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G

GB - Static variable in class edu.iastate.jtm.jmed.Limits
GBC - Static variable in class edu.iastate.jtm.jmed.Limits
GBWITHPARTS - Static variable in class edu.iastate.jtm.jmed.Limits
GDS - Static variable in class edu.iastate.jtm.jmed.Entrez
GENE - Static variable in class edu.iastate.jtm.jmed.Entrez
Gene - Interface in edu.iastate.metnet.datamodel.db: An Interface representing Gene.
genebankAccess - Variable in class edu.iastate.metnet.dao.SoybeanHomology: genebank access
GeneColor - Class in edu.iastate.metnet.birdseyeview: The GeneColor Class determines the color of a gene panel based on the experimental variance of the gene product.
GeneColor() - Constructor for class edu.iastate.metnet.birdseyeview.GeneColor
genedotCapacity - Variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
geneFamily - Variable in class edu.iastate.metnet.dao.SoybeanHomology: gene family
GeneImpl - Class in edu.iastate.metnet.datamodel.db: Class implementing interface Gene
GeneImpl(String) - Constructor for class edu.iastate.metnet.datamodel.db.GeneImpl
GeneList - Class in edu.iastate.metnet.metaomgraph
GeneList(String, boolean) - Constructor for class edu.iastate.metnet.metaomgraph.GeneList
GeneList(String, int[]) - Constructor for class edu.iastate.metnet.metaomgraph.GeneList
GeneName - Interface in edu.iastate.metnet.datamodel.attributes: Interface representing GeneName
GenePanel - Class in edu.iastate.metnet.birdseyeview.cellview: The GenePanel Class displays gene product information for the Cell View.
GenePanel(Annotation, Point, BirdsEyeView) - Constructor for class edu.iastate.metnet.birdseyeview.cellview.GenePanel
GenePanel(ArrayList, Point, BirdsEyeView) - Constructor for class edu.iastate.metnet.birdseyeview.cellview.GenePanel
GenePanel - Class in edu.iastate.metnet.birdseyeview: The GenePanel Class displays gene product information.
GenePanel(Annotation, BirdsEyeView) - Constructor for class edu.iastate.metnet.birdseyeview.GenePanel
GenePanel(ArrayList, BirdsEyeView) - Constructor for class edu.iastate.metnet.birdseyeview.GenePanel
GenePanelBuffer - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
GenePanelLayout - Class in edu.iastate.metnet.birdseyeview: The GenePanelLayout Class constructs a layout in which components are bounded by a square and the individual components are laid out in grid fashion starting in the center of the square.
GenePanelLayout(int, int) - Constructor for class edu.iastate.metnet.birdseyeview.GenePanelLayout
GenePanelLayout() - Constructor for class edu.iastate.metnet.birdseyeview.GenePanelLayout
GenePanelListener - Class in edu.iastate.metnet.birdseyeview: The GenePanelListener Class handles mouse events on the gene panel components.
GenePanelListener(BirdsEyeView, Annotation) - Constructor for class edu.iastate.metnet.birdseyeview.GenePanelListener: Constructor.
GenePanelListener(BirdsEyeView, ArrayList) - Constructor for class edu.iastate.metnet.birdseyeview.GenePanelListener: Constructor.
GenePanelListener - Class in edu.iastate.metnet.birdseyeview.goview: The GenePanelListener Class handles mouse events on the gene panel components in the GO views.
GenePanelListener(BirdsEyeView, Annotation) - Constructor for class edu.iastate.metnet.birdseyeview.goview.GenePanelListener: Constructor.
GenePanelSize - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
generateGUID(Object) - Static method in class edu.iastate.metnet.interfaces.MyFacadeUtil: A 32 byte GUID generator (Globally Unique ID).
generateGUID(Object) - Static method in class edu.iastate.metnet.interfaces.MyMetnetServiceUtil: A 32 byte GUID generator (Globally Unique ID).
generateGUID(Object) - Static method in class edu.iastate.metnet.interfaces.MyPaperUtil: A 32 byte GUID generator (Globally Unique ID).
generateGUID(Object) - Static method in class edu.iastate.metnet.utils.Utils: A 32 byte GUID generator (Globally Unique ID).
generateHistory(Integer, Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: generate the history and the version graph record
generateHistory(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: generate the history and the version graph record.
generateHistory(Integer, Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper: generate the history and the version graph record
generateHistory(Integer) - Method in interface edu.iastate.metnet.interfaces.MyPaper: generate the history and the version graph record.
generateNegativeBasedUUID() - Static method in class edu.iastate.metnet.utils.Utils: get the next unique id for the null vertex
generateSequenceBasedUUID() - Static method in class edu.iastate.biocyc.utils.BiocycUtils: get the next value of the normal graph element
generateSoybeanNetwork() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: generate soybean network from arabidopsis network
generateSoybeanNetwork() - Method in interface edu.iastate.metnet.interfaces.MyPaper: generate soybean network from arabidopsis network
generateSynonyms() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: generate the synonyms
generateSynonyms() - Method in interface edu.iastate.metnet.interfaces.MyPaper: generate the synonyms
generateSynonyms() - Method in class edu.iastate.metnet.ui.AbbreviationRules
GenericTree - Class in edu.iastate.metnet.aracyc: tree structure
GenericTree() - Constructor for class edu.iastate.metnet.aracyc.GenericTree
geneSearch(String) - Method in class edu.iastate.metnet.hivemindService.Browser: Search a gene using AtGeneSearch, opens broweser to the result page
GeneType - Static variable in class edu.iastate.metnet.birdseyeview.Annotation
GENOME - Static variable in class edu.iastate.jtm.jmed.Entrez
GENOMEPRJ - Static variable in class edu.iastate.jtm.jmed.Entrez
GENSAT - Static variable in class edu.iastate.jtm.jmed.Entrez
GEO - Static variable in class edu.iastate.jtm.jmed.Entrez
get(String) - Method in class edu.iastate.jtm.dic.Trie: Find and return the value associated with a key.
get() - Method in class edu.iastate.jtm.gui.SwingWorker: Return the value created by the construct method.
get() - Method in class edu.iastate.metnet.metaomgraph.AnimatedSwingWorker: Return the value created by the construct method.
get() - Method in class edu.iastate.metnet.metaomgraph.SwingWorker: Return the value created by the construct method.
get() - Method in class edu.iastate.metnet.utils.SwingWorker: Return the value created by the construct method.
get() - Method in class edu.iastate.metnet.utils.SwingWorker2: Return the value created by the construct method, waiting if necessary until it is ready.
get(OutputStream, String) - Method in class fcmodeler.pathbinder.MedLeaseClient
get(String, String) - Method in class fcmodeler.pathbinder.MedLeaseClient
get(String) - Method in class fcmodeler.pathbinder.MedLeaseClient
get(File, FTPFile) - Method in class fcmodeler.pathbinder.MedLeaseClient
GET_FASTA - Static variable in class edu.iastate.jtm.jmed.EFetch
GET_FASTA - Static variable in class edu.iastate.jtm.jmed.PubMedFetcher
GET_XML - Static variable in class edu.iastate.jtm.jmed.EFetch
GET_XML - Static variable in class edu.iastate.jtm.jmed.PubMedFetcher
getA() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the account name
getA() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the account name
getAB(HiddenLink.Link, Entity[]) - Method in class fcmodeler.pathbinder.HiddenLink
getAbbreviation() - Method in class edu.iastate.metnet.dao.AbbreviationObject
getAbbreviation() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitabbreviation: Return the value of the Abbreviation column.
getAbbreviation() - Method in class edu.iastate.metnet.hibernate.Entityabbreviation
getAbbreviation() - Method in class edu.iastate.metnet.hibernate.EntityabbreviationKey: Returns the value of the abbreviation property.
getAbbreviationObject(int) - Method in class edu.iastate.metnet.model.AbbreviationTableModel
getAbbreviationObjectList() - Method in class edu.iastate.metnet.hibernate.Blockunit
getAbbreviationRules() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the abbreviation rule as "object list", mainly for SQL->Java Object
getAbbreviationRules() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the abbreviation rule as "object list", mainly for SQL->Java Object
getAbbreviations() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getAbbreviations() - Method in class edu.iastate.metnet.hibernate.Blockunit: abbreviation
getAbbreviations() - Method in class edu.iastate.metnet.hibernate.Entity: abbreviation
getAbbreviations() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject: abbreviation list of the blockunit
getAbbreviations() - Method in class edu.iastate.metnet.model.CompositionBlockunit
getAbbreviations() - Method in class edu.iastate.metnet.model.SelectedBlockunit
getAboutIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getAbstract(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getAbstract_() - Method in class edu.iastate.metnet.dao.TairReferenceObject
getAbstract_() - Method in interface edu.iastate.metnet.hiveface.TairReference
getAc() - Method in class edu.iastate.metnet.hibernate.ExternaldbKey: Returns the value of the ac property.
getAccessionInt() - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession: Return the value of the accession_int column.
getActionTime() - Method in class edu.iastate.metnet.dao.HistoryInformation
getActionType() - Method in class edu.iastate.metnet.dao.HistoryInformation
getActivatingcompound() - Method in class edu.iastate.metnet.hibernate.BrendaactivatingcompoundKey: Returns the value of the activatingcompound property.
getActiveColumn() - Method in class fcmodeler.pathbinder.gui.EntityPanel
getActiveProject() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph: Fetches the active MetaOmProject.
getActiveTable() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph: Fetches the MetaOmTablePanel for the active project.
getActiveValues() - Method in class edu.iastate.metnet.metaomgraph.DualListPanel
getActiveValues() - Method in class edu.iastate.metnet.metaomgraph.DualTablePanel: Fetches the values in the active table
getAddEntityForm() - Method in class edu.iastate.metnet.ui.MainWindow2: the window instance of Edit Entity window
getAddPathwayController() - Method in class edu.iastate.metnet.ui.AddPathwayForm
getAddPathwayForm() - Method in class edu.iastate.metnet.controller.AddPathwayController
getAddPathwayModel() - Method in class edu.iastate.metnet.controller.AddPathwayController
getAffiliation() - Method in class edu.iastate.metnet.hibernate.AbstractUser: Return the value of the Affiliation column.
getAffy25kID() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of affy25k id
getAffy25kID() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getAffy25kID() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getAffy25kID() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAffy25kID() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of affy25k id
getAffy25kidList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAffy25kidList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAffy25kidList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAffy8kID() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of affy8k id
getAffy8kID() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getAffy8kID() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getAffy8kID() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAffy8kID() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of affy8k id
getAffy8kidList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAffy8kidList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAffy8kidList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAfgcID() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of afgc id
getAfgcID() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getAfgcID() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getAfgcID() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAfgcID() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of afgc id
getAfgcidList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAfgcidList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAfgcidList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAgrisActivedBy() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of activated by locus list
getAgrisActivedBy() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisActivedBy() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of activated by locus list
getAgrisActivedByList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisActivedByList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisActivedByList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAgrisActives() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of activates locus list
getAgrisActives() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisActives() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of activates locus list
getAgrisActivesList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisActivesList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisActivesList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAgrisAffectedBy() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the affected by locus list
getAgrisAffectedBy() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisAffectedBy() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the affected by locus list
getAgrisAffectedByList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisAffectedByList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisAffectedByList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAgrisAffects() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the affects locus list
getAgrisAffects() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisAffects() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the affects locus list
getAgrisAffectsList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisAffectsList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisAffectsList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAgrisCisBindingSite() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisCisBindingSite() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisCisBindingSiteList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisCisBindingSiteList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisReference() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the agris reference
getAgrisReference() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisReference() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the agris reference
getAgrisReferenceList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisReferenceList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisReferenceList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAgrisRepressedBy() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the repressed by locus list
getAgrisRepressedBy() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisRepressedBy() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the repressed by locus list
getAgrisRepressedByList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisRepressedByList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisRepressedByList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAgrisRepresses() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the represses locus list
getAgrisRepresses() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisRepresses() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the represses locus list
getAgrisRepressesList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAgrisRepressesList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAgrisRepressesList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getAlignMap() - Method in class edu.iastate.metnet.dao.AlignmentObject
getAlignment() - Method in interface edu.iastate.metnet.dao.MultiPathwayGraph
getAlignment() - Method in class edu.iastate.metnet.dao.MultiPathwayGraphImpl
getAlignment() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm
getAlignmentIndex() - Method in class edu.iastate.metnet.ui.PathwayEditor
getAlignmentMbidMap() - Method in interface edu.iastate.metnet.dao.PathwayAlignment: get the mapping betweem member blockid since the isomorphism is a one-to-one mapping, we only need Map data structure
getAlignmentMbidMap() - Method in class edu.iastate.metnet.dao.PathwayAlignmentImpl
getAll() - Method in class edu.iastate.jtm.SentenceParser
getAllEbidEidMap() - Method in interface edu.iastate.metnet.dao.PathwayGraph: get the entity blockid->entityid mapping for comparison
getAllEbidEidMap() - Method in class edu.iastate.metnet.dao.PathwayGraphImpl: get the entity blockid->entityid mapping for comparison
getAllEbidList() - Method in interface edu.iastate.metnet.dao.PathwayGraph: get all entity node bid list
getAllEbidList() - Method in class edu.iastate.metnet.dao.PathwayGraphImpl: get all entity node bid list
getAllElementNodeBlockIDList(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get all member element node's blockid list for client to test the pathway membership
getAllElementNodeBlockIDList(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get all member element node's blockid list for client to test the pathway membership
getAllGenesLocusID() - Static method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame
getAllGenesLocusID() - Static method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame
getAllGenesLocusID() - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
getAllIbidList() - Method in interface edu.iastate.metnet.dao.PathwayGraph: get all interaction node bid list
getAllIbidList() - Method in class edu.iastate.metnet.dao.PathwayGraphImpl: get all interaction node bid list
getAllIbidSet() - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph: get all interaction blockid in the mapping view
getAllLocationInfo() - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method retrieves all of the cellular location information from the database.
getAllLocationInfo() - Method in class edu.iastate.metnet.hivemindService.AnnotationService: returns all locations in MetNetDB
getAllLocationList() - Method in class edu.iastate.metnet.export.GraphExporterImpl
getAllLocationList() - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get all location in the database
getAllLocationList() - Method in class edu.iastate.metnet.hivemindService.RequestGeneData
getAllLocationMap() - Static method in class edu.iastate.metnet.hivemindService.AnnotationService
getAllNames() - Method in class edu.iastate.metnet.dao.ChebiOntologyName
getAllowsChildren() - Method in class edu.iastate.jtm.jmed.Query.CompositeTerm
getAllowsChildren() - Method in class edu.iastate.jtm.jmed.Query.SimpleTerm
getAllowsChildren() - Method in class fcmodeler.pathbinder.gui.VerbNode
getAllPathwayList() - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
getAllPathwayNameList() - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
getAllPathwayObjectList2(String) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get all pathway objects in the database for displaying in pathway selector
getAllPathwayObjectList2(String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get all pathway objects in the database for displaying in pathway selector
getAllText() - Method in class edu.iastate.jtm.util.SlidingWindow
getAllTrueRows() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
getAllUserList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get all users in the system
getAllUserList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get all users in the system
getAllUserList() - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: get all users in the system
getAllUserList() - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: get all users in the system
getAnnotation() - Method in class edu.iastate.metnet.birdseyeview.AnnotationTextPanel: This method returns the annotation data associated with this panel.
getAnnotation() - Method in class edu.iastate.metnet.birdseyeview.cellview.GenePanel: This method returns the description of this gene product.
getAnnotation() - Method in class edu.iastate.metnet.birdseyeview.GenePanel: This method returns the description of this gene product.
getAnnotationDatabase() - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Return the value of the annotation_database column.
getAnnotations() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: This method returns the gene product annotation list.
getAnnotationTable() - Static method in class edu.iastate.metnet.hivemindService.AnnotationService
getAnnotationText() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
getAnnotator() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
getAppend1Box() - Method in class fcmodeler.pathbinder.gui.EntityPanel
getAppend2Box() - Method in class fcmodeler.pathbinder.gui.EntityPanel
getAracycid() - Method in class edu.iastate.metnet.aracyc.AracycEntity: return the aracyc unique id
getAracycID() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
getAracycid() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Return the value of the AracycID column.
getAracycId() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getAracycId() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getAracycId() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
getAracycPathway() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of aracyc pathway
getAracycPathway() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getAracycPathway() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getAracycPathway() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAracycPathway() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of aracyc pathway
getAracycPathwayList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getAracycPathwayList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getAracycPathwayList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getArgs() - Method in class edu.iastate.metnet.launch.RunCytoscape
getArrayElementName() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Return the value of the array_element_name column.
getArrayElementName() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Return the value of the array_element_name column.
getArrayElementName() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the array_element_name column.
getArrayElementType() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Return the value of the array_element_type column.
getArrayElementType() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Return the value of the array_element_type column.
getArrayElementType() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the array_element_type column.
getAscendant(Object) - Method in class edu.iastate.metnet.aracyc.GenericTree: get the ascendant of te current node
getAspect() - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Return the value of the aspect column.
getAtGeneSearchAttributeList() - Method in class edu.iastate.metnet.export.GraphExporterImpl
getAtGeneSearchAttributeList() - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get all attributes in the AtGeneSearch application
getAtGeneSearchLocusObject(int) - Method in class edu.iastate.metnet.model.LocusInformationTableModel: get the row data object
getAtGeneSearchObject(String) - Method in class edu.iastate.metnet.export.GraphExporterImpl
getAtGeneSearchObject(String) - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get one data object based on the affyId
getAthLocus() - Method in class edu.iastate.metnet.dao.SoybeanHomology
getAttr(Class<A>) - Method in interface edu.iastate.metnet.datamodel.Entity
getAttr(Class<A>) - Method in class edu.iastate.metnet.datamodel.EntityImpl
getAttributeList() - Method in class edu.iastate.metnet.hivemindService.RequestGene: Returns the list of attributes that exist in a gene.
getAttributeList() - Method in class edu.iastate.metnet.hivemindService.RequestGeneData
getAttributeMap(GraphCell, Rectangle2D) - Method in class edu.iastate.reload.ui.MyMarqueeHandler: You can override how the view attributes of the cell are created
getAttributes() - Method in class edu.iastate.metnet.soft.Entity
getAuthorFullnames(Element, boolean) - Static method in class edu.iastate.jtm.jmed.CitationManager
getAuthorInitials(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getAuthors() - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Return the value of the AUTHORS column.
getAutoscrollInsets() - Method in class edu.iastate.metnet.metaomgraph.ListTree
getAvgIntensity() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the avg_intensity column.
getAvgIntensityStdErr() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the avg_intensity_std_err column.
getAvgLogRatio() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the avg_log_ratio column.
getAvgLogRatioStdErr() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the avg_log_ratio_std_err column.
getBackground() - Method in class edu.iastate.metnet.birdseyeview.AbstractView: Subclasses must indicate their background color so the parent can blend in if the display area is bigger than the view.
getBackground() - Method in class edu.iastate.metnet.birdseyeview.cellview.CellView
getBackground() - Method in class edu.iastate.metnet.birdseyeview.goview.GoView
getBackground() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.PathwayView
getBackIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getBackPlayIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getBasicInformation(Map) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: get the basic information, name, location nad biological type for collection of blockid
getBasicInformation(Map) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: get the basic information, name, location nad biological type for collection of blockid
getBC(HiddenLink.Link, Entity[]) - Method in class fcmodeler.pathbinder.HiddenLink
getBeanAddIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getBestJournalId(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getBiocycId() - Method in class edu.iastate.biocyc.dao.rdb.ClassName
getBiocycId() - Method in class edu.iastate.metnet.hibernate.AbstractClassName
getBiologicalType(DirectedGraph) - Static method in class edu.iastate.biocyc.dao.txt.BiocycClass: this is an extension of protein type detection.
getBiologicalType() - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
getBiologicalType() - Method in class edu.iastate.metnet.dao.HistoryInformation
getBiologicalType() - Method in interface edu.iastate.metnet.dao.PathwayElementNode: get the biological type for the data instance
getBiologicalType(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get thebiological type like entitywithcontext, interaction or pathway
getBiologicalType(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get thebiological type like entitywithcontext, interaction or pathway
getBirdsEyeView() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: This method returns the component that contains the Bird's Eye View.
getBirdsEyeView() - Static method in class edu.iastate.metnet.launch.LaunchMetNet
getBirdsEyeViewFrame() - Static method in class edu.iastate.metnet.launch.LaunchMetNet
getBlack() - Method in class edu.iastate.metnet.ui.Oasis
getBlack() - Method in class edu.iastate.metnet.ui.PropertiesMetalTheme
getBlack() - Method in class edu.iastate.reload.skin.OceanThemeX: Returns the OceanTheme's color for black, the RGB value (51, 51, 51).
getBlack() - Method in class javax.swing.plaf.metal.OceanTheme: Returns the OceanTheme's color for black, the RGB value (51, 51, 51).
getBlankValue() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
getBlankValue() - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog
getBlockId() - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
getBlockid() - Method in class edu.iastate.metnet.dao.Candidate
getBlockId() - Method in interface edu.iastate.metnet.dao.HistoryBlockunit: get the blockid
getBlockId() - Method in class edu.iastate.metnet.dao.HistoryBlockunitImpl
getBlockId() - Method in class edu.iastate.metnet.dao.HistoryInformation
getBlockid() - Method in class edu.iastate.metnet.dao.InteractionInformation
getBlockId() - Method in class edu.iastate.metnet.dao.MyVersionNode
getBlockid() - Method in class edu.iastate.metnet.dao.PathwayA
getBlockId() - Method in interface edu.iastate.metnet.dao.PathwayElementNode: the blockid of the blockunit (version)
getBlockid() - Method in class edu.iastate.metnet.dao.ZVertex
getBlockid() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getBlockid() - Method in class edu.iastate.metnet.graphmodel.MetaphorTypeInformation
getBlockid() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Return the simple primary key value that identifies this object.
getBlockid() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitabbreviation: Return the simple primary key value that identifies this object.
getBlockid() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitconfidence: Return the simple primary key value that identifies this object.
getBlockId() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getBlockId() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getBlockId() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
getBlockid() - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Return the simple primary key value that identifies this object.
getBlockid() - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Return the simple primary key value that identifies this object.
getBlockid() - Method in class edu.iastate.metnet.hibernate.Blockunitcomment
getBlockid() - Method in class edu.iastate.metnet.hibernate.BlockunitcommentKey: Returns the value of the blockid property.
getBlockid() - Method in class edu.iastate.metnet.hibernate.Blockunitref
getBlockid() - Method in class edu.iastate.metnet.hibernate.BlockunitrefKey: Returns the value of the blockid property.
getBlockid() - Method in class edu.iastate.metnet.hibernate.Blockunitsynonym
getBlockID() - Method in class edu.iastate.metnet.hibernate.BlockunitSynonymCandidate
getBlockid() - Method in class edu.iastate.metnet.hibernate.BlockunitsynonymKey: Returns the value of the blockid property.
getBlockid() - Method in class edu.iastate.metnet.hibernate.Entitywithcontext: Returns the value of the blockid property.
getBlockid() - Method in class edu.iastate.metnet.hibernate.EntitywithcontextKey: Returns the value of the blockid property.
getBlockid() - Method in class edu.iastate.metnet.hibernate.GroupShareKey: Returns the value of the blockid property.
getBlockid() - Method in class edu.iastate.metnet.hibernate.Interactionparts
getBlockid() - Method in class edu.iastate.metnet.hibernate.InteractionpartsKey: Returns the value of the blockid property.
getBlockid() - Method in class edu.iastate.metnet.hibernate.Pathwayparts
getBlockid() - Method in class edu.iastate.metnet.hibernate.PathwaypartsKey: Returns the value of the blockid property.
getBlockid() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject: blockid of the blockunit
getBlockID() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo
getBlockid() - Method in class edu.iastate.metnet.model.CheckCandidate
getBlockid() - Method in class edu.iastate.metnet.model.CompositionBlockunit
getBlockID() - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
getBlockid() - Method in class edu.iastate.metnet.model.GroupShareTableModel
getBlockid() - Method in class edu.iastate.metnet.model.IntermediumEntityInformation
getBlockid() - Method in class edu.iastate.metnet.model.SelectedBlockunit
getBlockIdList(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: get the blockid based on the entityid
getBlockIdList(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: get the blockid based on the entityid
getBlockunit() - Method in class edu.iastate.biocyc.dao.rdb.BlockunitChoice
getBlockunit() - Method in interface edu.iastate.metnet.dao.IMetnetBlockUnit: get the blockunit, can be changed in the user interface
getBlockunit() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
getBlockunit() - Method in class edu.iastate.metnet.model.AbstractBlockunitDecorator
getBlockunit() - Method in class edu.iastate.metnet.model.CompositionBlockunit
getBlockunit(int) - Method in class edu.iastate.metnet.model.EntityNameModel
getBlockunit() - Method in class edu.iastate.metnet.model.SelectedBlockunit
getBlockunitabbreviationSet() - Method in class edu.iastate.metnet.hibernate.Blockunit
getBlockunitComment(int) - Method in class edu.iastate.reload.model.CommentTableModel
getBlockunitcommentSet() - Method in class edu.iastate.metnet.hibernate.Blockunit
getBlockunitconfidence() - Method in class edu.iastate.metnet.hibernate.Blockunit
getBlockUnitConfidence(int) - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
getBlockunitMap(Collection) - Method in class edu.iastate.metnet.graphmodel.PathwayModel
getBlockunitReference(int) - Method in class edu.iastate.reload.model.ReferenceTableModel
getBlockunitrefSet() - Method in class edu.iastate.metnet.hibernate.Blockunit
getBlockunitSynonym(int) - Method in class edu.iastate.reload.model.SynonymTableModel
getBlockunitsynonymSet() - Method in class edu.iastate.metnet.hibernate.Blockunit
getBmid() - Method in class edu.iastate.metnet.hibernate.AbstractUser: Return the value of the BMID column.
getBridgeMap() - Method in class edu.iastate.metnet.graphmodel.PathwayModel
getBtnNewEdge() - Method in class edu.iastate.reload.ui.NetworkEditForm
getBtnNewInteraction() - Method in class edu.iastate.reload.ui.NetworkEditForm
getBuffer() - Method in class edu.iastate.jtm.util.RunningBuffer
getBuffer() - Method in interface edu.iastate.metnet.dao.IMetnetBlockUnit: get the buffered blockunit, never touched for comparison when things are being saved
getBuffer() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit: get the buffered blockunit, never touched for comparison when things are being saved
getButtonPanel() - Method in class edu.iastate.metnet.birdseyeview.RootPanel
getCandidate() - Method in class edu.iastate.metnet.dao.Candidate
getCandidate() - Method in interface edu.iastate.metnet.interfaces.MyFacade
getCandidate(int) - Method in interface edu.iastate.metnet.interfaces.MyFacade
getCandidate() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
getCandidate(int) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
getCandidate() - Method in class edu.iastate.metnet.model.CheckCandidate
getCandy() - Method in class edu.iastate.metnet.model.CheckCandidate
getCapacity() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
getCapacity() - Method in class edu.iastate.metnet.birdseyeview.ViewInfo
getCAS() - Method in class edu.iastate.metnet.aracyc.AracycCompound
getCasList() - Method in class edu.iastate.metnet.dao.ChebiObject
getCasList() - Method in class edu.iastate.metnet.export.MetaboliteObjectImpl
getCasList() - Method in interface edu.iastate.metnet.hiveface.MetaboliteObject
getCasListX() - Method in class edu.iastate.metnet.dao.ChebiObject
getCasListX() - Method in class edu.iastate.metnet.export.MetaboliteObjectImpl
getCasListX() - Method in interface edu.iastate.metnet.hiveface.MetaboliteObject
getCategoryGraph() - Method in class edu.iastate.metnet.ui.ClassEditForm
getCellEditor(int, int) - Method in class edu.iastate.metnet.ui.MyJTableEx
getCellEditorValue() - Method in class edu.iastate.jtm.assistant.QueryTreeCellEditor
getCellEditorValue() - Method in class edu.iastate.metnet.StripedTable.ColorEditor
getCellLocation(String) - Method in class edu.iastate.metnet.birdseyeview.cellview.PanelLocationsFactory
getChart() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
getChartPanel() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
getChebiAccession() - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Return the value of the chebi_accession column.
getChebiCid() - Method in class edu.iastate.metnet.export.MetaboliteObjectImpl
getChebiCid() - Method in interface edu.iastate.metnet.hiveface.MetaboliteObject
getChebiDbAccession() - Method in class edu.iastate.metnet.dao.ChebiObject
getChebiDbAccession() - Method in class edu.iastate.metnet.export.MetaboliteObjectImpl
getChebiDbAccession() - Method in interface edu.iastate.metnet.hiveface.MetaboliteObject
getChebiFormula() - Method in class edu.iastate.metnet.dao.ChebiObject
getChebiFormula() - Method in class edu.iastate.metnet.export.MetaboliteObjectImpl
getChebiFormula() - Method in interface edu.iastate.metnet.hiveface.MetaboliteObject
getChebiid() - Method in class edu.iastate.metnet.dao.ChebiOntologyName
getChebiidName() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the map of id and name
getChebiidName() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the map of id and name
getChebiInChI() - Method in class edu.iastate.metnet.dao.ChebiObject
getChebiInChI() - Method in class edu.iastate.metnet.export.MetaboliteObjectImpl
getChebiInChI() - Method in interface edu.iastate.metnet.hiveface.MetaboliteObject
getChebiName() - Method in class edu.iastate.metnet.dao.ChebiObject
getChebiName() - Method in class edu.iastate.metnet.export.MetaboliteObjectImpl
getChebiName() - Method in interface edu.iastate.metnet.hiveface.MetaboliteObject
getChebiObjectByBlockID(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the chebi information based on the compound id.
getChebiObjectByBlockID(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the chebi information based on the compound id.
getChebiObjectByBlockID(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: get the chebi information based on the compound id.
getChebiObjectByBlockID(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: get the chebi information based on the compound id.
getChebiOntologyName(int) - Method in class edu.iastate.metnet.model.ChebiOntologyTableModel
getChebiSmiles() - Method in class edu.iastate.metnet.dao.ChebiObject
getChebiSmiles() - Method in class edu.iastate.metnet.export.MetaboliteObjectImpl
getChebiSmiles() - Method in interface edu.iastate.metnet.hiveface.MetaboliteObject
getCheckBoxList() - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
getChecked() - Method in class edu.iastate.metnet.mapbuilder.TrivialNodePanel
getCheckedBoxes() - Method in class edu.iastate.metnet.mapbuilder.SelectPathwayPanel: Returns an ArrayList containing only the checked pathway boxes.
getCheckedString() - Method in class edu.iastate.metnet.mapbuilder.TrivialNodePanel
getChild(Element, int) - Method in class edu.iastate.jtm.util.ParenParser
getChild(Object, int) - Method in class edu.iastate.metnet.model.CategoryTreeModel: return the child node at the index position.
getChildAt(int) - Method in class fcmodeler.pathbinder.gui.VerbNode
getChildCount(Element) - Method in class edu.iastate.jtm.util.ParenParser
getChildCount(Object) - Method in class edu.iastate.metnet.model.CategoryTreeModel: get the size of the children
getChildCount() - Method in class fcmodeler.pathbinder.gui.VerbNode
getChildNodeIDs() - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode: This method returns the IDs of the child nodes
getChildren() - Method in class edu.iastate.jtm.dic.AbstractTrieNode: Return a node's child node array.
getChildren() - Method in interface edu.iastate.jtm.dic.TrieNode: Return a node's child node array.
getChildren(Object) - Method in class edu.iastate.metnet.aracyc.GenericTree: get the child node
getChildren() - Method in class edu.iastate.metnet.birdseyeview.goview.GoTerm: Returns the children.
getChildren(CellView) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: get the children cell view of one cell view
getChildren() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.TreeNode: get the children
getChildToParentMap() - Method in class edu.iastate.metnet.dao.RelationMap
getChloroplastTransitPeptideScore() - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Return the value of the chloroplast_transit_peptide_score column.
getChoice(int) - Method in class edu.iastate.biocyc.ui.PathwayChoiceModel: get the selected object
getChromosome() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Return the value of the chromosome column.
getChromosome() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Return the value of the chromosome column.
getChromosome() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the chromosome column.
getChromosome() - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Return the value of the chromosome column.
getCidList() - Method in class edu.iastate.metnet.dao.ChebiObject
getCidListX() - Method in class edu.iastate.metnet.dao.ChebiObject
getCitation(int) - Method in class edu.iastate.jtm.assistant.CitationPool
getCitationList() - Method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement: get the pubmed id list
getCitations() - Method in class edu.iastate.metnet.aracyc.AracycEntity: return the citations
getClassFilename() - Method in class edu.iastate.biocyc.io.BiocycImporter
getClassId() - Method in class edu.iastate.biocyc.dao.rdb.ClassName
getClassId() - Method in class edu.iastate.metnet.dao.CategoryNode
getClassId() - Method in class edu.iastate.metnet.export.PathwayCategoryNodeImpl
getClassId() - Method in class edu.iastate.metnet.hibernate.AbstractClassName
getClassId() - Method in interface edu.iastate.metnet.hiveface.PathwayCategoryNode
getClassification() - Method in class edu.iastate.metnet.hibernate.AbstractUser: Return the value of the Classification column.
getClassNet(boolean) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get current class network
getClassNet(boolean) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get current class network
getClassNet(boolean) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: get current class network
getClassNet(boolean) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: get current class network
getClassNet() - Method in class edu.iastate.metnet.model.CategoryTreeModel
getClassTree(String) - Method in class edu.iastate.metnet.aracyc.ClassesDatReader: return the classtree of the parentid and childid of class
getCode(char) - Static method in class edu.iastate.jtm.gui.KeyCoder
getCode() - Method in class edu.iastate.metnet.hibernate.AbstractCodeconfidence: Return the simple primary key value that identifies this object.
getCode() - Method in class edu.iastate.metnet.hibernate.AbstractCodedatasource: Return the simple primary key value that identifies this object.
getCode() - Method in class edu.iastate.metnet.hibernate.AbstractCodeentitytype: Return the simple primary key value that identifies this object.
getCode() - Method in class edu.iastate.metnet.hibernate.AbstractCodeinteractiontype: Return the simple primary key value that identifies this object.
getCode() - Method in class edu.iastate.metnet.hibernate.AbstractCodelocation: Return the simple primary key value that identifies this object.
getCode() - Method in class edu.iastate.metnet.hibernate.AbstractCodeorganism: Return the simple primary key value that identifies this object.
getCode() - Method in class edu.iastate.metnet.hibernate.AbstractCodereferencetype: Return the simple primary key value that identifies this object.
getCodeconfidenceList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the codeconfidence
getCodeconfidenceList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the codeconfidence
getCodedatasourceList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the codeconfidence
getCodedatasourceList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the codeconfidence
getCodeentitytypeList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the codeentitytype
getCodeentitytypeList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the codeentitytype
getCodeinteractiontypeList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the codeinteractiontype
getCodeinteractiontypeList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the codeinteractiontype
getCodelocationList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the codelocation
getCodelocationList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the codelocation
getCodelocationList() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getCodeorganismList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the codeorganism
getCodeorganismList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the codeorganism
getCodePresentationSQL() - Method in class edu.iastate.metnet.db.TableCodeConfidence
getCodereferencetypeList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the codereferencetype
getCodereferencetypeList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the codereferencetype
getCoderule() - Method in class edu.iastate.metnet.hibernate.Abbreviationrules: this is a customized method, so use interface is ok.
getCoderuleList() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the coderule
getCoderuleList() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the coderule
getCoderules() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the coderule as "object list", mainly for SQL->Java Object
getCoderules() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the coderule as "object list", mainly for SQL->Java Object
getCodes() - Method in class edu.iastate.metnet.birdseyeview.cellview.CellularLocation: Returns the codes.
getCoefficient(String) - Method in class edu.iastate.biocyc.dao.txt.BiocycProtein
getCoefficient(String) - Method in class edu.iastate.biocyc.dao.txt.BiocycReaction
getCoefficient() - Method in class edu.iastate.metnet.hibernate.AbstractInteractionparts: Return the value of the Coefficient column.
getCoefficient() - Method in class edu.iastate.metnet.model.EntityPart
getCoefficientMap(ArrayList, ArrayList) - Method in interface edu.iastate.metnet.interfaces.MyFacade: collect the coeffiecient given the interaction and entitywithlocation
getCoefficientMap(ArrayList, ArrayList) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: collect the coeffiecient given the interaction and entitywithlocation
getCoeffMap() - Method in class edu.iastate.metnet.graphmodel.PathwayModel
getCofactor() - Method in class edu.iastate.metnet.hibernate.BrendacofactorKey: Returns the value of the cofactor property.
getColArray() - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog
getColor() - Method in class edu.iastate.metnet.ColorChooseButton
getColor() - Method in class edu.iastate.metnet.metaomgraph.chart.RangeMarker
getColor() - Method in class edu.iastate.metnet.metaomgraph.PolygonPanel.BouncingPolygon
getColor(Point) - Method in class edu.iastate.metnet.metaomgraph.test.ColorPicker
getColor1() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.
getColor1() - Method in class edu.iastate.metnet.metaomgraph.ProjectPropertiesPanel
getColor2() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the default color used for the top-right portion of new MetaOmChartPanels' background gradient.
getColor2() - Method in class edu.iastate.metnet.metaomgraph.ProjectPropertiesPanel
getColorMap(JGraph) - Method in class edu.iastate.metnet.graphmodel.ComparativeMetaphor: assign the color map
getColumn() - Method in class edu.iastate.metnet.db.ResultSetAdapter: get the first column of the resultset
getColumn(int) - Method in class edu.iastate.metnet.db.ResultSetAdapter: return the column of the resultset
getColumnClass(int) - Method in class com.jgoodies.binding.extras.DelegatingTableModel: Returns the most specific superclass for all the cell values in the column.
getColumnClass(int) - Method in class edu.iastate.biocyc.ui.PathwayChoiceModel
getColumnClass(int) - Method in class edu.iastate.jtm.assistant.CitationPool
getColumnClass(int) - Method in class edu.iastate.jtm.gui.TableMap
getColumnClass(int) - Method in class edu.iastate.metnet.dataManager.TableDataModel
getColumnClass(int) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel
getColumnClass(int) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
getColumnClass(int) - Method in class edu.iastate.metnet.model.CandidateModel
getColumnClass(int) - Method in class edu.iastate.metnet.model.CompositionSelectionModel
getColumnClass(int) - Method in class edu.iastate.metnet.model.GroupShareTableModel
getColumnClass(int) - Method in class edu.iastate.metnet.model.MultiSelectionModel
getColumnClass(int) - Method in class edu.iastate.metnet.model.SpeciesTableModel: get the column class
getColumnClass(int) - Method in class edu.iastate.metnet.model.TableMap
getColumnClass(int) - Method in class edu.iastate.metnet.newgui.NoneditableTableModel
getColumnClass(int) - Method in class edu.iastate.metnet.NoneditableTableModel
getColumnClass(int) - Method in class edu.iastate.metnet.ui.PathwayChoiceTableModel: get the column class
getColumnCount() - Method in class com.jgoodies.binding.extras.DelegatingTableModel: Returns the number of columns in the model.
getColumnCount() - Method in class edu.iastate.jtm.assistant.CitationPool
getColumnCount() - Method in class edu.iastate.jtm.gui.TableMap
getColumnCount() - Method in class edu.iastate.metnet.dataManager.TableDataModel
getColumnCount() - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel
getColumnCount() - Method in class edu.iastate.metnet.metaomgraph.TableSorter
getColumnCount() - Method in class edu.iastate.metnet.model.AbbreviationRulesModel: get the number of the columns of the table model
getColumnCount() - Method in class edu.iastate.metnet.model.CandidateModel
getColumnCount() - Method in class edu.iastate.metnet.model.TableMap
getColumnCount() - Method in class edu.iastate.metnet.newgui.NoneditableTableModel
getColumnCount() - Method in class edu.iastate.metnet.NoneditableTableModel
getColumnEditorModel() - Method in class edu.iastate.metnet.ui.MyJTableEx
getColumnHeaders() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
getColumnName(int) - Method in class com.jgoodies.binding.extras.DelegatingTableModel: Returns the name of the column at columnIndex.
getColumnName(int) - Method in class edu.iastate.jtm.assistant.CitationPool
getColumnName(int) - Method in class edu.iastate.jtm.gui.TableMap
getColumnName() - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet
getColumnName() - Method in interface edu.iastate.metnet.analysis.IExcelSheet
getColumnName(int) - Method in class edu.iastate.metnet.dataManager.TableDataModel
getColumnName() - Method in class edu.iastate.metnet.db.ResultSetAdapter: match JDBCModel.setColumnNames() with Vector.toArray()
getColumnName(int) - Method in class edu.iastate.metnet.db.ResultSetAdapter
getColumnName(int) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel
getColumnName(int) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
getColumnName(int) - Method in class edu.iastate.metnet.model.AbbreviationRulesModel: get the column name of the table model
getColumnName(int) - Method in class edu.iastate.metnet.model.CandidateModel
getColumnName(int) - Method in class edu.iastate.metnet.model.TableMap
getColumnName(int) - Method in class edu.iastate.metnet.newgui.NoneditableTableModel
getColumnName(int) - Method in class edu.iastate.metnet.NoneditableTableModel
getColumns() - Method in class edu.iastate.metnet.dataManager.FileData
getColumns() - Method in class edu.iastate.metnet.dataManager.TableDataModel
getColumnStatus(int) - Method in class edu.iastate.jtm.gui.TableSorter
getComboBoxModel() - Method in class edu.iastate.metnet.model.DomainObjectListModel: get the presentation list for ComboBoxModel
getComment() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of comment
getComment() - Method in class edu.iastate.metnet.dao.CommentObject
getComment() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getComment() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getComment() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getComment() - Method in class edu.iastate.metnet.hibernate.Blockunitcomment
getComment() - Method in class edu.iastate.metnet.hibernate.BlockunitcommentKey: Returns the value of the comment property.
getComment() - Method in class edu.iastate.metnet.hibernate.Entitycomment
getComment() - Method in class edu.iastate.metnet.hibernate.EntitycommentKey: Returns the value of the comment property.
getComment() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of comment
getCommentList() - Method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement: get the comment list
getCommentList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getCommentList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getCommentList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getCommentObject(int) - Method in class edu.iastate.metnet.model.CommentTableModel
getCommentObjectList() - Method in class edu.iastate.metnet.hibernate.Blockunit: return the list of comment object
getCommentOrigin() - Method in class edu.iastate.reload.ui.CommentEditForm
getComments() - Method in class edu.iastate.metnet.aracyc.AracycEntity: return the comments
getComments() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getComments() - Method in class edu.iastate.metnet.hibernate.Blockunit: comments
getComments() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject: comment list of the blockunit
getComments() - Method in class edu.iastate.metnet.mapbuilder.NodeInfo
getCommentTuple() - Method in class edu.iastate.metnet.dao.CommentObject
getCommentTupleObject() - Method in class edu.iastate.metnet.dao.CommentObject
getCommonName() - Method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement: get the common name
getCommonName() - Method in interface edu.iastate.biocyc.dao.txt.BiocycElement: common name
getCommonName() - Method in class edu.iastate.metnet.aracyc.AbstractAracycEntity
getCommonName() - Method in class edu.iastate.metnet.aracyc.AracycClass
getCommonName() - Method in class edu.iastate.metnet.aracyc.AracycCompound
getCommonName() - Method in interface edu.iastate.metnet.aracyc.IAracycEntity
getComparator(int) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
getCompartment() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway: This method returns the name of the cellular compartment (location) for this pathway.
getCompleteKey(TrieNode) - Method in class edu.iastate.jtm.dic.Trie
getCompleteList() - Static method in class edu.iastate.metnet.metaomgraph.GeneList
getComplexID() - Method in class edu.iastate.metnet.graphmodel.RelationObject
getComplexList() - Method in class edu.iastate.biocyc.dao.txt.BiocycProtein: get the complex list that this is a component of
getComponent() - Method in class edu.iastate.metnet.birdseyeview.AbstractView: Subclasses must return some sort of component to display as their view.
getComponent() - Method in class edu.iastate.metnet.birdseyeview.cellview.CellView
getComponent() - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode: This method returns the panel.
getComponent() - Method in class edu.iastate.metnet.birdseyeview.goview.GoView
getComponent() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Compartment: This method causes the genes to be packaged and displayed, and then returns the finished image panel.
getComponent() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway: This method causes the genes to be packaged and displayed, and then returns the finished image panel.
getComponent() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.PathwayView
getComponent() - Method in class edu.iastate.metnet.newgui.LabelledComponent
getComponentCoefficient() - Method in class edu.iastate.metnet.graphmodel.RelationObject
getComponentID() - Method in class edu.iastate.metnet.graphmodel.RelationObject
getComponentList() - Method in class edu.iastate.biocyc.dao.txt.BiocycProtein: get the component list
getCompoundChildId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiVertices: Return the value of the compound_child_id column.
getCompoundFilename() - Method in class edu.iastate.biocyc.io.BiocycImporter
getCompoundFilename() - Method in class edu.iastate.metnet.aracyc.ChangeName
getCompoundID() - Method in class edu.iastate.metnet.dao.ChebiObject
getCompoundId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiChemicalData: Return the value of the compound_id column.
getCompoundId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Return the value of the compound_id column.
getCompoundId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession: Return the value of the compound_id column.
getCompoundId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames: Return the value of the compound_id column.
getCompoundId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference: Return the value of the compound_id column.
getConfidence() - Method in class edu.iastate.metnet.dao.InteractionObject
getConfidence() - Method in class edu.iastate.metnet.dao.MetnetInteraction
getConfidence() - Method in class edu.iastate.metnet.graphmodel.MetaphorTypeInformation
getConfidence() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getConfidence() - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Return the value of the Confidence column.
getConfidence() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo
getConfidenceList() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getConfiguration() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: This method returns the configuration object.
getContainer() - Static method in class edu.iastate.metnet.launch.LaunchMetNet
getContext(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph: get all entity id around the interaction in specified steps
getContext(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl: get all entity id around the interaction in specified steps.
getContextInstance() - Static method in class edu.iastate.metnet.utils.ContextFactory
getContextualHelpIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getControlEbid() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getControlTextColor() - Method in class edu.iastate.reload.skin.OceanThemeX: Returns the color for control text, which is the value of the theme's black value.
getControlTextColor() - Method in class javax.swing.plaf.metal.OceanTheme: Returns the color for control text, which is the value of the theme's black value.
getControlTextFont() - Method in class edu.iastate.reload.skin.DefaultMetalThemeX: Returns the font used for text on controls.
getControlTextFont() - Method in class javax.swing.plaf.metal.DefaultMetalTheme: Returns the font used for text on controls.
getCopyIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getCorrelationColumns() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
getCorrelations() - Method in class edu.iastate.metnet.metaomgraph.GeneList
getCost() - Method in class edu.iastate.metnet.dao.AlignmentObject
getCount() - Method in class edu.iastate.jtm.SentenceParser
getCounter() - Method in interface edu.iastate.metnet.interfaces.MyFacade: a test of state in stateless session bean
getCounter() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: a test of state in stateless session bean
getCounter() - Method in interface edu.iastate.metnet.interfaces.MyPaper: a test of state in stateless session bean
getCreatedOn() - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Return the value of the created_on column.
getCrosshairPoint() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
getCuratorToolWindow() - Static method in class edu.iastate.metnet.launch.LaunchMetNet
getCurrentBlockID() - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
getCurrentBlockIDSubSystemMap() - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
getCurrentDescFile() - Method in class edu.iastate.metnet.dataManager.DataManager
getCurrentGoLevel() - Method in class edu.iastate.metnet.birdseyeview.goview.GoView: This method returns the level object for the current level.
getCurrentInteraction() - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
getCurrentIntermediumMap() - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
getCurrentLiveEntity() - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
getCurrentNodeSubSystemMap() - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
getCurrentPathway() - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
getCurrentSQLDate() - Static method in class edu.iastate.metnet.utils.Utils: get current data with 'yyyy-mm-dd' format
getCurrentValidEdgeMap() - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
getCurrentValidity() - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
getCurrentValidNodeMap() - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
getCurrentView() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
getcurrentView() - Method in class edu.iastate.metnet.birdseyeview.ButtonPanel
getCutIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getData() - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet
getData() - Method in interface edu.iastate.metnet.analysis.IExcelSheet
getData(String) - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree: Retrieves the metadata for a given node.
getData() - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree.InfoNode: Gets the information associated with this node.
getData(int) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the numerical data from the given row.
getData() - Method in class edu.iastate.metnet.NoneditableTableModel
getData(int) - Method in class edu.iastate.metnet.threads.DataThread
getDatabase() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: This method returns the database object.
getDataColumnCount() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
getDataColumnHeader(int) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Fetches the header of a given column of data, ignoring the infocolumns.
getDataColumnHeader(int, boolean) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Fetches the header of a given column of data, ignoring the infocolumns.
getDataColumnHeaders() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
getDataFromMemory(int) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the numerical data from the given row for projects created from a stream.
getDataManager() - Static method in class edu.iastate.metnet.launch.LaunchMetNet
getDataMap() - Method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement: get the data map
getDataMap() - Method in interface edu.iastate.biocyc.dao.txt.BiocycElement: general data map for all attributes
getDataObject() - Method in class edu.iastate.metnet.dao.MyVersionNode
getDataset() - Method in class edu.iastate.metnet.model.AbstractPlotData
getDataset() - Method in interface edu.iastate.metnet.model.IPlotData
getDataSorter() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
getDataSource() - Method in class edu.iastate.metnet.controller.AddPathwayController
getDataSource() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getDataSource() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getDataSource() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
getDataSourceList() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getDataTable() - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
getDatatype() - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Return the value of the datatype column.
getDatatypeId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Return the value of the datatype_id column.
getDate() - Method in class edu.iastate.metnet.dao.InteractionInformation
getDate() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
getDate() - Method in class edu.iastate.metnet.dataManager.Properties
getDate() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Return the value of the Date column.
getDate() - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Return the value of the Date column.
getDate() - Method in class edu.iastate.metnet.hibernate.AbstractUser: Return the value of the Date column.
getDateAnnotated() - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Return the value of the date_annotated column.
getDB() - Method in class edu.iastate.metnet.aracyc.ConsoleApplication: get the database name setting
getDb() - Method in class edu.iastate.metnet.hibernate.ExternaldbKey: Returns the value of the db property.
getDB() - Static method in class edu.iastate.metnet.utils.Utils
getDblinkList() - Method in class edu.iastate.biocyc.dao.txt.BiocycCompound: get the external database link
getDblinkList() - Method in class edu.iastate.biocyc.dao.txt.BiocycEnzrxn: get the external database link
getDblinkList() - Method in class edu.iastate.biocyc.dao.txt.BiocycGene: get the external database link
getDblinkList() - Method in class edu.iastate.biocyc.dao.txt.BiocycPathway: get the external database link
getDblinkList() - Method in class edu.iastate.biocyc.dao.txt.BiocycProtein: get the external database link
getDblinkList() - Method in class edu.iastate.biocyc.dao.txt.BiocycReaction: get the external database link
getDbNames() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway: This method returns the list of database names for this pathway.
getDefaultCodeSQL() - Method in class edu.iastate.metnet.db.TableCodeConfidence
getDefaultColumn() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the index of the "default" info column.
getDefaultModel() - Method in class edu.iastate.metnet.metaomgraph.ListTree
getDefaultTitle() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the title used on all new MetaOmChartPanels.
getDefaultXAxis() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the label used for the x-axis of all new MetaOmChartPanels.
getDefaultYAxis() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the label used for the y-axis of all new MetaOmChartPanels.
getDefinition() - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds
getDegree() - Method in class edu.iastate.jtm.dic.AbstractTrieNode: Return the degree of this trie (size of the trie's alphabet).
getDegree() - Method in class edu.iastate.jtm.dic.AsciiTrieNode: Return the degree of this trie (size of the trie's alphabet).
getDegree() - Method in class edu.iastate.jtm.dic.DigitTrieNode: Return the degree of this trie (size of the trie's alphabet).
getDegree() - Method in class edu.iastate.jtm.dic.FuzzyTrieNode
getDegree() - Method in class edu.iastate.jtm.dic.LetterDigitTrieNode: Return the degree of this trie (size of the trie's alphabet).
getDegree() - Method in class edu.iastate.jtm.dic.LetterTrieNode: Return the degree of this trie (size of the trie's alphabet).
getDegree() - Method in class edu.iastate.jtm.dic.LowerTrieNode: Return the degree of this trie (size of the trie's alphabet).
getDegree() - Method in interface edu.iastate.jtm.dic.TrieNode: Return the degree of this trie (size of the trie's alphabet).
getDegree() - Method in class edu.iastate.jtm.dic.WordTrieNode: Return the degree of this trie (size of the trie's alphabet).
getDegree() - Method in class edu.iastate.metnet.dao.TrivialMetabolite
getDelay() - Method in class edu.iastate.metnet.metaomgraph.throbber.FlippingSquaresThrobber
getDelay() - Method in class edu.iastate.metnet.metaomgraph.throbber.Throbber
getDelegate() - Method in class com.jgoodies.binding.extras.DelegatingTableModel: Returns the current TableModel delegate.
getDeleteIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getDelimiter() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
getDelimiter() - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog
getDescendant(Object) - Method in class edu.iastate.metnet.aracyc.GenericTree: get all descendant of the current vertex
getDescendantList(DirectedGraph, Object) - Static method in class edu.iastate.biocyc.dao.txt.BiocycClass: get descendant list.
getDescendentValue() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getDescription() - Method in class edu.iastate.metnet.dao.HistoryInformation
getDescription() - Method in class edu.iastate.metnet.dataManager.FileFilterImpl
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractCodeconfidence: Return the value of the Description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractCodedatasource: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractCodeentitytype: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractCodeinteractiontype: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractCodelocation: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractCodeorganism: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractCodereferencetype: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractCoderule: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Return the value of the description column.
getDescription() - Method in class edu.iastate.metnet.hibernate.BackgroundTask
getDescription() - Method in class edu.iastate.metnet.metaomgraph.GraphFileFilter: Gets a description of this filter.
getDesktop() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph: Fetches the desktop used in the main JFrame.
getDesktop() - Method in class edu.iastate.metnet.ui.MainWindow2: the desktop instance
getDesktopColor() - Method in class edu.iastate.reload.skin.OceanThemeX: Returns the desktop color, which is the theme's white color.
getDesktopColor() - Method in class javax.swing.plaf.metal.OceanTheme: Returns the desktop color, which is the theme's white color.
getDestination() - Method in class edu.iastate.metnet.soft.SOFTParserOptionPanel
getDetailedDate(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getDifferenceWithCase(List, List) - Static method in class edu.iastate.metnet.utils.Utils: get differnece a-b, case sensitive
getDifferenceWithoutCase(List, List) - Static method in class edu.iastate.metnet.utils.Utils: get the difference a-b, case insensitive
getDifferenceXWithCase(List, List) - Static method in class edu.iastate.metnet.utils.Utils: get differnece of (a-b) + (b-a), case sensitive
getDifferenceXWithoutCase(List, List) - Static method in class edu.iastate.metnet.utils.Utils: get the difference (a-b) + (b-a), case insensitive
getDirected() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo
getDirectedGraph(Integer) - Method in class edu.iastate.metnet.hivemindService.CytoscapeHMService: returns a directed graph based on pathway ID
getDirectory() - Method in class edu.iastate.biocyc.io.BiocycImporter
getDisplay() - Method in class edu.iastate.metnet.model.DisplayObject
getDocBevItem() - Method in class edu.iastate.metnet.launch.LaunchMetNet
getDocCytoItem() - Method in class edu.iastate.metnet.launch.LaunchMetNet
getDocMenu() - Method in class edu.iastate.metnet.launch.LaunchMetNet
getDocMogItem() - Method in class edu.iastate.metnet.launch.LaunchMetNet
getDocPbItem() - Method in class edu.iastate.metnet.launch.LaunchMetNet
getDocPumaItem() - Method in class edu.iastate.metnet.launch.LaunchMetNet
getDocumentCount(Object) - Method in class edu.iastate.jtm.util.VocabularyCounter
getDocumentFrequency(Object) - Method in class edu.iastate.jtm.util.VocabularyCounter
getDomainObject(String) - Method in class edu.iastate.metnet.model.DomainObjectListModel: get the domain object
getDomainValue(Object) - Method in class edu.iastate.metnet.model.CodelocationListModel
getDomainValue(Object) - Method in class edu.iastate.metnet.model.DomainObjectListModel
getDoubleValue() - Method in class edu.iastate.metnet.model.AbstractCodePresentation
getDoubleValue() - Method in interface edu.iastate.metnet.model.ICodePresentation
getDownIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getDownstreamEntityNodeIdList(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph: get the downstream entity node id list
getDownstreamEntityNodeIdList(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl
getDownstreamEntityNodeIdList(Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph: get the downstream entity node id list
getDownstreamGuidSet() - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
getDownstreamGuidSet() - Method in interface edu.iastate.metnet.dao.PathwayElementNode: get the outgoing node id
getDownstreamInteractionNodeIdList(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph: get the downstream interaction node id list
getDownstreamInteractionNodeIdList(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl
getDownstreamInteractionNodeIdList(Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph: get the downstream interaction node id list
getDownstreamNodeIdList(Integer) - Method in class edu.iastate.metnet.dao.MyVersionGraph: get the list of new version record
getDownstreamNodeIdList(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph: get the list of new version record
getDownstreamNodeIdList(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl
getDownstreamNodeIdList(Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph: get the list of new version record
getDownstreamNodeIdSet() - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
getDownstreamNodeIdSet() - Method in class edu.iastate.metnet.dao.MyVersionNode
getDownstreamNodeIdSet() - Method in interface edu.iastate.metnet.dao.PathwayElementNode: get the outgoing node id
getEC() - Method in class edu.iastate.metnet.dao.MetnetInteraction
getEc() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getEc() - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Return the value of the EC column.
getEcid() - Method in class edu.iastate.metnet.hibernate.AbstractBrendarecommendname: Return the simple primary key value that identifies this object.
getEcid() - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Return the value of the ECID column.
getEcid() - Method in class edu.iastate.metnet.hibernate.BrendaactivatingcompoundKey: Returns the value of the ecid property.
getEcid() - Method in class edu.iastate.metnet.hibernate.BrendacofactorKey: Returns the value of the ecid property.
getEcid() - Method in class edu.iastate.metnet.hibernate.BrendainhibitorKey: Returns the value of the ecid property.
getEcid() - Method in class edu.iastate.metnet.hibernate.BrendametalionKey: Returns the value of the ecid property.
getEcid() - Method in class edu.iastate.metnet.hibernate.BrendaproductKey: Returns the value of the ecid property.
getEcid() - Method in class edu.iastate.metnet.hibernate.BrendasubstrateKey: Returns the value of the ecid property.
getEcid() - Method in class edu.iastate.metnet.hibernate.BrendasynonymsKey: Returns the value of the ecid property.
getECID() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo
getECList() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getECnumber() - Method in class edu.iastate.biocyc.dao.txt.BiocycReaction: get the ec number of the reaction
getEdge(JGraph, GraphCell, GraphCell) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper: get the JGraph edge based on JGraph node
getEdgeAttributeFiles() - Method in class edu.iastate.metnet.launch.RunCytoscape
getEdgeCell(Edge) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter: Returns the JGraph edge cell that corresponds to the specified JGraphT edge.
getEdgeList() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo
getEdgeSeparation() - Method in class edu.iastate.reload.ui.JGraphParallelEdgeRouter
getEdgeSet() - Method in class edu.iastate.metnet.dao.MetnetInteraction
getEdgeType(Blockunit, Blockunit) - Static method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor: searching rule: node A, and node B, edge (A, B) A and B both are entitywithcontext get the intersection of the interactions? require the entity join the interaction A is interaction and B is entitywithcontext type of A A is entitywithcontext and B is interaction see if catalysis A and B both are interaction, never occurred
getEditIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getEditor(int) - Method in class edu.iastate.metnet.model.ColumnEditorModel
getEditor(int) - Method in class edu.iastate.metnet.model.RowEditorModel
getEidByName(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: search the entity exact match the search string.
getEidByName(String, String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: search the entity exact match the search string.
getEidByName(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: search the entity exact match the search string.
getEidByName(String, String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: search the entity exact match the search string.
getElementAt(int) - Method in class com.jgoodies.binding.extras.ListModelHolder: Returns the value at the specified index, or null if the current value is null
getElementAt(int) - Method in class edu.iastate.metnet.model.JDBCComboModel: get the value object in the list model
getEmail() - Method in class edu.iastate.metnet.hibernate.AbstractUser: Return the value of the Email column.
getEnd() - Method in class edu.iastate.jtm.util.SlidingWindow.Stride
getEnd() - Method in class edu.iastate.metnet.metaomgraph.chart.RangeMarker
getEnt1List() - Method in class fcmodeler.pathbinder.gui.EntityPanel
getEnt2List() - Method in class fcmodeler.pathbinder.gui.EntityPanel
getEntities() - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
getEntitiesFound() - Method in class edu.iastate.jtm.EntityFinder
getEntity() - Method in class edu.iastate.metnet.hibernate.Blockunit
getEntity(int) - Method in class edu.iastate.metnet.model.EntityListModel
getEntityabbreviationSet() - Method in class edu.iastate.metnet.hibernate.Entity
getEntitycommentSet() - Method in class edu.iastate.metnet.hibernate.Entity
getEntityCount() - Method in class edu.iastate.jtm.EntityFinder
getEntityexternaldbSet() - Method in class edu.iastate.metnet.hibernate.Blockunit
getEntityexternaldbSet() - Method in class edu.iastate.metnet.hibernate.Entity
getEntityID() - Method in class edu.iastate.metnet.birdseyeview.Protein: Returns the entityID.
getEntityID() - Method in class edu.iastate.metnet.dao.ChebiObject
getEntityId() - Method in class edu.iastate.metnet.dao.EntityNode
getEntityId() - Method in class edu.iastate.metnet.dao.TrivialMetabolite
getEntityId() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getEntityid() - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Return the simple primary key value that identifies this object.
getEntityid() - Method in class edu.iastate.metnet.hibernate.AbstractEntityOntology: Return the value of the entityid column.
getEntityid() - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchem: Return the value of the entityid column.
getEntityid() - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchemName: Return the value of the entityid column.
getEntityId() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getEntityId() - Method in class edu.iastate.metnet.hibernate.Blockunit
getEntityid() - Method in class edu.iastate.metnet.hibernate.Entityabbreviation
getEntityid() - Method in class edu.iastate.metnet.hibernate.EntityabbreviationKey: Returns the value of the entityid property.
getEntityid() - Method in class edu.iastate.metnet.hibernate.Entitycomment
getEntityid() - Method in class edu.iastate.metnet.hibernate.EntitycommentKey: Returns the value of the entityid property.
getEntityid() - Method in class edu.iastate.metnet.hibernate.Entityref
getEntityid() - Method in class edu.iastate.metnet.hibernate.EntityrefKey: Returns the value of the entityid property.
getEntityid() - Method in class edu.iastate.metnet.hibernate.Entitysynonym
getEntityid() - Method in class edu.iastate.metnet.hibernate.EntitysynonymKey: Returns the value of the entityid property.
getEntityid() - Method in class edu.iastate.metnet.hibernate.Entitywithcontext: Returns the value of the blockid property.
getEntityid() - Method in class edu.iastate.metnet.hibernate.EntitywithcontextKey: Returns the value of the entityid property.
getEntityid() - Method in class edu.iastate.metnet.hibernate.Externaldb
getEntityid() - Method in class edu.iastate.metnet.hibernate.ExternaldbKey: Returns the value of the entityid property.
getEntityId() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject
getEntityIdListOfPathway(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the entity id list of specified pathway
getEntityIdListOfPathway() - Method in interface edu.iastate.metnet.interfaces.MyFacade: collection version of getEntityIdListOfPathway()
getEntityIdListOfPathway(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the entity id list of specified pathway
getEntityIdListOfPathway() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: collection version of getEntityIdListOfPathway()
getEntityIdOfUniqueId(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacade: collection version of getEntityIdOfUniqueId().
getEntityIdOfUniqueId(Blockunit) - Method in interface edu.iastate.metnet.interfaces.MyFacade: this function is used to test if the given AraCyc entry has a corresponding entity id in MetNetDB.
getEntityIdOfUniqueId(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: collection version of getEntityIdOfUniqueId().
getEntityIdOfUniqueId(Blockunit) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: this function is used to test if the given AraCyc entry has a corresponding entity id in MetNetDB.
getEntityIDs(boolean) - Method in class fcmodeler.pathbinder.gui.EntityPanel
getEntityList(boolean, boolean) - Method in class fcmodeler.pathbinder.gui.EntityPanel
getEntityList(boolean, boolean) - Method in class fcmodeler.pathbinder.gui.PbFrame
getEntityLocationList() - Method in class edu.iastate.metnet.dao.PathwayObject
getEntityLocationList() - Method in class edu.iastate.metnet.export.PathwayInfoImpl
getEntityLocationList() - Method in interface edu.iastate.metnet.hiveface.PathwayInfo
getEntityLocationString() - Method in class edu.iastate.metnet.dao.PathwayObject: return the entity location string
getEntityLocationString() - Method in class edu.iastate.metnet.model.PathwayObjectChoice
getEntityName() - Method in class edu.iastate.metnet.dao.MetnetLiveEntity
getEntityOntologySet() - Method in class edu.iastate.metnet.hibernate.Entity
getEntityPanel() - Method in class fcmodeler.pathbinder.gui.PbFrame
getEntityPart(int) - Method in class edu.iastate.metnet.model.InteractionPartsModel
getEntityrefSet() - Method in class edu.iastate.metnet.hibernate.Entity
getEntityStrings(boolean) - Method in class fcmodeler.pathbinder.gui.EntityPanel
getEntitysynonymSet() - Method in class edu.iastate.metnet.hibernate.Entity
getEntityTermID(int) - Method in class fcmodeler.pathbinder.PathBinder
getEntityTermName(int) - Method in class fcmodeler.pathbinder.PathBinder
getEntityType() - Method in class edu.iastate.metnet.dao.MetnetLiveEntity
getEntityType() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getEntityType() - Method in class edu.iastate.metnet.export.GobiNodeImpl: get the entity type, if null, means all types
getEntitytype() - Method in class edu.iastate.metnet.hibernate.AbstractCodeentitytype: Return the value of the entitytype column.
getEntityType() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getEntityType() - Method in class edu.iastate.metnet.hibernate.Blockunit: entity type
getEntityType() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject: get the entity type of the blockunit.
getEntityType() - Method in interface edu.iastate.metnet.hiveface.GobiNode: get the entity type of one node.
getEntityType() - Method in class edu.iastate.metnet.hivetest.GobiNodeImpl: get the entity type, if null, means all types
getEntityType() - Method in class edu.iastate.metnet.model.CompositionBlockunit
getEntityType() - Method in class edu.iastate.metnet.model.EntityPart
getEntityType() - Method in class edu.iastate.metnet.model.SelectedBlockunit
getEntityTypeList() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getEnvironment() - Static method in class edu.iastate.metnet.utils.ContextFactory
getEnzrxnFilename() - Method in class edu.iastate.biocyc.io.BiocycImporter
getEnzrxnList() - Method in class edu.iastate.biocyc.dao.txt.BiocycProtein: get the catalyzed enzrxn reaction list
getEnzrxnList() - Method in class edu.iastate.biocyc.dao.txt.BiocycReaction: get the control interaction list
getEnzyme() - Method in class edu.iastate.biocyc.dao.txt.BiocycEnzrxn: get enzyme list
getEnzyme() - Method in class edu.iastate.metnet.dao.MetnetInteraction
getEnzyme() - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Return the value of the Enzyme column.
getEnzymeName() - Method in class edu.iastate.metnet.hibernate.AbstractTairAracycDump: Return the value of the enzyme_name column.
getEnzymes() - Method in class edu.iastate.metnet.dao.InteractionInformation
getErrorList() - Method in class edu.iastate.jtm.jmed.ESearch
getErrorList() - Method in class edu.iastate.jtm.jmed.PubMedQuerier
getErrorMessage(Integer) - Method in class edu.iastate.metnet.graphmodel.GraphValidity: get the error message for model id
getErrors() - Method in class edu.iastate.metnet.graphmodel.GraphValidity: get the errors
getEsAlignmentList() - Method in class edu.iastate.metnet.ui.PathwayEditor
getEValue() - Method in class edu.iastate.metnet.dao.SoybeanHomology
getEvidenceCode() - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Return the value of the evidence_code column.
getException() - Method in class edu.iastate.metnet.utils.SwingWorker2: Get the exception, or null if there isn't one (yet).
getExitValue() - Method in class edu.iastate.jtm.util.ProcessWrapper
getExperimentCount() - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
getExperimentData(int) - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
getExperimentIndex() - Method in class edu.iastate.metnet.birdseyeview.ExperimentChooserPanel: This method returns the index of the selected item.
getExperimentIndex() - Method in class edu.iastate.metnet.birdseyeview.LoadWindow: This method returns the index of the chosen experiment.
getExperimentName() - Method in class edu.iastate.metnet.birdseyeview.LoadController: Added by Mohammed Alabsi - April 13th, 2006 Method to get the name of current experiment.
getExperimentName(int) - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
getExperiments() - Method in class edu.iastate.metnet.birdseyeview.LoadController: Added by Mohammed Alabsi - April 13th, 2006 Method to get list of experiments names
getExperiments() - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
getExperimentsTable() - Method in class edu.iastate.metnet.birdseyeview.LoadController: Added by Mohammed Alabsi - April 13th, 2006 Returned data from all experiments
getExpressionFiles() - Method in class edu.iastate.metnet.launch.RunCytoscape
getExtendedInfo() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the root node of this project's extended info tree.
getExtendedInfoFile() - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog
getExtension(File) - Method in class edu.iastate.metnet.dataManager.FileFilterImpl
getExtension(File) - Static method in class edu.iastate.metnet.metaomgraph.ComponentToImage: Determines the extension of a given file.
getExtension(File) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils: Determines the extension of a given file.
getExtension(String) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils
getExternaldb(int) - Method in class edu.iastate.metnet.model.EntityDBModel
getFastForwardIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getFcmlFile() - Method in class edu.iastate.metnet.ui.SBMLExporter
getFD() - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile: Returns the opaque file descriptor object associated with this file.
getFD() - Method in class edu.iastate.metnet.soft.RandomAccessFile: Returns the opaque file descriptor object associated with this file.
getField() - Method in class edu.iastate.jtm.jmed.Limits
getField(String) - Static method in class edu.iastate.jtm.jmed.Query.Field
getFields() - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree: Retrieves a list of leaf node names in this tree.
getFileData() - Method in class edu.iastate.metnet.dataManager.DataManager
getFileExitItem() - Method in class edu.iastate.metnet.launch.LaunchMetNet
getFileIndex(int) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Fetches the file index that marks the start of a given entry.
getFileLines(String) - Method in class edu.iastate.metnet.aracyc.AbstractAracycFileReader: get the file lines as the linked list, and remove any comment line which are preceded by #
getFileLines(InputStream) - Method in class edu.iastate.metnet.aracyc.AbstractAracycFileReader
getFileName() - Method in class edu.iastate.metnet.dataManager.Properties
getFilePointer() - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile: Returns the current position in the file, where the next read or write will occur.
getFilePointer() - Method in class edu.iastate.metnet.soft.RandomAccessFile: Returns the current position in the file, where the next read or write will occur.
getFilesToParse() - Method in class edu.iastate.metnet.soft.SOFTParserOptionPanel
getFilterCount() - Method in class fcmodeler.pathbinder.PmidFilter
getFilteredColumns(String[]) - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph
getFilterTaxonomy() - Method in class fcmodeler.pathbinder.PmidFilter
getFinalId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiRelation: Return the value of the final_id column.
getFindAgainIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getFindIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getFinishTime() - Method in class edu.iastate.metnet.hibernate.BackgroundTask
getFirst(Map, Object) - Method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement: get first object in the map.
getFirst(Map, Object) - Static method in class edu.iastate.metnet.utils.Utils
getFirstAuthor(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getFirstname() - Method in class edu.iastate.metnet.hibernate.AbstractUser: Return the value of the Firstname column.
getFocusColor() - Method in class edu.iastate.metnet.ui.Desert
getFocusColor() - Method in class edu.iastate.metnet.ui.Oasis
getFont(String, int, int) - Method in class edu.iastate.metnet.utils.Utils
getFormat() - Method in class edu.iastate.jtm.assistant.Exporter
getFormatedSentence(List, String, String, boolean) - Method in class fcmodeler.pathbinder.PbSentence
getFormatedSentence(List, String) - Method in class fcmodeler.pathbinder.PbSentence
getFormatter() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
getFormDBLink() - Method in class edu.iastate.metnet.ui.MainWindow2: the window instance of web database source window
getFormEditPathway() - Method in class edu.iastate.metnet.ui.MainWindow2: the window instance of edit pathway window
getFormInteraction() - Method in class edu.iastate.metnet.ui.MainWindow2: the window instance of Edit Interaction window
getFormReference() - Method in class edu.iastate.metnet.ui.MainWindow2: the window instance of reference service window
getFormSynonym() - Method in class edu.iastate.metnet.ui.MainWindow2: the window instance of name service window
getFormula() - Method in class edu.iastate.metnet.aracyc.AracycCompound
getFormula() - Method in class edu.iastate.metnet.hibernate.AbstractChebiChemicalData: Return the value of the formula column.
getForwardIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getFrameCount() - Method in class edu.iastate.metnet.metaomgraph.throbber.MetaOmThrobber
getFullCitation(int) - Method in class edu.iastate.jtm.assistant.CitationPool
getFullFieldList() - Static method in class edu.iastate.jtm.jmed.Query.Field
getFullGeneAnnotationAttributeList() - Method in class edu.iastate.metnet.export.GraphExporterImpl
getFullGeneAnnotationAttributeList() - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get all attributes in function getFullGeneAnnotationList()
getFullGeneAnnotationList() - Method in class edu.iastate.metnet.export.GraphExporterImpl
getFullGeneAnnotationList() - Method in interface edu.iastate.metnet.hiveface.GraphExporter: return all possible gene annnotation.
getFullGeneAnnotationList() - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: batch model query, not an object
getFullGeneAnnotationList() - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: batch model query, not an object
getFullJournal(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getFullPublicationTypes() - Static method in class edu.iastate.jtm.jmed.Query.SimpleTerm
getFullString() - Method in class fcmodeler.pathbinder.FilterEntry
getFullUrl() - Method in class edu.iastate.jtm.assistant.GoogleScholar
getFuncCon() - Method in class edu.iastate.metnet.mapbuilder.NodeInfo
getFunctionCategory() - Method in class edu.iastate.metnet.dao.SoybeanHomology
getFunctionconfidence() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getFunctionconfidence() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitconfidence: Return the value of the FunctionConfidence column.
getFunctionConfidence() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getFunctionconfidence() - Method in class edu.iastate.metnet.hibernate.Blockunit
getFunctionconfidence() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject
getFunctionConfidence() - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
getGenbankAccession() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the genbank_accession column.
getGenebankAccess() - Method in class edu.iastate.metnet.dao.SoybeanHomology
getGeneByID(String) - Method in class edu.iastate.metnet.hivemindService.RequestGene: Search a gene by ID.
getGeneByID(String, ArrayList<String>) - Method in class edu.iastate.metnet.hivemindService.RequestGene: Searches for genes by ID, and populates only the required attributes
getGeneByID(String) - Method in class edu.iastate.metnet.hivemindService.RequestGeneData: Method returns a Gene obj containing all attributes data
getGeneByID(String, ArrayList<String>) - Method in class edu.iastate.metnet.hivemindService.RequestGeneData: Method gets a gene id and list of attributes to be retreieved from DB and returns Gene obj populated with found data if any.
getGeneFamily() - Method in class edu.iastate.metnet.dao.SoybeanHomology
getGeneFilename() - Method in class edu.iastate.biocyc.io.BiocycImporter
getGeneFilename() - Method in class edu.iastate.metnet.aracyc.ChangeName
getGeneId() - Method in class edu.iastate.metnet.hivemindService.SimpleGeneObj
getGeneInfo(String, ArrayList<String>) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils: Gets gene info from AtGeneSearch for a given list of genes.
getGeneList() - Method in class edu.iastate.biocyc.dao.txt.BiocycProtein: get the gene list
getGeneListFlavor() - Static method in class edu.iastate.metnet.metaomgraph.GeneList
getGeneListNames() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Fetches the names of all the gene lists in this project.
getGeneListRowNames(String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the row names of all the rows in the given list.
getGeneListRowNumbers(String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the row numbers of all the rows in the given list.
getGeneLists() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
getGeneName() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get gene name list
getGeneName() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getGeneName() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getGeneName() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGeneName() - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Return the value of the gene_name column.
getGeneName() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get gene name list
getGeneNameList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getGeneNameList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGeneNameList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getGeneObj(String) - Static method in class edu.iastate.metnet.hivemindService.AnnotationService: The Gene object returned by this method is not fully populated.
getGenes() - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode: This method returns the list of genes.
getGlobalDictionary() - Method in class edu.iastate.jtm.EntityFinder
getGobiNodeList() - Static method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame
getGobiNodeList() - Static method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame
getGobiNodeList() - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
getGoBiologicalProcess() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of biological process
getGoBiologicalProcess() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getGoBiologicalProcess() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getGoBiologicalProcess() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoBiologicalProcess() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of biological process
getGoBiologicalProcessList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getGoBiologicalProcessList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoBiologicalProcessList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getGoBiologicalProcessWithLinks() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of biological process with hyperlinks
getGoBiologicalProcessWithLinks() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoBioProcesses() - Method in class edu.iastate.metnet.birdseyeview.Annotation: This method returns the node IDs of the GO biological processes in which this gene product participates.
getGoBioProcesses(Integer) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method returns a list of GO biological process term IDs in which the given entity participates.
getGoBioProcesses(Integer) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getGoCellularComponent() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of cellular component
getGoCellularComponent() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getGoCellularComponent() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getGoCellularComponent() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoCellularComponent() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of cellular component
getGoCellularComponentList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getGoCellularComponentList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoCellularComponentList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getGoCellularComponentWithLinks() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of cellular component with hyperlinks
getGoCellularComponentWithLinks() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoChildren(Integer) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method retrieves a list of the child nodes for the given node.
getGoChildren(Integer) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getGoFunctions() - Method in class edu.iastate.metnet.birdseyeview.Annotation: This method returns the node IDs of the GO molecular functions of this gene product.
getGoFunctions(Integer) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method returns a list of GO molecular function term IDs in which the given entity is involved.
getGoFunctions(Integer) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getGoGeneProductID() - Method in class edu.iastate.metnet.birdseyeview.Annotation: Returns the gene ontology gene product ID.
getGoGeneProductID(String) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method converts the given locus ID into a GO gene product ID querying the GO database in the Metnet DB.
getGoGeneProductID(String) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getGoID() - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode: This method returns the GO term ID.
getGoID() - Method in class edu.iastate.metnet.birdseyeview.goview.GoTerm: Returns the goID.
getGoId() - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Return the value of the go_id column.
getGoMolecularFunction() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of molecular function
getGoMolecularFunction() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getGoMolecularFunction() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getGoMolecularFunction() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoMolecularFunction() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of molecular function
getGoMolecularFunctionList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getGoMolecularFunctionList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoMolecularFunctionList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getGoMolecularFunctionWithLinks() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of molecular function with hyperlinks
getGoMolecularFunctionWithLinks() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getGoNodeName(Integer) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method retrieves the name of the GO node with the given ID.
getGoNodeName(Integer) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getGoNodesWithinDistance(Integer, int) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method retrieves a unique list of the nodes of the hierarchy for the given root within the given distance from the root.
getGoNodesWithinDistance(Integer, int) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getGoslimTerm() - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Return the value of the goslim_term column.
getGoTerm() - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Return the value of the go_term column.
getGoTermAncestors(Integer) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method returns a list of terms which are the ancestors (parents, itself, etc.) for the given term.
getGoTermAncestors(Integer) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getGrandDocumentCount() - Method in class edu.iastate.jtm.util.VocabularyCounter
getGrandTermCount() - Method in class edu.iastate.jtm.util.VocabularyCounter
getGraphFiles() - Method in class edu.iastate.metnet.launch.RunCytoscape
getGraphModel(JGraph) - Method in class edu.iastate.metnet.ui.StructureQueryHelper: try to recognize the graph data model from the user interface
getGraphModelByEntity(GobiNode) - Method in class edu.iastate.metnet.export.GraphExporterImpl
getGraphModelByEntity(GobiNode) - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get the graph model from the node info.
getGraphModelByEntityList(Collection) - Method in class edu.iastate.metnet.export.GraphExporterImpl
getGraphModelByEntityList(Collection) - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get the graph model from the node list.
getGraphModelByPathway(Collection) - Method in class edu.iastate.metnet.export.GraphExporterImpl
getGraphModelByPathway(Collection) - Method in interface edu.iastate.metnet.hiveface.GraphExporter: return the graph model based on the pathway id list.
getGraphModelByStep(Collection, int) - Method in class edu.iastate.metnet.export.GraphExporterImpl
getGraphModelByStep(Collection, int) - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get the p-neighborhood graph
getGraphValidity() - Method in class edu.iastate.metnet.graphmodel.ValidityMetaphor
getGroupid() - Method in class edu.iastate.metnet.dao.GroupObject
getGroupid() - Method in class edu.iastate.metnet.hibernate.AbstractGroupList: Return the simple primary key value that identifies this object.
getGroupid() - Method in class edu.iastate.metnet.hibernate.GroupMemberKey: Returns the value of the groupid property.
getGroupid() - Method in class edu.iastate.metnet.hibernate.GroupShareKey: Returns the value of the groupid property.
getGroupid() - Method in class edu.iastate.metnet.ui.MemberManagerForm
getGroupList() - Method in class edu.iastate.metnet.dao.GroupObject
getGroupMemberList() - Method in class edu.iastate.metnet.dao.GroupObject
getGroupMemberList(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the member of the specified group
getGroupMemberList(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the member of the specified group
getGroupname() - Method in class edu.iastate.metnet.dao.GroupObject
getGroupname() - Method in class edu.iastate.metnet.hibernate.AbstractGroupList: Return the value of the groupname column.
getGroupName() - Method in class edu.iastate.metnet.ui.MemberManagerForm
getGroupNum() - Method in class edu.iastate.jtm.jmed.PubMedSampler
getGroupObject(int) - Method in class edu.iastate.metnet.model.GroupListTableModel
getGroupObject(int) - Method in class edu.iastate.metnet.model.GroupShareTableModel
getGroupShareList() - Method in class edu.iastate.metnet.dao.GroupObject
getGroupSize() - Method in class edu.iastate.jtm.jmed.PubMedSampler
getGuid() - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode
getGuid() - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
getGuid() - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode
getGuid() - Method in interface edu.iastate.metnet.dao.PathwayElementNode
getHeader() - Method in class edu.iastate.jtm.jmed.StreamXMLParser
getHeaderDescriptor(String) - Method in class edu.iastate.metnet.soft.Entity
getHeaderRendererIcon(int, int) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
getHeaders() - Static method in class edu.iastate.metnet.metaomgraph.AtGeneSearch
getHeaders() - Method in class edu.iastate.metnet.NoneditableTableModel
getHeight() - Method in class edu.iastate.metnet.dao.ZVertex
getHeight() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.TreeNode: get the total height of the tree node
getHelpAboutItem() - Method in class edu.iastate.metnet.launch.LaunchMetNet
getHelper() - Method in class edu.iastate.reload.ui.NetworkEditForm
getHelpListener() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph: Fetches the ActionListener used to display a Help frame.
getHelpResource() - Method in class edu.iastate.reload.ui.HelpResource
getHighlightedRow() - Method in class edu.iastate.jtm.gui.DnDTree
getHint() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: Get a human readable hint for using this layout.
getHistoryIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getHistoryInformation(int) - Method in class edu.iastate.metnet.model.HistoryTableModel: get the selected object
getHistoryReport(Date, Date, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the history report
getHistoryReport(Date, Date, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the history report
getHit(int) - Method in class edu.iastate.jtm.EntityFinder
getHits() - Method in class edu.iastate.jtm.jmed.ESearch
getHits() - Method in class edu.iastate.jtm.jmed.PubMedQuerier
getHitsCount() - Method in class edu.iastate.jtm.EntityFinder
getHome() - Static method in class edu.iastate.metnet.interfaces.MyFacadeUtil: Obtain remote home interface from default initial context
getHome(Hashtable) - Static method in class edu.iastate.metnet.interfaces.MyFacadeUtil: Obtain remote home interface from parameterised initial context
getHome() - Static method in class edu.iastate.metnet.interfaces.MyMetnetServiceUtil: Obtain remote home interface from default initial context
getHome(Hashtable) - Static method in class edu.iastate.metnet.interfaces.MyMetnetServiceUtil: Obtain remote home interface from parameterised initial context
getHome() - Static method in class edu.iastate.metnet.interfaces.MyPaperUtil: Obtain remote home interface from default initial context
getHome(Hashtable) - Static method in class edu.iastate.metnet.interfaces.MyPaperUtil: Obtain remote home interface from parameterised initial context
getHomeIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getHost() - Method in class edu.iastate.jtm.util.RemoteControl
getHtml() - Method in class edu.iastate.jtm.jmed.MeshDescriptor
getIbid() - Method in class edu.iastate.metnet.dao.InteractionStructure
getIbidList() - Method in class edu.iastate.metnet.hibernate.HistoryFlatPathway: get the ibid list
getIcon(String) - Static method in class edu.iastate.jtm.gui.IconLib
getIconImage() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph: Fetches the MetaOmGraph icon as an Image.
getId() - Method in class edu.iastate.metnet.birdseyeview.ViewInfo: Returns the id.
getId() - Method in class edu.iastate.metnet.dao.AbbreviationObject
getId() - Method in class edu.iastate.metnet.dao.Candidate
getId() - Method in class edu.iastate.metnet.dao.CommentObject
getId() - Method in class edu.iastate.metnet.dao.GoTermID
getID() - Method in interface edu.iastate.metnet.dao.IMetnetBlockUnit: get the identity in the pathway graph
getId() - Method in interface edu.iastate.metnet.dao.IMetnetBlockUnit: same as getID() but return object
getID() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
getId() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
getId() - Method in class edu.iastate.metnet.dao.ReferenceObject
getId() - Method in class edu.iastate.metnet.dao.SynonymObject
getId() - Method in class edu.iastate.metnet.export.GoTermID
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitcomment: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitref: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitsynonym: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBrendaactivatingcompound: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBrendacofactor: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBrendainhibitor: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBrendametalion: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBrendaproduct: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBrendasubstrate: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractBrendasynonyms: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiChemicalData: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiOntology: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiRelation: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiVertices: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractCoderule: Return the simple primary key value that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractEntityabbreviation: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractEntitycomment: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractEntityref: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractEntitysynonym: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractEntitywithcontext: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractExternaldb: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractGroupMember: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractGroupShare: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractInteractionparts: Return the composite id instance that identifies this object.
getId() - Method in class edu.iastate.metnet.hibernate.AbstractPathwayparts: Return the composite id instance that identifies this object.
getID() - Method in class edu.iastate.metnet.hibernate.BlockunitSynonymCandidate
getId() - Method in class edu.iastate.metnet.model.CheckCandidate
getID() - Method in class fcmodeler.pathbinder.gui.LocationNode
getID() - Method in class fcmodeler.pathbinder.gui.VerbNode
getIdColumn() - Method in class edu.iastate.metnet.dataManager.DataManager
getIdColumn() - Method in class edu.iastate.metnet.dataManager.FileData
getIdentifier() - Method in class edu.iastate.metnet.soft.Entity
getIdf(Object) - Method in class edu.iastate.jtm.util.VocabularyCounter
getIdType() - Method in class edu.iastate.metnet.dataManager.FileData
getIdType() - Method in class edu.iastate.metnet.hivemindService.SimpleGeneObj
getIDType(String) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils: Determines whether the given String is a Locus ID, Affy8k ID, Affy8k ID, or none of the above.
getIgnoreConsecutiveDelimiters() - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog
getImage() - Method in class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel
getImportDate() - Method in class edu.iastate.metnet.dao.MyVersionNode
getImportDateRepresentation() - Method in class edu.iastate.metnet.dao.MyVersionNode
getInactiveControlTextColor() - Method in class edu.iastate.reload.skin.OceanThemeX: Returns the color for inactive control text, which is the RGB value (153, 153, 153).
getInactiveControlTextColor() - Method in class javax.swing.plaf.metal.OceanTheme: Returns the color for inactive control text, which is the RGB value (153, 153, 153).
getInactiveValues() - Method in class edu.iastate.metnet.metaomgraph.DualTablePanel: Fetches the values in the inactive table
getIncomingBlockunitSet() - Method in class edu.iastate.metnet.hibernate.Blockunit
getIncomingEdges(JGraph, Object, CellView) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor: get the incoming edges use CellView[] views = graph.getGraphLayoutCache().getMapping(cells); to get views
getIncomingInteractionIDList() - Method in class edu.iastate.metnet.model.IntermediumEntityInformation
getIncomingNodes(JGraph, Object, CellView) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor: get the predecessor nodes
getIndex(char) - Method in class edu.iastate.jtm.dic.AbstractTrieNode: Return the index of a character in this node's child array.
getIndex(char[]) - Method in class edu.iastate.jtm.dic.AbstractTrieNode
getIndex(CharSequence) - Method in class edu.iastate.jtm.dic.AbstractTrieNode
getIndex(char) - Method in class edu.iastate.jtm.dic.AsciiTrieNode: Return the index of a character in this node's child array.
getIndex(char) - Method in class edu.iastate.jtm.dic.DigitTrieNode: Return the index of a character in this node's child array.
getIndex(char) - Method in class edu.iastate.jtm.dic.FuzzyTrieNode: Return the index of a character in this node's child array.
getIndex(char) - Method in class edu.iastate.jtm.dic.LetterDigitTrieNode: Return the index of a character in this node's child array.
getIndex(char) - Method in class edu.iastate.jtm.dic.LetterTrieNode: Return the index of a character in this node's child array.
getIndex(char) - Method in class edu.iastate.jtm.dic.LowerTrieNode: Return the index of a character in this node's child array.
getIndex(char) - Method in interface edu.iastate.jtm.dic.TrieNode: Return the index of a character in this node's child array.
getIndex(char[]) - Method in interface edu.iastate.jtm.dic.TrieNode
getIndex(CharSequence) - Method in interface edu.iastate.jtm.dic.TrieNode
getIndex(char) - Method in class edu.iastate.jtm.dic.WordTrieNode: Return the index of a character in this node's child array.
getIndex() - Method in class edu.iastate.metnet.metaomgraph.SortableData
getIndex(TreeNode) - Method in class fcmodeler.pathbinder.gui.VerbNode
getIndexOfChild(Object, Object) - Method in class edu.iastate.metnet.model.CategoryTreeModel: get the index of one child
getInfoColumnCount() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
getInfoColumnNames() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Returns cleaned String representations of the names of the information columns.
getInfoColumns() - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog
getInfoPanel() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
getInformation() - Method in class edu.iastate.metnet.dao.MyVersionNode
getInhibitor() - Method in class edu.iastate.metnet.hibernate.BrendainhibitorKey: Returns the value of the inhibitor property.
getInitId() - Method in class edu.iastate.metnet.hibernate.AbstractChebiRelation: Return the value of the init_id column.
getInput() - Method in class edu.iastate.metnet.dao.AlignmentObject
getInputUsed() - Method in class edu.iastate.metnet.dao.AlignmentObject
getInsertTime() - Method in class edu.iastate.biocyc.dao.rdb.ClassName
getInsertTime() - Method in interface edu.iastate.metnet.dao.HistoryBlockunit: get the insert time
getInsertTime() - Method in class edu.iastate.metnet.dao.HistoryBlockunitImpl
getInsertTime() - Method in class edu.iastate.metnet.hibernate.AbstractClassName
getInsertTime() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getInsertTime() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getInsertTime() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
getInstance() - Static method in class edu.iastate.jtm.jmed.PubMedTimer: Get an instance of PubMedTimer.
getInstance() - Static method in class edu.iastate.metnet.analysis.MySolver
getInstance() - Static method in class edu.iastate.metnet.aracyc.GraphStatistics
getInstance() - Static method in class edu.iastate.metnet.aracyc.InteractionFix
getInstance() - Static method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame
getInstance() - Static method in class edu.iastate.metnet.birdseyeview.ExploRaseExpFrame
getInstance() - Static method in class edu.iastate.metnet.dataManager.DataManager
getInstance() - Static method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame
getInstance() - Static method in class edu.iastate.metnet.export.GraphExporterImpl: singleton pattern
getInstance() - Static method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
getInstance(String) - Method in class edu.iastate.metnet.hivemindService.Launcher: launches passed application if it is not launched already, and changes it to visible if it not.
getInstance() - Static method in class edu.iastate.metnet.hivemindService.RequestGene: used to get instance of this class
getInstance() - Static method in class edu.iastate.metnet.metaomgraph.ExploRaseFrame
getInstance() - Static method in class edu.iastate.metnet.metaomgraph.ListTransferHandler
getInstance() - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
getInstance() - Static method in class edu.iastate.metnet.newgui.MetNetStatusbar
getInstance() - Static method in class edu.iastate.metnet.threads.DataThread
getInstance() - Static method in class edu.iastate.metnet.ui.BlockunitFinder
getInstance() - Static method in class edu.iastate.metnet.utils.MyFacadeFactory: factory pattern
getInstance() - Static method in class edu.iastate.metnet.utils.MyMetnetServiceFactory: factory pattern
getInstance() - Static method in class edu.iastate.metnet.utils.MyPaperFactory: factory pattern
getInstance() - Static method in class edu.iastate.metnet.utils.MyXmlRpcClientFactory: get the instance of the client
getInstance() - Static method in class edu.iastate.metnet.utils.Utils
getIntegerValue() - Method in class edu.iastate.metnet.model.AbstractCodePresentation
getIntegerValue() - Method in class edu.iastate.metnet.model.CodeRulePresentation
getIntegerValue() - Method in interface edu.iastate.metnet.model.ICodePresentation
getInteraction() - Method in class edu.iastate.metnet.hibernate.Blockunit
getInteraction(int) - Method in class edu.iastate.reload.model.InteractionSearchTableModel
getInteractionChange(HistoryFlatInteraction) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the summary report about the change of version
getInteractionChange(HistoryFlatInteraction) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the summary report about the change of version
getInteractionColorForEdge(String) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor: get the color for interaction type
getInteractionInformation(int) - Method in class edu.iastate.metnet.model.InteractionSelectorModel
getInteractionList() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
getInteractionObject(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get more interaction information
getInteractionObject(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get more interaction information
getInteractionSet() - Method in class edu.iastate.metnet.dao.MetnetPathway
getInteractionSourceList() - Method in class edu.iastate.metnet.dao.PathwayObject
getInteractionSourceList() - Method in class edu.iastate.metnet.export.PathwayInfoImpl
getInteractionSourceList() - Method in interface edu.iastate.metnet.hiveface.PathwayInfo
getInteractionSourceString() - Method in class edu.iastate.metnet.dao.PathwayObject: return the string representation of interaction source
getInteractionSourceString() - Method in class edu.iastate.metnet.model.PathwayObjectChoice
getInteractionType() - Method in class edu.iastate.metnet.dao.MetnetInteraction
getInteractionType() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getInteractionType() - Method in class edu.iastate.metnet.graphmodel.MetaphorTypeInformation
getInteractionType() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getInteractionType() - Method in class edu.iastate.metnet.hibernate.Blockunit: (non-Javadoc)
getInteractionType() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject
getInteractionType() - Method in class edu.iastate.metnet.model.CompositionBlockunit
getInteractionType() - Method in class edu.iastate.metnet.model.SelectedBlockunit
getInteractionTypeList() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getInteractionUserList() - Method in class edu.iastate.metnet.dao.PathwayObject
getInteractionUserList() - Method in class edu.iastate.metnet.export.PathwayInfoImpl
getInteractionUserList() - Method in interface edu.iastate.metnet.hiveface.PathwayInfo
getInteractionUserString() - Method in class edu.iastate.metnet.dao.PathwayObject: return string representation of interaction user
getInteractionUserString() - Method in class edu.iastate.metnet.model.PathwayObjectChoice
getInteractionWidthForEdge(String) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor: get the line width for interaction type
getIntersectionNodes(Blockunit, Blockunit) - Static method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor: if the intermedia dummy node is removed already, guess the interaction from the two enity nodes
getIntersectionWithCase(List, List) - Static method in class edu.iastate.metnet.utils.Utils: get unique intersection of two vectors, case sensitive for string
getIntersectionWithoutCase(List, List) - Static method in class edu.iastate.metnet.utils.Utils: get the intersection of two vectors, case insensitive
getIntValue() - Method in class edu.iastate.metnet.db.ReturnCode
getInvolvedPbidSet(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the involved pathway list
getInvolvedPbidSet(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the involved pathway list
getIsAmbiguous() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Return the value of the is_ambiguous column.
getIsAmbiguous() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Return the value of the is_ambiguous column.
getIsAmbiguous() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the is_ambiguous column.
getIsControl() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Return the value of the is_control column.
getIsControl() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Return the value of the is_control column.
getIsControl() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the is_control column.
getISSN(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getIssue(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getItem(int) - Method in class edu.iastate.metnet.model.ConfidenceModel
getItemCount() - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet
getItemCount(int) - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet
getItemCount() - Method in interface edu.iastate.metnet.analysis.IExcelSheet
getItemCount(int) - Method in interface edu.iastate.metnet.analysis.IExcelSheet
getItemCount() - Method in class edu.iastate.metnet.model.AbstractPlotData
getItemCount(int) - Method in class edu.iastate.metnet.model.AbstractPlotData
getJGraph() - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
getJgraph() - Method in class edu.iastate.metnet.ui.PathwayEditor
getJournal(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getJournal() - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Return the value of the JOURNAL column.
getJournalLink(String) - Static method in class edu.iastate.jtm.jmed.MedCitation
getKey() - Method in class edu.iastate.jtm.dic.AbstractTrieNode: Return a node's key.
getKey() - Method in interface edu.iastate.jtm.dic.TrieNode: Return a node's key.
getKey() - Method in class edu.iastate.metnet.soft.Attribute
getKeyString() - Method in class edu.iastate.jtm.dic.AbstractTrieNode
getKeyString() - Method in interface edu.iastate.jtm.dic.TrieNode
getKi() - Method in class edu.iastate.metnet.dao.MetnetInteraction
getKi() - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Return the value of the Ki column.
getKm() - Method in class edu.iastate.metnet.dao.MetnetInteraction
getKm() - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Return the value of the Km column.
getLabel() - Method in class edu.iastate.metnet.dao.ZVertex
getLabel() - Method in class edu.iastate.metnet.metaomgraph.chart.RangeMarker
getLabel() - Method in class edu.iastate.metnet.newgui.LabelledComponent
getLanguages() - Static method in class edu.iastate.jtm.jmed.Query.SimpleTerm
getLastCorrelation() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
getLastDir() - Static method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
getLastDir() - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils: Retrieves the directory last accessed by the user (as set by Utils.setLastDir(File).
getLastDir() - Method in class edu.iastate.metnet.soft.SOFTParser
getLastMadeTransferable() - Method in class edu.iastate.metnet.metaomgraph.ListTransferHandler
getLastModifiedDate() - Method in class edu.iastate.metnet.dao.PathwayObject
getLastModifiedDate() - Method in class edu.iastate.metnet.export.PathwayInfoImpl
getLastModifiedDate() - Method in interface edu.iastate.metnet.hiveface.PathwayInfo
getLastModifiedDate() - Method in class edu.iastate.metnet.model.PathwayObjectChoice
getLastname() - Method in class edu.iastate.metnet.hibernate.AbstractUser: Return the value of the Lastname column.
getLastSearchResult() - Method in class edu.iastate.metnet.metaomgraph.TreeSearcher
getLatestHistory(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade: always get the latest history so we can determine if something is changed during the data load and update session.
getLatestHistory(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: always get the latest history so we can determine if something is changed during the data load and update session.
getLayout() - Method in class edu.iastate.metnet.birdseyeview.AbstractView: This method returns a layout which centers the view in the parent.
getLayout() - Method in class edu.iastate.metnet.birdseyeview.goview.GoView
getLeaves() - Method in class edu.iastate.metnet.aracyc.GenericTree: get the outdegree = 0's node in this graph
getLeaves(Object) - Method in class edu.iastate.metnet.aracyc.GenericTree: get the leaves in the subtree rooted by current node
getLeft() - Method in class edu.iastate.jtm.EntityFinder.Hit: Getter for property left.
getLeft(Object) - Method in class edu.iastate.metnet.dao.BidiMultiHashMap
getLeftEbidEidMap() - Method in class edu.iastate.metnet.dao.InteractionStructure
getLeftGraph() - Method in interface edu.iastate.metnet.dao.PathwayAlignment: get one pathway graph
getLeftGraph() - Method in class edu.iastate.metnet.dao.PathwayAlignmentImpl
getLeftId(int) - Method in class edu.iastate.jtm.util.ParenFinder: Get the pair ID for the left parenthesis.
getLeftIterator() - Method in class edu.iastate.metnet.dao.BidiMultiHashMap
getLeftList() - Method in class edu.iastate.biocyc.dao.txt.BiocycReaction: get left list
getLeftMostX(MyTreeAlgorithm.TreeNode) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: get the most left child tree node in this tree specified by the root node
getLeftNode() - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode
getLeftNode() - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode
getLeftPart() - Method in class edu.iastate.metnet.dao.MetnetInteraction
getLeftPart() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getLeftPart() - Method in class edu.iastate.metnet.hibernate.Interaction
getLeftPartEbidList() - Method in class edu.iastate.metnet.hibernate.HistoryFlatInteraction: get the mapping of the left ebid and coefficient
getLeftPartIDList() - Method in class edu.iastate.metnet.hibernate.Interaction
getLeftPosition(int) - Method in class edu.iastate.jtm.util.ParenFinder: Get the position of left parenthesis for pair "count".
getLeftSize() - Method in class edu.iastate.metnet.dao.BidiMultiHashMap
getLeftToRightMap() - Method in class edu.iastate.metnet.dao.BidiMultiHashMap
getLeftUnit() - Method in class edu.iastate.metnet.model.AbstractMultiBlockunitDecorator
getLeftWidth() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.TreeNode: get the total width of the left contour XXX !!! this algorithm has issues on graphs containing cycle (even the direction is not)
getLevel() - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode: This method returns the hierarchy level.
getLevelColors() - Method in class edu.iastate.metnet.birdseyeview.goview.GoBioProcessView
getLevelColors() - Method in class edu.iastate.metnet.birdseyeview.goview.GoFunctionView
getLevelColors() - Method in class edu.iastate.metnet.birdseyeview.goview.GoView: Subclasses must provide the different level colors.
getLevelDistance() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm
getLineValue(int) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile
getLineValues() - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile
getLink(String, String) - Method in class edu.iastate.reload.ui.HelpResource: get the help document for specific help
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.iastate.jtm.gui.RowHeaderRenderer
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.iastate.jtm.gui.RowHeaderTable.TableRowHeaderRenderer
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.iastate.metnet.birdseyeview.AnnotationRenderer
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.iastate.metnet.soft.SOFTParserOptionPanel
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class fcmodeler.pathbinder.gui.TipRenderer
getListDataListeners() - Method in class com.jgoodies.binding.extras.ListModelHolder: Returns an array of all the list data listeners registered on this ArrayListModel.
getListDisplay() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
getListModel() - Method in class edu.iastate.reload.ui.CommentEditForm
getListModel() - Method in class edu.iastate.reload.ui.ReferenceEditForm
getListModel() - Method in class edu.iastate.reload.ui.SynonymEditForm
getListTransferHandler() - Method in class edu.iastate.metnet.metaomgraph.ListPanel
getListTransferHandler() - Method in class edu.iastate.metnet.metaomgraph.ListTree
getLiveEntity() - Method in class edu.iastate.metnet.dao.InputNode
getLiveEntity(int) - Method in class edu.iastate.reload.model.EntitySearchTableModel
getLiveEntityChange(HistoryFlatLiveEntity) - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the summary report about the change of version
getLiveEntityChange(HistoryFlatLiveEntity) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the summary report about the change of version
getLoadController() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
getLocalGraph() - Method in class edu.iastate.metnet.graphmodel.MultiPathwayModel: return the local multi-pathway graph.
getLocalHome() - Static method in class edu.iastate.metnet.interfaces.MyFacadeUtil: Obtain local home interface from default initial context
getLocalHome() - Static method in class edu.iastate.metnet.interfaces.MyMetnetServiceUtil: Obtain local home interface from default initial context
getLocalPathwayMap() - Method in class edu.iastate.metnet.graphmodel.PathwayModel
getLocation() - Method in class edu.iastate.biocyc.dao.txt.BiocycGene: get the gene location for database
getLocation() - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
getLocation() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
getLocation() - Method in interface edu.iastate.metnet.dao.PathwayElementNode: get the subcellular location
getLocation() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getLocation() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Return the value of the Location column.
getLocation() - Method in class edu.iastate.metnet.hibernate.AbstractGtairProperty: Return the value of the Location column.
getLocation() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getLocation() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getLocation() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
getLocation() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject
getLocation() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo
getLocation() - Method in class edu.iastate.metnet.mapbuilder.NodeInfo
getLocation() - Method in class edu.iastate.metnet.model.CompositionBlockunit
getLocation() - Method in class edu.iastate.metnet.model.EntityPart
getLocation() - Method in class edu.iastate.metnet.model.SelectedBlockunit
getLocationColorForVertex(String) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor: return the vertext background color
getLocationConfideceMap() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getLocationConfideceMap() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getLocationConfideceMap() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getLocationConfidence(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getLocationConfidence(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getLocationconfidence() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getLocationconfidence() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitconfidence: Return the value of the LocationConfidence column.
getLocationConfidence() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getLocationconfidence() - Method in class edu.iastate.metnet.hibernate.Blockunit
getLocationConfidence(String) - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getLocationconfidence() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject
getLocationConfidence() - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
getLocationInRef() - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference: Return the value of the location_in_ref column.
getLocationList() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getLocationNameList() - Method in class edu.iastate.metnet.ui.BlockunitFinder
getLocations() - Method in class edu.iastate.metnet.birdseyeview.Annotation: Returns the locations.
getLocations(Integer) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method returns a list of cellular locations for the given entity.
getLocations(Integer) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getLocationString() - Method in class edu.iastate.metnet.birdseyeview.Annotation: Returns the location string.
getLocCon() - Method in class edu.iastate.metnet.mapbuilder.NodeInfo
getLocusID() - Method in class edu.iastate.metnet.birdseyeview.Annotation: Returns the locus ID.
getLocusid() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the locus id
getLocusid() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getLocusid() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getLocusid() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getLocusId() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Return the value of the locus_id column.
getLocusId() - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Return the value of the locus_id column.
getLocusId() - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Return the value of the locus_id column.
getLocusId() - Method in class edu.iastate.metnet.hibernate.AbstractTairAgiToUniprot: Return the value of the locus_id column.
getLocusId() - Method in class edu.iastate.metnet.hibernate.AbstractTairAracycDump: Return the value of the locus_id column.
getLocusId() - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Return the value of the locus_id column.
getLocusId() - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Return the value of the locus_id column.
getLocusId() - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Return the value of the locus_id column.
getLocusid() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the locus id
getLocusIDs(String) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method converts the given affymetrix ID (..._at) into Locus IDs (AT-G----...) by querying a cross-ref table in the Metnet DB.
getLocusIDs(String) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getLongterm() - Method in class edu.iastate.metnet.hibernate.AbstractAbbreviationrules: Return the value of the longterm column.
getLongTerm(int) - Method in class edu.iastate.metnet.model.AbbreviationRulesModel
getM_jtGraph() - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter
getMainWindow() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph: Fetches the main JFrame used by this program
getMainWindow2() - Static method in class edu.iastate.metnet.ui.MainWindow2: get the current main window instance
getMapmanBinId() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getMapmanBinId() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMapmanBinId() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getMapmanBinIdList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getMapmanBinIdList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMapmanBinIdList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getMapmanCategory() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getMapmanCategory() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMapmanCategory() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getMapmanCategoryList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getMapmanCategoryList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMapmanCategoryList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getMapmanDescription() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getMapmanDescription() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMapmanDescription() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getMapmanDescriptionList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getMapmanDescriptionList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMapmanDescriptionList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getMapping(Object, boolean) - Method in class edu.iastate.metnet.ui.OverviewPanel.ViewRedirector
getMapping(Object, boolean) - Method in class edu.iastate.reload.ui.OverviewPanel.ViewRedirector
getMatchedKey() - Method in class edu.iastate.jtm.dic.AbstractDictionary
getMatchedKey() - Method in class edu.iastate.jtm.dic.HashDictionary
getMatchedKey() - Method in class edu.iastate.jtm.dic.TrieDictionary
getMatchedValue() - Method in class edu.iastate.jtm.dic.AbstractDictionary
getMaxNameLength() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the length of the longest data column header in this project.
getMaxWidth() - Method in class edu.iastate.metnet.dataManager.JMultilineLabel
getMbidPbidMap() - Method in class edu.iastate.metnet.graphmodel.PathwayModel: get the relation among all member blockid and pathway blockid mapping relation
getMD5Digest(String) - Static method in class edu.iastate.metnet.utils.MD5Digest: get the MD5 digest of the input string
getMember() - Method in class edu.iastate.metnet.hibernate.GroupMemberKey: Returns the value of the member property.
getMenuAlignAracyc() - Method in class edu.iastate.metnet.ui.PathwayEditor: create menu for aligning pathway
getMenuDisabledForeground() - Method in class edu.iastate.reload.skin.OceanThemeX: Returns the OceanTheme's color for disabled menu foreground,
getMenuDisabledForeground() - Method in class javax.swing.plaf.metal.OceanTheme: Returns the OceanTheme's color for disabled menu foreground,
getMenuHighlightDelta() - Method in class edu.iastate.metnet.ui.PathwayEditor: menu for comparing pathways
getMenuItemSelectedBackground() - Method in class edu.iastate.metnet.ui.Desert
getMenuItemSelectedBackground() - Method in class edu.iastate.metnet.ui.Oasis
getMenuItemSelectedForeground() - Method in class edu.iastate.metnet.ui.Desert
getMenuItemSelectedForeground() - Method in class edu.iastate.metnet.ui.Oasis
getMenuSaveVersion() - Method in class edu.iastate.metnet.ui.VersionEditor
getMenuSelectedBackground() - Method in class edu.iastate.metnet.ui.Desert
getMenuSelectedBackground() - Method in class edu.iastate.metnet.ui.Oasis
getMenuTextFont() - Method in class edu.iastate.reload.skin.DefaultMetalThemeX: Returns the font used for text in menus.
getMenuTextFont() - Method in class javax.swing.plaf.metal.DefaultMetalTheme: Returns the font used for text in menus.
getMeshHeadingList(Element) - Static method in class edu.iastate.jtm.jmed.CitationManager
getMessage() - Method in class edu.iastate.jtm.assistant.CitationPool
getMessage() - Method in class edu.iastate.jtm.gui.DefaultMonitorable
getMessage() - Method in interface edu.iastate.jtm.gui.Monitorable
getMessage() - Method in exception edu.iastate.metnet.birdseyeview.FieldNotFoundException
getMessage() - Method in class fcmodeler.pathbinder.MedLeaseClient
getMetaboliteMap() - Method in class edu.iastate.metnet.export.GraphExporterImpl
getMetaboliteMap() - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get the map from metabolite blockid to name
getMetaboliteMap() - Method in interface edu.iastate.metnet.interfaces.MyFacade: get the map from metabolite blockid to name
getMetaboliteMap() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: get the map from metabolite blockid to name
getMetaboliteMap() - Method in interface edu.iastate.metnet.interfaces.MyMetnetService: get the map from metabolite blockid to name
getMetaboliteMap() - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal: get the map from metabolite blockid to name
getMetaboliteObject(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl
getMetaboliteObject(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter: get additional metabolite information.
getMetalion() - Method in class edu.iastate.metnet.hibernate.BrendametalionKey: Returns the value of the metalion property.
getMetaOmGraph() - Static method in class edu.iastate.metnet.launch.LaunchMetNet
getMetaphorGraph() - Method in class edu.iastate.reload.ui.NetworkEditForm: current jgraph object
getMetnetEntityID() - Method in class edu.iastate.metnet.birdseyeview.Annotation: Returns the metnet entity ID.
getMetnetEntityID(String) - Method in class edu.iastate.metnet.birdseyeview.db.Database: This method converts the given locus ID into a Metnet Entity ID by querying the Metnet DB.
getMetnetEntityID(String) - Method in class edu.iastate.metnet.hivemindService.AnnotationService
getMetNetInfo(Object[]) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils
getMetNetInfo(String) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils
getMetnetInteraction(int) - Method in class edu.iastate.reload.model.InteractionObjectTableModel
getMetnetLiveEntity(int) - Method in class edu.iastate.reload.model.EntityObjectTableModel
getMetnetLocation() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of metnet location
getMetnetLocation() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getMetnetLocation() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getMetnetLocation() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMetnetLocation() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of metnet location
getMetnetLocationList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getMetnetLocationList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMetnetLocationList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getMetnetPathway() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: get the list of metnet pathway
getMetnetPathway() - Method in interface edu.iastate.metnet.datamodel.db.Gene
getMetnetPathway() - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
getMetnetPathway() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMetnetPathway() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject: get the list of metnet pathway
getMetnetPathwayList() - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject
getMetnetPathwayList() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
getMetnetPathwayList() - Method in interface edu.iastate.metnet.hiveface.AtGeneSearchObject
getMinCapacity() - Method in class edu.iastate.metnet.birdseyeview.goview.GoLevel: This method returns current level's capacity
getminCapacity() - Method in class edu.iastate.metnet.birdseyeview.ViewInfo
getMinimumSize() - Method in class edu.iastate.metnet.birdseyeview.GenePanel
getMinimumSize() - Method in class edu.iastate.metnet.birdseyeview.ImagePanel
getMinimumSize() - Method in class edu.iastate.metnet.dataManager.JMultilineLabel
getMinX() - Method in class edu.iastate.metnet.dao.ZVertex
getMinY() - Method in class edu.iastate.metnet.dao.ZVertex
getMissingAttributes() - Method in class edu.iastate.metnet.soft.Entity
getMitochondrialTargetingPeptideScore() - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Return the value of the mitochondrial_targeting_peptide_score column.
getMitochondrionFamily() - Static method in class edu.iastate.metnet.graphmodel.NetworkEditHelper: get the location belongs to mitochondrion.
getModalMaker() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph: Fetches the WindowListener used to make a frame/dialog modal, but still be able to access the Help frame.
getMode() - Method in class edu.iastate.metnet.launch.RunCytoscape
getModel() - Method in class edu.iastate.jtm.gui.TableMap
getModel() - Method in class edu.iastate.metnet.dao.AlignmentObject
getModel() - Method in class edu.iastate.metnet.model.TableMap
getModelIdCellMap() - Method in class edu.iastate.metnet.graphmodel.ValidityMetaphor
getModelUsed() - Method in class edu.iastate.metnet.dao.AlignmentObject
getModifyPanel() - Method in class edu.iastate.metnet.ui.RefService
getModifyPanel() - Method in class edu.iastate.metnet.ui.WebDBService
getMolecularWeight() - Method in class edu.iastate.biocyc.dao.txt.BiocycCompound: get the molecular weight of the compound
getMolecularWeight() - Method in class edu.iastate.metnet.aracyc.AracycCompound
getMolID() - Method in class edu.iastate.metnet.mapbuilder.NodeInfo
getMultiNodeFlag() - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph
getMultiSelectionModel() - Method in class edu.iastate.metnet.ui.NodeSelectionForm
getMyPlatform() - Method in class edu.iastate.metnet.soft.Series
getMyVersionGraph() - Method in class edu.iastate.metnet.graphmodel.VersionGraphModel: get the version graph structure
getMyVersionGraph() - Method in class edu.iastate.metnet.ui.VersionEditor
getName() - Method in class edu.iastate.biocyc.dao.rdb.ClassName
getName() - Method in class edu.iastate.jtm.jmed.MeshDescriptor
getName() - Method in class edu.iastate.metnet.aracyc.AracycEntity: return the name
getName() - Method in class edu.iastate.metnet.birdseyeview.Annotation: Returns the name.
getName() - Method in class edu.iastate.metnet.birdseyeview.goview.GoTerm: Returns the name.
getName() - Static method in class edu.iastate.metnet.birdseyeview.pathwayview.Compartment: This method returns the name of the compartment.
getName() - Method in class edu.iastate.metnet.birdseyeview.Protein: Returns the name.
getName() - Method in class edu.iastate.metnet.birdseyeview.ViewInfo: Returns the name.
getName() - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode
getName() - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
getName() - Method in class edu.iastate.metnet.dao.CategoryNode
getName() - Method in class edu.iastate.metnet.dao.ChebiOntologyName: return the chebiname
getName() - Method in interface edu.iastate.metnet.dao.HistoryBlockunit: get the name of the history stuff
getName() - Method in class edu.iastate.metnet.dao.HistoryBlockunitImpl
getName() - Method in class edu.iastate.metnet.dao.HistoryInformation
getName() - Method in interface edu.iastate.metnet.dao.IMetnetBlockUnit: get the name
getName() - Method in class edu.iastate.metnet.dao.InteractionInformation
getName() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
getName() - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode: used to display the name of the node
getName() - Method in class edu.iastate.metnet.dao.NameSource
getName() - Method in interface edu.iastate.metnet.dao.PathwayElementNode: get the name of the data instance
getName() - Method in class edu.iastate.metnet.dao.PathwayObject
getName() - Method in class edu.iastate.metnet.dao.TrivialMetabolite
getName() - Method in interface edu.iastate.metnet.datamodel.Entity
getName() - Method in class edu.iastate.metnet.datamodel.EntityImpl
getName() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl
getName() - Method in class edu.iastate.metnet.export.GobiNodeImpl: get the search string
getName() - Method in class edu.iastate.metnet.export.PathwayCategoryNodeImpl
getName() - Method in class edu.iastate.metnet.export.PathwayInfoImpl
getName() - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Return the value of the Name column.
getName() - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Return the value of the name column.
getName() - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames: Return the value of the name column.
getName() - Method in class edu.iastate.metnet.hibernate.AbstractClassName
getName() - Method in class edu.iastate.metnet.hibernate.AbstractCodedatasource: Return the value of the name column.
getName() - Method in class edu.iastate.metnet.hibernate.AbstractCodeinteractiontype: Return the value of the name column.
getName() - Method in class edu.iastate.metnet.hibernate.AbstractCodelocation: Return the value of the name column.
getName() - Method in class edu.iastate.metnet.hibernate.AbstractCodereferencetype: Return the value of the name column.
getName() - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Return the value of the Name column.
getName() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
getName() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
getName() - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
getName() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject
getName() - Method in interface edu.iastate.metnet.hiveface.GobiNode: get the search string for one node
getName() - Method in interface edu.iastate.metnet.hiveface.PathwayCategoryNode
getName() - Method in interface edu.iastate.metnet.hiveface.PathwayInfo
getName() - Method in class edu.iastate.metnet.hivetest.GobiNodeImpl: get the search string
getName() - Method in class edu.iastate.metnet.model.CompositionBlockunit
getName() - Method in class edu.iastate.metnet.model.EntityPart
getName() - Method in class edu.iastate.metnet.model.NodeSelectionModel
getName() - Method in class edu.iastate.metnet.model.PathwayObjectChoice
getName() - Method in class edu.iastate.metnet.model.SelectedBlockunit
getName() - Method in class edu.iastate.metnet.ui.Desert
getName() - Method in class edu.iastate.metnet.ui.HelpWindow.HelpPage
getName() - Method in class edu.iastate.metnet.ui.Oasis
getName() - Method in class edu.iastate.metnet.ui.PropertiesMetalTheme
getName() - Method in class edu.iastate.reload.skin.DefaultMetalThemeX: Returns the name of the theme.
getName() - Method in class edu.iastate.reload.skin.OceanThemeX: Returns the name of this theme, "Ocean"
getName() - Method in class javax.swing.plaf.metal.DefaultMetalTheme: Returns the name of the theme.
getName() - Method in class javax.swing.plaf.metal.OceanTheme: Returns the name of this theme, "Ocean"
getNameLength() - Method in class edu.iastate.metnet.metaomgraph.chart.ChartToolBar
getNameMap() - Method in class edu.iastate.metnet.aracyc.ChangeName
getNames() - Method in class edu.iastate.metnet.birdseyeview.cellview.CellularLocation: Returns the names.
getNames() - Method in class edu.iastate.metnet.dao.Candidate
getNames() - Method in class edu.iastate.metnet.model.CheckCandidate
getNameSource() - Method in class edu.iastate.metnet.dao.ChebiOntologyName
getNewIcon(boolean) - Static method in class edu.iastate.jtm.gui.IconLib
getNext() - Method in class edu.iastate.metnet.launch.ListNode
getNextName() - Method in class edu.iastate.metnet.newgui.oldWizardPanel
getNextRecordId() - Method in class edu.iastate.metne