object.common
Class Link

java.lang.Object
  object.common.Link

All Implemented Interfaces:

java.io.Serializable

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

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

See Also:

Serialized Form

Field Summary

protected static java.lang.String	begin Beginning of a Http Url link (	protected static java.lang.String	end End of a Http Url link ()
protected static java.lang.String	href_microcible_1 Http Url link to Internal Microcible
protected static java.lang.String	href_microcible_2
protected static java.lang.String	href_microcible_3
protected static java.lang.String	href_microcible_4
protected static java.lang.String	href_microcible_5
protected static java.lang.String	href_mirbasetarget_1 Http Url link to TargetScan 5.0
protected static java.lang.String	href_mirbasetarget_2
protected static java.lang.String	href_mirbasetarget_3
protected static java.lang.String	href_targetscan_1 Http Url link to TragetScan 5.0
protected static java.lang.String	href_targetscan_2
protected static java.lang.String	href_targetscan_3
protected static java.lang.String	href_targetscan_4
protected static java.lang.String	href_tp_1
protected static java.lang.String	href_tp_2
protected static java.lang.String	hrefEnsg Http Url link to Ensembl database for viewing a Homo sapiens Gene details
protected static java.lang.String	hrefEnsgMouse Http Url link to Ensembl database for viewing a Mus musculus Gene details
protected static java.lang.String	hrefEnsgRattus Http Url link to Ensembl database for viewing a Mus musculus Gene details
protected static java.lang.String	hrefEnst Http Url link to Ensembl database for viewing a Homo sapiens Transcript details
protected static java.lang.String	hrefEnstMouse Http Url link to Ensembl database for viewing a Mus musculus Transcript details
protected static java.lang.String	hrefEnstRattus Http Url link to Ensembl database for viewing a Mus musculus Transcript details
protected static java.lang.String	hrefEST Http Url link to NCBI website to see EST details
protected static java.lang.String	hrefGb_gene_id Http Url link to GENBANK_GENE_ID database for viewing GENBANK_GENE id cluster details
protected static java.lang.String	hrefGBLink_mgi Http Url link to MGD database
protected static java.lang.String	hrefGBLink_mim Http Url link to OMIM database
protected static java.lang.String	hrefGBLink_rgd Http Url link to RGD database
protected static java.lang.String	hrefGenbank_gene_id Http Url link to NCBI website to see Gene details
protected static java.lang.String	hrefGeneCard Http Url link to GENE CARDS
protected static java.lang.String	hrefGi Http Url link to NCBI website to see GI details
protected static java.lang.String	hrefGo Http Url link to GO(Gene Ontology) database
protected static java.lang.String	hrefMICIB_1 Http Url link to IPMC CIBLE tool
protected static java.lang.String	hrefMICIB_2
protected static java.lang.String	hrefMiranda Http Url link to Sanger institute to see Miranda targets
protected static java.lang.String	hrefMiRNAMAP_1 Http Url link to miRNA MAP 2.0
protected static java.lang.String	hrefMiRNAMAP_2
protected static java.lang.String	hrefmiRNASanger Http Url link to Sanger website miRNA informations
protected static java.lang.String	hrefProtein Http Url link to NCBI for protein
protected static java.lang.String	hrefPubmed Http Url link to NCBI website to see PUbmed publication
protected static java.lang.String	hrefRefseq Http Url link to NCBI website to see Refseq accession number details
protected static java.lang.String	hrefSRS_1 Http Url link to SwissProt SRS
protected static java.lang.String	hrefSRS_2
protected static java.lang.String	hrefSRS_3
protected static java.lang.String	hrefUCSC_1 Http Url link to UCSC genome browser
protected static java.lang.String	hrefUCSC_2
protected static java.lang.String	hrefUnigene Http Url link to Unigene database for viewing cluster Unigene id detail, first part
protected static java.lang.String	hrefUnigene2
protected static java.lang.String	hrefUnigeneEST Http Url link to NCBI website to see Unigene est profiler system
protected static java.lang.String	middle Middle of a Http Url link (" target="_blank">)
protected static java.lang.String	middle_main
protected static java.lang.String	middle_navig

Constructor Summary

Link()
Default constructor

Method Summary

java.lang.String	getHitLink(BlastBase blastbase, java.lang.String hit) Return a link to the database selected with type parameter concatenate with the ID received
java.lang.String	getHitLink(java.lang.String type, java.lang.String hit) Return a link to the database selected with type parameter concatenate with the ID received
java.lang.String	getLink(GenomicPosition genomicPosition) Return a link corresponding to the GenomicPosition Object received
java.lang.String	getLink(java.lang.String type, Organism organism, java.lang.String id) Return a link to the database selected
java.lang.String	getLink(java.lang.String type, java.lang.String id) Return a link to the database selected with type parameter concatenate with the ID received
java.lang.String	getLink(java.lang.String type, java.lang.String id, int org_id)
java.lang.String	getLink(java.lang.String type, java.lang.String view, java.lang.String id) Return a link to the database selected with type parameter concatenate with the GI and Refseq AN received
java.lang.String	getLinkTargetPrediction(java.lang.String mature_acc, int organism_id)
java.lang.String	getMicrocibleLink(java.lang.String seed, java.lang.String seq, java.lang.String symbol, java.lang.String mature_acc, java.lang.String label, int org_id)
java.lang.String	getMirbaseTargetLink(java.lang.String specie, java.lang.String symbol, java.lang.String micro)
java.lang.String	getTargetScanLink(java.lang.String tax_id, java.lang.String symbol, java.lang.String micro)

Methods inherited from class java.lang.Object

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

Field Detail

begin

protected static final java.lang.String begin

Beginning of a Http Url link (Constant Field Values

middle

protected static final java.lang.String middle

Middle of a Http Url link (" target="_blank">)

See Also:

Constant Field Values

middle_main

protected static final java.lang.String middle_main

See Also:

Constant Field Values

middle_navig

protected static final java.lang.String middle_navig

See Also:

Constant Field Values

end

protected static final java.lang.String end

End of a Http Url link ()

See Also:

Constant Field Values

hrefEnsg

protected static final java.lang.String hrefEnsg

Http Url link to Ensembl database for viewing a Homo sapiens Gene details

See Also:

Constant Field Values

hrefEnsgMouse

protected static final java.lang.String hrefEnsgMouse

Http Url link to Ensembl database for viewing a Mus musculus Gene details

See Also:

Constant Field Values

hrefEnsgRattus

protected static final java.lang.String hrefEnsgRattus

Http Url link to Ensembl database for viewing a Mus musculus Gene details

See Also:

Constant Field Values

hrefEnst

protected static final java.lang.String hrefEnst

Http Url link to Ensembl database for viewing a Homo sapiens Transcript details

See Also:

Constant Field Values

hrefEnstMouse

protected static final java.lang.String hrefEnstMouse

Http Url link to Ensembl database for viewing a Mus musculus Transcript details

See Also:

Constant Field Values

hrefEnstRattus

protected static final java.lang.String hrefEnstRattus

Http Url link to Ensembl database for viewing a Mus musculus Transcript details

See Also:

Constant Field Values

hrefGb_gene_id

protected static final java.lang.String hrefGb_gene_id

Http Url link to GENBANK_GENE_ID database for viewing GENBANK_GENE id cluster details

See Also:

Constant Field Values

hrefRefseq

protected static final java.lang.String hrefRefseq

Http Url link to NCBI website to see Refseq accession number details

See Also:

Constant Field Values

hrefGenbank_gene_id

protected static final java.lang.String hrefGenbank_gene_id

Http Url link to NCBI website to see Gene details

See Also:

Constant Field Values

hrefUnigene

protected static final java.lang.String hrefUnigene

Http Url link to Unigene database for viewing cluster Unigene id detail, first part

See Also:

Constant Field Values

hrefUnigene2

protected static final java.lang.String hrefUnigene2

See Also:

Constant Field Values

hrefGo

protected static final java.lang.String hrefGo

Http Url link to GO(Gene Ontology) database

See Also:

Constant Field Values

hrefGi

protected static final java.lang.String hrefGi

Http Url link to NCBI website to see GI details

See Also:

Constant Field Values

hrefEST

protected static final java.lang.String hrefEST

Http Url link to NCBI website to see EST details

See Also:

Constant Field Values

hrefUnigeneEST

protected static final java.lang.String hrefUnigeneEST

Http Url link to NCBI website to see Unigene est profiler system

See Also:

Constant Field Values

hrefmiRNASanger

protected static final java.lang.String hrefmiRNASanger

Http Url link to Sanger website miRNA informations

See Also:

Constant Field Values

hrefPubmed

protected static final java.lang.String hrefPubmed

Http Url link to NCBI website to see PUbmed publication

See Also:

Constant Field Values

hrefMiranda

protected static final java.lang.String hrefMiranda

Http Url link to Sanger institute to see Miranda targets

See Also:

Constant Field Values

hrefProtein

protected static final java.lang.String hrefProtein

Http Url link to NCBI for protein

See Also:

Constant Field Values

hrefGBLink_mim

protected static final java.lang.String hrefGBLink_mim

Http Url link to OMIM database

See Also:

Constant Field Values

hrefGBLink_mgi

protected static final java.lang.String hrefGBLink_mgi

Http Url link to MGD database

See Also:

Constant Field Values

hrefGBLink_rgd

protected static final java.lang.String hrefGBLink_rgd

Http Url link to RGD database

See Also:

Constant Field Values

hrefSRS_1

protected static final java.lang.String hrefSRS_1

Http Url link to SwissProt SRS

See Also:

Constant Field Values

hrefSRS_2

protected static final java.lang.String hrefSRS_2

See Also:

Constant Field Values

hrefSRS_3

protected static final java.lang.String hrefSRS_3

See Also:

Constant Field Values

hrefUCSC_1

protected static final java.lang.String hrefUCSC_1

Http Url link to UCSC genome browser

See Also:

Constant Field Values

hrefUCSC_2

protected static final java.lang.String hrefUCSC_2

See Also:

Constant Field Values

hrefMICIB_1

protected static final java.lang.String hrefMICIB_1

Http Url link to IPMC CIBLE tool

See Also:

Constant Field Values

hrefMICIB_2

protected static final java.lang.String hrefMICIB_2

See Also:

Constant Field Values

hrefGeneCard

protected static final java.lang.String hrefGeneCard

Http Url link to GENE CARDS

See Also:

Constant Field Values

hrefMiRNAMAP_1

protected static final java.lang.String hrefMiRNAMAP_1

Http Url link to miRNA MAP 2.0

See Also:

Constant Field Values

hrefMiRNAMAP_2

protected static final java.lang.String hrefMiRNAMAP_2

See Also:

Constant Field Values

href_tp_1

protected static final java.lang.String href_tp_1

See Also:

Constant Field Values

href_tp_2

protected static final java.lang.String href_tp_2

See Also:

Constant Field Values

href_targetscan_1

protected static final java.lang.String href_targetscan_1

Http Url link to TragetScan 5.0

See Also:

Constant Field Values

href_targetscan_2

protected static final java.lang.String href_targetscan_2

See Also:

Constant Field Values

href_targetscan_3

protected static final java.lang.String href_targetscan_3

See Also:

Constant Field Values

href_targetscan_4

protected static final java.lang.String href_targetscan_4

See Also:

Constant Field Values

href_mirbasetarget_1

protected static final java.lang.String href_mirbasetarget_1

Http Url link to TargetScan 5.0

See Also:

Constant Field Values

href_mirbasetarget_2

protected static final java.lang.String href_mirbasetarget_2

See Also:

Constant Field Values

href_mirbasetarget_3

protected static final java.lang.String href_mirbasetarget_3

See Also:

Constant Field Values

href_microcible_1

protected static final java.lang.String href_microcible_1

Http Url link to Internal Microcible

See Also:

Constant Field Values

href_microcible_2

protected static final java.lang.String href_microcible_2

See Also:

Constant Field Values

href_microcible_3

protected static final java.lang.String href_microcible_3

See Also:

Constant Field Values

href_microcible_4

protected static final java.lang.String href_microcible_4

See Also:

Constant Field Values

href_microcible_5

protected static final java.lang.String href_microcible_5

See Also:

Constant Field Values

Constructor Detail

Link

public Link()

Default constructor

Method Detail

getLink

public java.lang.String getLink(java.lang.String type,
                                java.lang.String id)

Return a link to the database selected with type parameter concatenate with the ID received

Parameters:

type - type of link you want to create, it could be :
- 'ENSG' for Ensembl gene link
- 'ENST' for Ensembl transcript link
- 'GENBANK_GENE_ID' for GENBANK_GENE_ID cluster link
- 'GO' for Gene Ontology term link
- 'EST' for EST link with the Gi number
- 'REFSEQ' for Refseq transcript link
- 'UNIGENE' for Unigene cluster link

id - ID of the reference link you want to create

Returns:

link String containing the all link ( 'id' )

See Also:

Common, Common.getGiFromRefseq(String)

getLink

public java.lang.String getLink(java.lang.String type,
                                java.lang.String view,
                                java.lang.String id)

Return a link to the database selected with type parameter concatenate with the GI and Refseq AN received

Parameters:

type - type of link you want to create, it could be :
- 'EST' for Ensembl gene link

view - refseq reference view in the browser

id - reference for href link

Returns:

link String containing the all link( something like : 'view' )

getLink

public java.lang.String getLink(java.lang.String type,
                                Organism organism,
                                java.lang.String id)

Return a link to the database selected

Parameters:

type - type of link you want to create

organism - Organism Object concerning the link to create

id - reference for href link

Returns:

link String containing link( something like : 'view' )

getHitLink

public java.lang.String getHitLink(BlastBase blastbase,
                                   java.lang.String hit)

Return a link to the database selected with type parameter concatenate with the ID received

Parameters:

blastbase - Blastbase Mediante Object, the blastbase_type attribute of this Blastbase could be :
- 'oligo' for Oligo Mediante Database
- 'mediante' for Gene Mediante Database
- 'ensembl' for Ensembl Database
- 'refseq' for Refseq Database

hit - ID of the reference link you want to create (oligo_id,gene_id,ensembl_ref,refseq_ref)

Returns:

link String containing the href Html balise ( something like : 'hit' )

See Also:

BlastBase, Common, Common.getGiFromRefseq(String)

getHitLink

public java.lang.String getHitLink(java.lang.String type,
                                   java.lang.String hit)

Return a link to the database selected with type parameter concatenate with the ID received

Parameters:

type - type of link you want to create, it could be :
- 'oligo' for Oligo Mediante Database
- 'mediante' for Gene Mediante Database
- 'ensembl' for Ensembl Database
- 'refseq' for Refseq Database

hit - ID of the reference link you want to create (oligo_id,gene_id,ensembl_ref,refseq_ref)

Returns:

link String containing the href Html balise ( something like : 'hit' )

See Also:

Common, Common.getGiFromRefseq(String)

getLink

public java.lang.String getLink(GenomicPosition genomicPosition)

Return a link corresponding to the GenomicPosition Object received

Parameters:

genomicPosition - GenomicPosition Object

Returns:

link String containing link( something like : 'view' )

See Also:

GenomicPosition, Organism

getLink

public java.lang.String getLink(java.lang.String type,
                                java.lang.String id,
                                int org_id)

getTargetScanLink

public java.lang.String getTargetScanLink(java.lang.String tax_id,
                                          java.lang.String symbol,
                                          java.lang.String micro)

getMirbaseTargetLink

public java.lang.String getMirbaseTargetLink(java.lang.String specie,
                                             java.lang.String symbol,
                                             java.lang.String micro)

getMicrocibleLink

public java.lang.String getMicrocibleLink(java.lang.String seed,
                                          java.lang.String seq,
                                          java.lang.String symbol,
                                          java.lang.String mature_acc,
                                          java.lang.String label,
                                          int org_id)

getLinkTargetPrediction

public java.lang.String getLinkTargetPrediction(java.lang.String mature_acc,
                                                int organism_id)