edu.iastate.metnet.export
Class AtGeneSearchObjectImpl

java.lang.Object
  edu.iastate.metnet.export.AtGeneSearchObjectImpl

All Implemented Interfaces:

AtGeneSearchObject, java.io.Serializable

public class AtGeneSearchObjectImpl
extends java.lang.Object
implements java.io.Serializable, AtGeneSearchObject

delegate the data access object AtGeneSearch and implement some interfaces

Author:

Jie Li

See Also:

Serialized Form

Constructor Summary

AtGeneSearchObjectImpl(AtGeneSearchLocusObject dao)
default constructor

Method Summary

void	addAffy25kID(java.lang.String affy25kid)
void	addAffy8kID(java.lang.String affy8kid)
void	addAfgcID(java.lang.String afgcid)
void	addAllAffy25kID(java.util.Collection collection)
void	addAllAffy8kID(java.util.Collection collection)
void	addAllAfgcID(java.util.Collection collection)
void	addAllAgrisActivatedBy(java.util.Collection collection)
void	addAllAgrisActivates(java.util.Collection collection)
void	addAllAgrisAffectedBy(java.util.Collection collection)
void	addAllAgrisAffects(java.util.Collection collection)
void	addAllAgrisCisBinindSite(java.util.Collection collection)
void	addAllAgrisReference(java.util.Collection collection)
void	addAllAgrisRepressedBy(java.util.Collection collection)
void	addAllAgrisRepresses(java.util.Collection collection)
void	addAllAracycPathway(java.util.Collection collection)
void	addAllComment(java.util.Collection collection)
void	addAllGeneName(java.util.Collection collection)
void	addAllMapmanBinId(java.util.Collection collection)
void	addAllMapmanCategory(java.util.Collection collection)
void	addAllMapmanDescription(java.util.Collection collection)
void	addAllMetnetLocation(java.util.Collection collection)
void	addAllMetnetPathway(java.util.Collection collection)
void	addAllReference(java.util.Collection collection)
void	addAllTairAnnotation(java.util.Collection collection)
void	addAllUniprotID(java.util.Collection collection)
void	addAracycPathway(java.lang.String aracycPathway)
void	addComment(java.lang.String comment)
void	addGoBiologicalProcess(GoTermID goBiologicalProcess)
void	addGoCellularComponent(GoTermID goCellularComponent)
void	addGoMolecularFunction(GoTermID goMolecularFunction)
void	addMetnetLocation(java.lang.String metnetLocation)
void	addMetnetPathway(java.lang.String metnetPathway)
void	addTairAnnotation(java.lang.String tairAnnotation)
void	addUniprotID(java.lang.String uniprotid)
boolean	equals(java.lang.Object obj)
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()
java.lang.String	getGoCellularComponent() get the list of cellular component
java.util.ArrayList	getGoCellularComponentList()
java.lang.String	getGoCellularComponentWithLinks()
java.lang.String	getGoMolecularFunction() get the list of molecular function
java.util.ArrayList	getGoMolecularFunctionList()
java.lang.String	getGoMolecularFunctionWithLinks()
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() get the TAIR reference information
java.lang.String	getTairAnnotation()
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()
int	hashCode()
void	setLocusid(java.lang.String locusid)
void	setPredictedLocation(java.lang.String predictedLocation)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

AtGeneSearchObjectImpl

public AtGeneSearchObjectImpl(AtGeneSearchLocusObject dao)

default constructor

Parameters:

dao - datagated object

Method Detail

addAffy25kID

public void addAffy25kID(java.lang.String affy25kid)

addAffy8kID

public void addAffy8kID(java.lang.String affy8kid)

addAfgcID

public void addAfgcID(java.lang.String afgcid)

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)

addAllAgrisActivates

public void addAllAgrisActivates(java.util.Collection collection)

addAllAgrisAffectedBy

public void addAllAgrisAffectedBy(java.util.Collection collection)

addAllAgrisAffects

public void addAllAgrisAffects(java.util.Collection collection)

addAllAgrisCisBinindSite

public void addAllAgrisCisBinindSite(java.util.Collection collection)

addAllAgrisReference

public void addAllAgrisReference(java.util.Collection collection)

addAllAgrisRepressedBy

public void addAllAgrisRepressedBy(java.util.Collection collection)

addAllAgrisRepresses

public void addAllAgrisRepresses(java.util.Collection collection)

addAllAracycPathway

public void addAllAracycPathway(java.util.Collection collection)

addAllComment

public void addAllComment(java.util.Collection collection)

addAllMapmanBinId

public void addAllMapmanBinId(java.util.Collection collection)

addAllMapmanCategory

public void addAllMapmanCategory(java.util.Collection collection)

addAllMapmanDescription

public void addAllMapmanDescription(java.util.Collection collection)

addAllMetnetLocation

public void addAllMetnetLocation(java.util.Collection collection)

addAllMetnetPathway

public void addAllMetnetPathway(java.util.Collection collection)

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)

addComment

public void addComment(java.lang.String comment)

addGoBiologicalProcess

public void addGoBiologicalProcess(GoTermID goBiologicalProcess)

addGoCellularComponent

public void addGoCellularComponent(GoTermID goCellularComponent)

addGoMolecularFunction

public void addGoMolecularFunction(GoTermID goMolecularFunction)

addMetnetLocation

public void addMetnetLocation(java.lang.String metnetLocation)

addMetnetPathway

public void addMetnetPathway(java.lang.String metnetPathway)

addTairAnnotation

public void addTairAnnotation(java.lang.String tairAnnotation)

addUniprotID

public void addUniprotID(java.lang.String uniprotid)

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

getAffy25kID

public java.lang.String getAffy25kID()

Description copied from interface: AtGeneSearchObject

get the list of affy25k id

Specified by:

getAffy25kID in interface AtGeneSearchObject

Returns:

the list of affy25k id

getAffy25kidList

public java.util.ArrayList getAffy25kidList()

Specified by:

getAffy25kidList in interface AtGeneSearchObject

Returns:

the affy25kidList

getAffy8kID

public java.lang.String getAffy8kID()

Description copied from interface: AtGeneSearchObject

get the list of affy8k id

Specified by:

getAffy8kID in interface AtGeneSearchObject

Returns:

the list of affy8k id

getAffy8kidList

public java.util.ArrayList getAffy8kidList()

Specified by:

getAffy8kidList in interface AtGeneSearchObject

Returns:

the affy8kidList

getAfgcID

public java.lang.String getAfgcID()

Description copied from interface: AtGeneSearchObject

get the list of afgc id

Specified by:

getAfgcID in interface AtGeneSearchObject

Returns:

the list of afgc id

getAfgcidList

public java.util.ArrayList getAfgcidList()

Specified by:

getAfgcidList in interface AtGeneSearchObject

Returns:

the afgcidList

getAgrisActivedBy

public java.lang.String getAgrisActivedBy()

Description copied from interface: AtGeneSearchObject

get the list of activated by locus list

Specified by:

getAgrisActivedBy in interface AtGeneSearchObject

Returns:

the activated by locus list

getAgrisActivedByList

public java.util.ArrayList getAgrisActivedByList()

Specified by:

getAgrisActivedByList in interface AtGeneSearchObject

Returns:

the agrisActivedByList

getAgrisActives

public java.lang.String getAgrisActives()

Description copied from interface: AtGeneSearchObject

get the list of activates locus list

Specified by:

getAgrisActives in interface AtGeneSearchObject

Returns:

the activates locus list

getAgrisActivesList

public java.util.ArrayList getAgrisActivesList()

Specified by:

getAgrisActivesList in interface AtGeneSearchObject

Returns:

the agrisActivesList

getAgrisAffectedBy

public java.lang.String getAgrisAffectedBy()

Description copied from interface: AtGeneSearchObject

get the affected by locus list

Specified by:

getAgrisAffectedBy in interface AtGeneSearchObject

Returns:

the affected by locus list

getAgrisAffectedByList

public java.util.ArrayList getAgrisAffectedByList()

Specified by:

getAgrisAffectedByList in interface AtGeneSearchObject

Returns:

the agrisAffectedByList

getAgrisAffects

public java.lang.String getAgrisAffects()

Description copied from interface: AtGeneSearchObject

get the affects locus list

Specified by:

getAgrisAffects in interface AtGeneSearchObject

Returns:

the affects locus list

getAgrisAffectsList

public java.util.ArrayList getAgrisAffectsList()

Specified by:

getAgrisAffectsList in interface AtGeneSearchObject

Returns:

the agrisAffectsList

getAgrisCisBindingSite

public java.lang.String getAgrisCisBindingSite()

getAgrisCisBindingSiteList

public java.util.ArrayList getAgrisCisBindingSiteList()

getAgrisReference

public java.lang.String getAgrisReference()

Description copied from interface: AtGeneSearchObject

get the agris reference

Specified by:

getAgrisReference in interface AtGeneSearchObject

Returns:

the agris reference

getAgrisReferenceList

public java.util.ArrayList getAgrisReferenceList()

Specified by:

getAgrisReferenceList in interface AtGeneSearchObject

Returns:

the agrisReferenceList

getAgrisRepressedBy

public java.lang.String getAgrisRepressedBy()

Description copied from interface: AtGeneSearchObject

get the repressed by locus list

Specified by:

getAgrisRepressedBy in interface AtGeneSearchObject

Returns:

the repressed by locus list

getAgrisRepressedByList

public java.util.ArrayList getAgrisRepressedByList()

Specified by:

getAgrisRepressedByList in interface AtGeneSearchObject

Returns:

the agrisRepressedByList

getAgrisRepresses

public java.lang.String getAgrisRepresses()

Description copied from interface: AtGeneSearchObject

get the represses locus list

Specified by:

getAgrisRepresses in interface AtGeneSearchObject

Returns:

the represses locus list

getAgrisRepressesList

public java.util.ArrayList getAgrisRepressesList()

Specified by:

getAgrisRepressesList in interface AtGeneSearchObject

Returns:

the agrisRepressesList

getAracycPathway

public java.lang.String getAracycPathway()

Description copied from interface: AtGeneSearchObject

get the list of aracyc pathway

Specified by:

getAracycPathway in interface AtGeneSearchObject

Returns:

the list of aracyc pathway

getAracycPathwayList

public java.util.ArrayList getAracycPathwayList()

Specified by:

getAracycPathwayList in interface AtGeneSearchObject

Returns:

the aracycPathwayList

getComment

public java.lang.String getComment()

Description copied from interface: AtGeneSearchObject

get the list of comment

Specified by:

getComment in interface AtGeneSearchObject

Returns:

the list of comment

getCommentList

public java.util.ArrayList getCommentList()

Specified by:

getCommentList in interface AtGeneSearchObject

Returns:

the commentList

getGoBiologicalProcess

public java.lang.String getGoBiologicalProcess()

Description copied from interface: AtGeneSearchObject

get the list of biological process

Specified by:

getGoBiologicalProcess in interface AtGeneSearchObject

Returns:

the list of biological process

getGoBiologicalProcessList

public java.util.ArrayList getGoBiologicalProcessList()

Specified by:

getGoBiologicalProcessList in interface AtGeneSearchObject

Returns:

the goBiologicalProcessList

getGoBiologicalProcessWithLinks

public java.lang.String getGoBiologicalProcessWithLinks()

getGoCellularComponent

public java.lang.String getGoCellularComponent()

Description copied from interface: AtGeneSearchObject

get the list of cellular component

Specified by:

getGoCellularComponent in interface AtGeneSearchObject

Returns:

the list of cellular component

getGoCellularComponentList

public java.util.ArrayList getGoCellularComponentList()

Specified by:

getGoCellularComponentList in interface AtGeneSearchObject

Returns:

the goCellularComponentList

getGoCellularComponentWithLinks

public java.lang.String getGoCellularComponentWithLinks()

getGoMolecularFunction

public java.lang.String getGoMolecularFunction()

Description copied from interface: AtGeneSearchObject

get the list of molecular function

Specified by:

getGoMolecularFunction in interface AtGeneSearchObject

Returns:

the list of molecular function

getGoMolecularFunctionList

public java.util.ArrayList getGoMolecularFunctionList()

Specified by:

getGoMolecularFunctionList in interface AtGeneSearchObject

Returns:

the goMolecularFunctionList

getGoMolecularFunctionWithLinks

public java.lang.String getGoMolecularFunctionWithLinks()

getLocationConfideceMap

public java.util.Map getLocationConfideceMap()

Specified by:

getLocationConfideceMap in interface AtGeneSearchObject

Returns:

the locationConfideceMap

getLocationConfidence

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

Specified by:

getLocationConfidence in interface AtGeneSearchObject

Returns:

the location confidence

getLocusid

public java.lang.String getLocusid()

Description copied from interface: AtGeneSearchObject

get the locus id

Specified by:

getLocusid in interface AtGeneSearchObject

Returns:

Returns the locusid.

getMapmanBinId

public java.lang.String getMapmanBinId()

Specified by:

getMapmanBinId in interface AtGeneSearchObject

Returns:

the mapmanBinId

getMapmanBinIdList

public java.util.ArrayList getMapmanBinIdList()

Specified by:

getMapmanBinIdList in interface AtGeneSearchObject

Returns:

the mapmanBinId

getMapmanCategory

public java.lang.String getMapmanCategory()

Specified by:

getMapmanCategory in interface AtGeneSearchObject

Returns:

the mapmanCategory

getMapmanCategoryList

public java.util.ArrayList getMapmanCategoryList()

Specified by:

getMapmanCategoryList in interface AtGeneSearchObject

Returns:

the mapmanCategory

getMapmanDescription

public java.lang.String getMapmanDescription()

Specified by:

getMapmanDescription in interface AtGeneSearchObject

Returns:

the mapmanDescription

getMapmanDescriptionList

public java.util.ArrayList getMapmanDescriptionList()

Specified by:

getMapmanDescriptionList in interface AtGeneSearchObject

Returns:

the mapmanDescription

getMetnetLocation

public java.lang.String getMetnetLocation()

Description copied from interface: AtGeneSearchObject

get the list of metnet location

Specified by:

getMetnetLocation in interface AtGeneSearchObject

Returns:

Returns the list of metnetLocation.

getMetnetLocationList

public java.util.ArrayList getMetnetLocationList()

Specified by:

getMetnetLocationList in interface AtGeneSearchObject

Returns:

the metnetLocationList

getMetnetPathway

public java.lang.String getMetnetPathway()

Description copied from interface: AtGeneSearchObject

get the list of metnet pathway

Specified by:

getMetnetPathway in interface AtGeneSearchObject

Returns:

the list of metnet pathway

getMetnetPathwayList

public java.util.ArrayList getMetnetPathwayList()

Specified by:

getMetnetPathwayList in interface AtGeneSearchObject

Returns:

the metnetPathwayList

getPredictedLocation

public java.lang.String getPredictedLocation()

Description copied from interface: AtGeneSearchObject

get predicted location

Specified by:

getPredictedLocation in interface AtGeneSearchObject

Returns:

Returns the predictedLocation.

getReference

public java.lang.String getReference()

getReferenceList

public java.util.ArrayList getReferenceList()

Description copied from interface: AtGeneSearchObject

get the TAIR reference information

Specified by:

getReferenceList in interface AtGeneSearchObject

Returns:

TAIR refence information

See Also:

TairReference

getTairAnnotation

public java.lang.String getTairAnnotation()

getTairAnnotationList

public java.util.ArrayList getTairAnnotationList()

Specified by:

getTairAnnotationList in interface AtGeneSearchObject

Returns:

the tairAnnotationList

getTooltip

public java.lang.String getTooltip()

getUniprotID

public java.lang.String getUniprotID()

Description copied from interface: AtGeneSearchObject

get the uniprot id list separated by semicolon

Specified by:

getUniprotID in interface AtGeneSearchObject

Returns:

the uniprot ids

getUniprotidList

public java.util.ArrayList getUniprotidList()

Specified by:

getUniprotidList in interface AtGeneSearchObject

Returns:

the uniprotidList

getUniprotIDWithLinks

public java.lang.String getUniprotIDWithLinks()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

setLocusid

public void setLocusid(java.lang.String locusid)

setPredictedLocation

public void setPredictedLocation(java.lang.String predictedLocation)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

addAllGeneName

public void addAllGeneName(java.util.Collection collection)

getGeneName

public java.lang.String getGeneName()

Description copied from interface: AtGeneSearchObject

get gene name list

Specified by:

getGeneName in interface AtGeneSearchObject

Returns:

the synonym of locus

getGeneNameList

public java.util.ArrayList getGeneNameList()

Specified by:

getGeneNameList in interface AtGeneSearchObject

Returns:

the geneNameList