edu.iastate.metnet.dao
Class AtGeneSearchLocusObject

java.lang.Object
  edu.iastate.metnet.dao.AtGeneSearchLocusObject

All Implemented Interfaces:

java.io.Serializable

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

get all information for locus id

Author:

Jie Li

See Also:

Serialized Form

Constructor Summary

AtGeneSearchLocusObject()
default constructor

Method Summary

void	addAffy25kID(java.lang.String affy25kid) add new affy25k id
void	addAffy8kID(java.lang.String affy8kid) add new affy8k id
void	addAfgcID(java.lang.String afgcid) add new afgc id
void	addAllAffy25kID(java.util.Collection collection)
void	addAllAffy8kID(java.util.Collection collection)
void	addAllAfgcID(java.util.Collection collection)
void	addAllAgrisActivatedBy(java.util.Collection collection) add all activated by loci
void	addAllAgrisActivates(java.util.Collection collection) add all activates loci
void	addAllAgrisAffectedBy(java.util.Collection collection) add all affected by loci
void	addAllAgrisAffects(java.util.Collection collection) add all affects loci
void	addAllAgrisCisBinindSite(java.util.Collection collection) add all binding site information
void	addAllAgrisReference(java.util.Collection collection) add all references
void	addAllAgrisRepressedBy(java.util.Collection collection) add all repressed by loci
void	addAllAgrisRepresses(java.util.Collection collection) add all represses loci
void	addAllAracycPathway(java.util.Collection collection) add all pathways
void	addAllComment(java.util.Collection collection) add new comment
void	addAllGeneName(java.util.Collection collection) add locus synonym and abbreviation
void	addAllMapmanBinId(java.util.Collection collection) add mapman bin id
void	addAllMapmanCategory(java.util.Collection collection) add mapman category
void	addAllMapmanDescription(java.util.Collection collection) add mapman description
void	addAllMetnetLocation(java.util.Collection collection)
void	addAllMetnetPathway(java.util.Collection collection) add new metnet pathway
void	addAllReference(java.util.Collection collection)
void	addAllTairAnnotation(java.util.Collection collection)
void	addAllUniprotID(java.util.Collection collection)
void	addAracycPathway(java.lang.String aracycPathway) add new aracyc pathway
void	addComment(java.lang.String comment) add new comment
void	addGoBiologicalProcess(GoTermID goBiologicalProcess) add new biological process
void	addGoCellularComponent(GoTermID goCellularComponent) add new cellular component
void	addGoMolecularFunction(GoTermID goMolecularFunction) add new molecular function
void	addMetnetLocation(java.lang.String metnetLocation) add new metnet location
void	addMetnetPathway(java.lang.String metnetPathway) add new metnet pathway
void	addTairAnnotation(java.lang.String tairAnnotation) add new tait annotation
void	addUniprotID(java.lang.String uniprotid) add another uniprot id
java.lang.String	getAffy25kID() get the list of affy25k id
java.util.ArrayList	getAffy25kidList()
java.lang.String	getAffy8kID() get the list of affy8k id
java.util.ArrayList	getAffy8kidList()
java.lang.String	getAfgcID() get the list of afgc id
java.util.ArrayList	getAfgcidList()
java.lang.String	getAgrisActivedBy() get the list of activated by locus list
java.util.ArrayList	getAgrisActivedByList()
java.lang.String	getAgrisActives() get the list of activates locus list
java.util.ArrayList	getAgrisActivesList()
java.lang.String	getAgrisAffectedBy() get the affected by locus list
java.util.ArrayList	getAgrisAffectedByList()
java.lang.String	getAgrisAffects() get the affects locus list
java.util.ArrayList	getAgrisAffectsList()
java.lang.String	getAgrisCisBindingSite()
java.util.ArrayList	getAgrisCisBindingSiteList()
java.lang.String	getAgrisReference() get the agris reference
java.util.ArrayList	getAgrisReferenceList()
java.lang.String	getAgrisRepressedBy() get the repressed by locus list
java.util.ArrayList	getAgrisRepressedByList()
java.lang.String	getAgrisRepresses() get the represses locus list
java.util.ArrayList	getAgrisRepressesList()
java.lang.String	getAracycPathway() get the list of aracyc pathway
java.util.ArrayList	getAracycPathwayList()
java.lang.String	getComment() get the list of comment
java.util.ArrayList	getCommentList()
java.lang.String	getGeneName() get gene name list
java.util.ArrayList	getGeneNameList()
java.lang.String	getGoBiologicalProcess() get the list of biological process
java.util.ArrayList	getGoBiologicalProcessList()
java.lang.String	getGoBiologicalProcessWithLinks() get the list of biological process with hyperlinks
java.lang.String	getGoCellularComponent() get the list of cellular component
java.util.ArrayList	getGoCellularComponentList()
java.lang.String	getGoCellularComponentWithLinks() get the list of cellular component with hyperlinks
java.lang.String	getGoMolecularFunction() get the list of molecular function
java.util.ArrayList	getGoMolecularFunctionList()
java.lang.String	getGoMolecularFunctionWithLinks() get the list of molecular function with hyperlinks
java.util.Map	getLocationConfideceMap()
java.lang.String	getLocationConfidence(java.lang.String location)
java.lang.String	getLocusid() get the locus id
java.lang.String	getMapmanBinId()
java.util.ArrayList	getMapmanBinIdList()
java.lang.String	getMapmanCategory()
java.util.ArrayList	getMapmanCategoryList()
java.lang.String	getMapmanDescription()
java.util.ArrayList	getMapmanDescriptionList()
java.lang.String	getMetnetLocation() get the list of metnet location
java.util.ArrayList	getMetnetLocationList()
java.lang.String	getMetnetPathway() get the list of metnet pathway
java.util.ArrayList	getMetnetPathwayList()
java.lang.String	getPredictedLocation() get predicted location
java.lang.String	getReference()
java.util.ArrayList	getReferenceList()
java.lang.String	getTairAnnotation() get the distinct annotation separated by semicolon
java.util.ArrayList	getTairAnnotationList()
java.lang.String	getTooltip()
java.lang.String	getUniprotID() get the uniprot id list separated by semicolon
java.util.ArrayList	getUniprotidList()
java.lang.String	getUniprotIDWithLinks() get the uniprot id list separated by semicolon with hyperlinks
void	setLocusid(java.lang.String locusid) set the locus id
void	setPredictedLocation(java.lang.String predictedLocation) set predicted location

Methods inherited from class java.lang.Object

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

Constructor Detail

AtGeneSearchLocusObject

public AtGeneSearchLocusObject()

default constructor

Method Detail

addAffy25kID

public void addAffy25kID(java.lang.String affy25kid)

add new affy25k id

Parameters:

affy25kid - new affy25k id

addAffy8kID

public void addAffy8kID(java.lang.String affy8kid)

add new affy8k id

Parameters:

affy8kid - the new affy8k id

addAllGeneName

public void addAllGeneName(java.util.Collection collection)

add locus synonym and abbreviation

Parameters:

collection - the list of synonym

addAfgcID

public void addAfgcID(java.lang.String afgcid)

add new afgc id

Parameters:

afgcid - the new afgc id

addAllAffy25kID

public void addAllAffy25kID(java.util.Collection collection)

addAllAffy8kID

public void addAllAffy8kID(java.util.Collection collection)

addAllAfgcID

public void addAllAfgcID(java.util.Collection collection)

addAllAgrisActivatedBy

public void addAllAgrisActivatedBy(java.util.Collection collection)

add all activated by loci

Parameters:

collection - activated by loci

addAllAgrisActivates

public void addAllAgrisActivates(java.util.Collection collection)

add all activates loci

Parameters:

collection - activates loci

addAllAgrisAffectedBy

public void addAllAgrisAffectedBy(java.util.Collection collection)

add all affected by loci

Parameters:

collection - affected by loci

addAllAgrisAffects

public void addAllAgrisAffects(java.util.Collection collection)

add all affects loci

Parameters:

collection - affects loci

addAllAgrisCisBinindSite

public void addAllAgrisCisBinindSite(java.util.Collection collection)

add all binding site information

Parameters:

collection - binding site information

addAllAgrisReference

public void addAllAgrisReference(java.util.Collection collection)

add all references

Parameters:

collection - references

addAllAgrisRepressedBy

public void addAllAgrisRepressedBy(java.util.Collection collection)

add all repressed by loci

Parameters:

collection - repressed by loci

addAllAgrisRepresses

public void addAllAgrisRepresses(java.util.Collection collection)

add all represses loci

Parameters:

collection - represses loci

addAllAracycPathway

public void addAllAracycPathway(java.util.Collection collection)

add all pathways

Parameters:

collection - pathways

addAllComment

public void addAllComment(java.util.Collection collection)

add new comment

Parameters:

comment - the new comment

addAllMapmanBinId

public void addAllMapmanBinId(java.util.Collection collection)

add mapman bin id

Parameters:

collection - the mapman bin id

addAllMapmanCategory

public void addAllMapmanCategory(java.util.Collection collection)

add mapman category

Parameters:

collection - mapman category

addAllMapmanDescription

public void addAllMapmanDescription(java.util.Collection collection)

add mapman description

Parameters:

collection - mapman description

addAllMetnetLocation

public void addAllMetnetLocation(java.util.Collection collection)

addAllMetnetPathway

public void addAllMetnetPathway(java.util.Collection collection)

add new metnet pathway

Parameters:

allMetnetPathway - the new metnet pathway

addAllReference

public void addAllReference(java.util.Collection collection)

addAllTairAnnotation

public void addAllTairAnnotation(java.util.Collection collection)

addAllUniprotID

public void addAllUniprotID(java.util.Collection collection)

addAracycPathway

public void addAracycPathway(java.lang.String aracycPathway)

add new aracyc pathway

Parameters:

aracycPathway - the new aracyc pathway

addComment

public void addComment(java.lang.String comment)

add new comment

Parameters:

comment - the new comment

addGoBiologicalProcess

public void addGoBiologicalProcess(GoTermID goBiologicalProcess)

add new biological process

Parameters:

goBiologicalProcess - the new biological process

addGoCellularComponent

public void addGoCellularComponent(GoTermID goCellularComponent)

add new cellular component

Parameters:

goCellularComponent - the new cellular component

addGoMolecularFunction

public void addGoMolecularFunction(GoTermID goMolecularFunction)

add new molecular function

Parameters:

goMolecularFunction - the new molecular function

addMetnetLocation

public void addMetnetLocation(java.lang.String metnetLocation)

add new metnet location

Parameters:

metnetLocation - the new metnet location

addMetnetPathway

public void addMetnetPathway(java.lang.String metnetPathway)

add new metnet pathway

Parameters:

metnetPathway - the new metnet pathway

addTairAnnotation

public void addTairAnnotation(java.lang.String tairAnnotation)

add new tait annotation

Parameters:

tairAnnotation - the new tair annotation

addUniprotID

public void addUniprotID(java.lang.String uniprotid)

add another uniprot id

Parameters:

uniprotid - the new uniprot id

getAffy25kID

public java.lang.String getAffy25kID()

get the list of affy25k id

Returns:

the list of affy25k id

getAffy25kidList

public java.util.ArrayList getAffy25kidList()

getAffy8kID

public java.lang.String getAffy8kID()

get the list of affy8k id

Returns:

the list of affy8k id

getAffy8kidList

public java.util.ArrayList getAffy8kidList()

getAfgcID

public java.lang.String getAfgcID()

get the list of afgc id

Returns:

the list of afgc id

getAfgcidList

public java.util.ArrayList getAfgcidList()

getAgrisActivedBy

public java.lang.String getAgrisActivedBy()

get the list of activated by locus list

Returns:

the activated by locus list

getAgrisActivedByList

public java.util.ArrayList getAgrisActivedByList()

getAgrisActives

public java.lang.String getAgrisActives()

get the list of activates locus list

Returns:

the activates locus list

getAgrisActivesList

public java.util.ArrayList getAgrisActivesList()

getAgrisAffectedBy

public java.lang.String getAgrisAffectedBy()

get the affected by locus list

Returns:

the affected by locus list

getAgrisAffectedByList

public java.util.ArrayList getAgrisAffectedByList()

getAgrisAffects

public java.lang.String getAgrisAffects()

get the affects locus list

Returns:

the affects locus list

getAgrisAffectsList

public java.util.ArrayList getAgrisAffectsList()

getAgrisCisBindingSite

public java.lang.String getAgrisCisBindingSite()

Returns:

the agrisCisBindingSiteList

getAgrisCisBindingSiteList

public java.util.ArrayList getAgrisCisBindingSiteList()

getAgrisReference

public java.lang.String getAgrisReference()

get the agris reference

Returns:

the agris reference

getAgrisReferenceList

public java.util.ArrayList getAgrisReferenceList()

getAgrisRepressedBy

public java.lang.String getAgrisRepressedBy()

get the repressed by locus list

Returns:

the repressed by locus list

getAgrisRepressedByList

public java.util.ArrayList getAgrisRepressedByList()

getAgrisRepresses

public java.lang.String getAgrisRepresses()

get the represses locus list

Returns:

the represses locus list

getAgrisRepressesList

public java.util.ArrayList getAgrisRepressesList()

getAracycPathway

public java.lang.String getAracycPathway()

get the list of aracyc pathway

Returns:

the list of aracyc pathway

getAracycPathwayList

public java.util.ArrayList getAracycPathwayList()

getComment

public java.lang.String getComment()

get the list of comment

Returns:

the list of comment

getCommentList

public java.util.ArrayList getCommentList()

getGoBiologicalProcess

public java.lang.String getGoBiologicalProcess()

get the list of biological process

Returns:

the list of biological process

getGoBiologicalProcessList

public java.util.ArrayList getGoBiologicalProcessList()

getGoBiologicalProcessWithLinks

public java.lang.String getGoBiologicalProcessWithLinks()

get the list of biological process with hyperlinks

Returns:

the list of biological process

getGoCellularComponent

public java.lang.String getGoCellularComponent()

get the list of cellular component

Returns:

the list of cellular component

getGoCellularComponentList

public java.util.ArrayList getGoCellularComponentList()

getGoCellularComponentWithLinks

public java.lang.String getGoCellularComponentWithLinks()

get the list of cellular component with hyperlinks

Returns:

the list of cellular component

getGoMolecularFunction

public java.lang.String getGoMolecularFunction()

get the list of molecular function

Returns:

the list of molecular function

getGoMolecularFunctionList

public java.util.ArrayList getGoMolecularFunctionList()

getGoMolecularFunctionWithLinks

public java.lang.String getGoMolecularFunctionWithLinks()

get the list of molecular function with hyperlinks

Returns:

the list of molecular function

getLocationConfideceMap

public java.util.Map getLocationConfideceMap()

getLocationConfidence

public java.lang.String getLocationConfidence(java.lang.String location)

Returns:

the location confidence. If nothing is there, return null

getLocusid

public java.lang.String getLocusid()

get the locus id

Returns:

Returns the locusid.

getMapmanBinId

public java.lang.String getMapmanBinId()

Returns:

the mapmanBinId

getMapmanBinIdList

public java.util.ArrayList getMapmanBinIdList()

getMapmanCategory

public java.lang.String getMapmanCategory()

Returns:

the mapmanCategory

getMapmanCategoryList

public java.util.ArrayList getMapmanCategoryList()

getMapmanDescription

public java.lang.String getMapmanDescription()

Returns:

the mapmanDescription

getMapmanDescriptionList

public java.util.ArrayList getMapmanDescriptionList()

getMetnetLocation

public java.lang.String getMetnetLocation()

get the list of metnet location

Returns:

Returns the list of metnetLocation.

getMetnetLocationList

public java.util.ArrayList getMetnetLocationList()

getMetnetPathway

public java.lang.String getMetnetPathway()

get the list of metnet pathway

Returns:

the list of metnet pathway

getMetnetPathwayList

public java.util.ArrayList getMetnetPathwayList()

getPredictedLocation

public java.lang.String getPredictedLocation()

get predicted location

Returns:

Returns the predictedLocation.

getReference

public java.lang.String getReference()

Returns:

the referenceList

getReferenceList

public java.util.ArrayList getReferenceList()

getTairAnnotation

public java.lang.String getTairAnnotation()

get the distinct annotation separated by semicolon

Returns:

the annotation

getTairAnnotationList

public java.util.ArrayList getTairAnnotationList()

getTooltip

public java.lang.String getTooltip()

getUniprotID

public java.lang.String getUniprotID()

get the uniprot id list separated by semicolon

Returns:

the uniprot ids

getUniprotidList

public java.util.ArrayList getUniprotidList()

getUniprotIDWithLinks

public java.lang.String getUniprotIDWithLinks()

get the uniprot id list separated by semicolon with hyperlinks

Returns:

the uniprot ids

setLocusid

public void setLocusid(java.lang.String locusid)

set the locus id

Parameters:

locusid - The locusid to set.

setPredictedLocation

public void setPredictedLocation(java.lang.String predictedLocation)

set predicted location

Parameters:

predictedLocation - The predictedLocation to set.

getGeneNameList

public java.util.ArrayList getGeneNameList()

getGeneName

public java.lang.String getGeneName()

get gene name list

Returns:

the synonym of locus