adhocRelation

public void setVectorOligo_adhocRelation(java.util.Vector vectorOligo_adhocRelation)

getVectorExons

public java.util.Vector getVectorExons()

Vector of Exons Object which composed this Gene object

setVectorExons

public void setVectorExons(java.util.Vector vectorExons)

getVectorAnnotations

public java.util.Vector getVectorAnnotations()

Vector of GoLink Object for this Gene object

setVectorAnnotations

public void setVectorAnnotations(java.util.Vector vectorAnnotations)

getVectorCytobands

public java.util.Vector getVectorCytobands()

Vector of Cytoband Object for this Gene object

setVectorCytobands

public void setVectorCytobands(java.util.Vector vectorCytobands)

getHashOligosExternes

public java.util.Hashtable getHashOligosExternes()

Hashtable of Oligo_externe Object matching this Gene object

setHashOligosExternes

public void setHashOligosExternes(java.util.Hashtable hashOligosExternes)

getHashOligosAffy

public java.util.Hashtable getHashOligosAffy()

Hashtable of Oligo_affy Object matching this Gene object

setHashOligosAffy

public void setHashOligosAffy(java.util.Hashtable hashOligosAffy)

getVectorGenbankRef

public java.util.Vector getVectorGenbankRef()

Vector of GenbankRef Object for this Gene object

setVectorGenbankRef

public void setVectorGenbankRef(java.util.Vector vectorGenbankRef)

getProtein_id

public java.lang.String getProtein_id()

ID from protein from NCBI genbank file

setProtein_id

public void setProtein_id(java.lang.String protein_id)

getGenbank_link

public java.lang.String getGenbank_link()

ID link from NCBI genbank file to database MIM, MGI, RGD

setGenbank_link

public void setGenbank_link(java.lang.String genbank_link)

getGenomicPosition

public GenomicPosition getGenomicPosition()

GenomicPosition Object concerning this Gene Object

setGenomicPosition

public void setGenomicPosition(GenomicPosition genomicPosition)

getEstMatch

public java.lang.String getEstMatch()

list of number of match EST along the transcript

setEstMatch

public void setEstMatch(java.lang.String estMatch)

getXhybridMatch

public java.lang.String getXhybridMatch()

list of Xhybrid match along the transcript

setXhybridMatch

public void setXhybridMatch(java.lang.String xhybridMatch)

getMap

public java.lang.String getMap()

map for images

setMap

public void setMap(java.lang.String map)

getMapEST

public MapEST getMapEST()

MapEST Object of this Gene Object

setMapEST

public void setMapEST(MapEST mapEST)

getHashMirna_target

public java.util.Hashtable getHashMirna_target()

Hashtable of Mirna_target for this Gene object

setHashMirna_target

public void setHashMirna_target(java.util.Hashtable hashMirna_target)

loadVectorOligos

public void loadVectorOligos()

This function load a Vector containing the List of Oligos Objects for this Gene Object

See Also:

Oligo, Oligo.Oligo(int)

loadVectorOligo_adhocRelation

public void loadVectorOligo_adhocRelation()

This function load a Vector containing the List of Oligo_adhocRelation for this Gene Object

See Also:

Oligo_adhocRelation, Oligo_adhocRelation.Oligo_adhocRelation(int,int,int,int,double)

loadVectorExons

public void loadVectorExons()

This function load a vector containing the list of Exons Objects composing the sequence of this Gene Object

See Also:

Exon, Exon.Exon(int,int,int,int)

loadVectorAnnotations

public void loadVectorAnnotations()

Thhis function load a vector containing the list of GoLink Objects for this Gene Object

See Also:

GoLink, GoLink.GoLink(int,Term)

loadVectorCytobands

public void loadVectorCytobands()

This function load a vector containing the list of Cytoband Objects for this Gene Object

See Also:

Cytoband, Cytoband.Cytoband(int)

loadHashMirna_target

public void loadHashMirna_target()

This function load a Vector containing the List of Mirna_target Objects for this Gene Object

See Also:

Mirna_target

loadHashOligosExternes

public void loadHashOligosExternes()

This function load all the Oligo_externe for the Gene Object
in a Hashtable ordered in fucntion of array_id of External Arrays

See Also:

Array, Oligo_externe, Oligo_externe.Oligo_externe(int)

loadHashOligosAffy

public void loadHashOligosAffy()

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

See Also:

Array, Oligo_affy, Oligo_affy.Oligo_affy(int)

loadVectorGenbankRef

public void loadVectorGenbankRef()

This function load a vector containing the list of GenbankRef Object for this Gene Object

See Also:

GenbankRef, GenbankRef.GenbankRef(int,int,String,String,String,String)

displayOligos

public java.lang.String displayOligos()
                               throws java.lang.Exception

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

Returns:

graph All the informations graph in one String (in a Html table)

Throws:

java.lang.Exception

See Also:

Gene, Exon, Oligo, Oligo_adhoc, Oligo_externe, Genoligo_rel, OnMouseOver, Oligo_adhocRelation, Microarray_project_type, Common