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Sample - Class in edu.iastate.metnet.soft
Sample(String) - Constructor for class edu.iastate.metnet.soft.Sample
SAMPLE - Static variable in class fcmodeler.pathbinder.MedLeaseClient
samplePlainFromParser(MedlineParser, String) - Method in class edu.iastate.jtm.jmed.PubMedSampler
samplePmidFromFile(File) - Method in class edu.iastate.jtm.jmed.PubMedSampler: Random sample PMIDs from a file containing a list of PMIDs: 1 PMID/line.
samplePmidFromParser(MedlineParser) - Method in class edu.iastate.jtm.jmed.PubMedSampler
samplePmidFromQuerier(PubMedQuerier) - Method in class edu.iastate.jtm.jmed.PubMedSampler
sampleXmlFromParser(MedlineParser, String, boolean) - Method in class edu.iastate.jtm.jmed.PubMedSampler
save(File) - Method in class edu.iastate.jtm.assistant.CitationPool
save(File) - Method in class edu.iastate.jtm.util.VocabularyCounter: Save word count to output.
SAVE_AS_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmGraph
SAVE_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmGraph
SAVE_CORRELATION_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
SAVE_SORT_ACTION_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog
saveAnnotations(OutputStream) - Method in class edu.iastate.metnet.birdseyeview.RootPanel: This method calls the text panel to save the selected gene annotations.
saveAnnotations(OutputStream) - Method in class edu.iastate.metnet.birdseyeview.TextPanel: This method saves the selected gene annotations as delimited text.
saveAnnotationsToFile() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: This method enables the user to save the selected gene annotations to a file.
saveAsPNG(File) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
saveAsPNG(File, int, int) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
saveAsPNG(Component, File, int, int) - Static method in class edu.iastate.metnet.metaomgraph.ComponentToImage
saveAsPNG(Component, File) - Static method in class edu.iastate.metnet.metaomgraph.ComponentToImage
SaveButtonListener - Class in edu.iastate.metnet.birdseyeview: The SaveButtonListener Class notifies the controller that the user would like to save the annotation data.
SaveButtonListener(BirdsEyeView) - Constructor for class edu.iastate.metnet.birdseyeview.SaveButtonListener: Constructor.
saveGraph(Integer, MetnetPathway, DirectedGraph, Map, MultiKeyMap, String, String, boolean) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: save graph to the database.
saveGraph(Integer, MetnetPathway, DirectedGraph, Map, MultiKeyMap, String, String, boolean) - Method in interface edu.iastate.metnet.interfaces.MyPaper: save graph to the database.
saveInteractionDeletionHistory(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: save the deletion history, who delete it and when it is deleted, we can use null name to determine this is a saved deletion history
saveInteractionDeletionHistory(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper: save the deletion history, who delete it and when it is deleted, we can use null name to determine this is a saved deletion history
saveKeywords(File) - Method in class edu.iastate.jtm.assistant.Highlighter
saveLiveEntityDeletionHistory(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: save the deletion history
saveLiveEntityDeletionHistory(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper: save the deletion history
saveNetwork4All() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: save all compilation in the database.
saveNetwork4All() - Method in interface edu.iastate.metnet.interfaces.MyPaper: save all compilation in the database.
savePathwayDeletionHistory(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: move the current pathway to the history.
savePathwayDeletionHistory(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper: move the current pathway to the history.
saveProject(File) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Saves this MetaOmProject to a given file.
saveQueries(TreeSearchQueryConstructionPanel.QuerySet, String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Stores the given metadata query
saveSort(CustomSortDialog.CustomSortObject, String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Stores the given custom sort.
saveToFile(File) - Method in class edu.iastate.jtm.dic.AbstractDictionary
SB - Static variable in class edu.iastate.jtm.jmed.Query.Field
SBMLExporter - Class in edu.iastate.metnet.ui
SBMLExporter() - Constructor for class edu.iastate.metnet.ui.SBMLExporter
SBMLExporter(String) - Constructor for class edu.iastate.metnet.ui.SBMLExporter
scaleChanged(double) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
scaleChanged(double) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
scaledHeight - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
scaledHeight - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
scaledWidth - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
scaledWidth - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
scanCitation(String, String) - Method in class fcmodeler.pathbinder.MedCrawler
scanFile(File) - Method in class fcmodeler.pathbinder.MedCrawler
Score - Variable in class fcmodeler.pathbinder.gui.EntityPanel.EntityScore
Score - Variable in class fcmodeler.pathbinder.gui.EntityPanel.InteractionScore
score(PbSentence[], Set[]) - Method in class fcmodeler.pathbinder.PathBinder
scoreSentence(String) - Method in class fcmodeler.pathbinder.SentenceScorer: Calculate the probability of a sentence describing an interaction.
scoreSentences(PbSentence[], Set[]) - Method in class fcmodeler.pathbinder.SentenceScorer: Score a list of sentences based on their interaction scores.
screenToChart(Point2D) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel: Converts a point on the screen to a point on the chart.
ScreenUtil - Class in edu.iastate.jtm.gui
ScreenUtil() - Constructor for class edu.iastate.jtm.gui.ScreenUtil
ScriptSink - Class in edu.iastate.metnet.aracyc
ScriptSink() - Constructor for class edu.iastate.metnet.aracyc.ScriptSink
ScrollingTexturePanel - Class in edu.iastate.metnet.metaomgraph
ScrollingTexturePanel(InputStream, int, int) - Constructor for class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel
ScrollingTexturePanel(File, int, int) - Constructor for class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel
ScrollingTexturePanel.ColorFader - Class in edu.iastate.metnet.metaomgraph
ScrollingTexturePanel.ColorFader(Color) - Constructor for class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel.ColorFader
scrollPaneInteraction - Variable in class edu.iastate.metnet.ui.InteractionSelector: scroll pane for the table
SE_CORNER - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
SE_CORNER - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
SEARCH - Variable in class edu.iastate.biocyc.io.AttributeFileReaderEx: file line scanner status for one unique-id record
search(String) - Method in class edu.iastate.jtm.assistant.PubMedAssistant
search() - Method in class edu.iastate.jtm.assistant.QueryPanel
SEARCH - Variable in class edu.iastate.metnet.aracyc.AttributeFileReader: file line scanner status for one unique-id record
SEARCH - Variable in class edu.iastate.metnet.aracyc.AttributeFileReaderEx: file line scanner status for one unique-id record
search(int) - Method in class fcmodeler.pathbinder.gui.EntityPanel
search() - Method in class fcmodeler.pathbinder.gui.TaxonomyPanel
search(Gene, Gene) - Method in class fcmodeler.pathbinder.SentenceService
SearchByPubMed - Class in edu.iastate.metnet.hivemindService: HiveMind service searches documents for a gene using PubMed
SearchByPubMed() - Constructor for class edu.iastate.metnet.hivemindService.SearchByPubMed
SearchDialog - Class in edu.iastate.metnet.ui
SearchDialog() - Constructor for class edu.iastate.metnet.ui.SearchDialog
SearchDialog(PathwayEditor) - Constructor for class edu.iastate.metnet.ui.SearchDialog
SearchDialog_btnAppply_actionAdapter - Class in edu.iastate.metnet.ui
SearchDialog_btnAppply_actionAdapter(SearchDialog) - Constructor for class edu.iastate.metnet.ui.SearchDialog_btnAppply_actionAdapter
SearchDialog_btnClose_actionAdapter - Class in edu.iastate.metnet.ui
SearchDialog_btnClose_actionAdapter(SearchDialog) - Constructor for class edu.iastate.metnet.ui.SearchDialog_btnClose_actionAdapter
searchEntities(Gene, Gene) - Method in class fcmodeler.pathbinder.SentenceService
searchEntities(String, String) - Method in class fcmodeler.pathbinder.SentenceService: Method used to search for two String from CytoScape.
searchEntitiesByName(String, String) - Method in class fcmodeler.pathbinder.SentenceService
searchEntityByName(String, boolean, boolean) - Method in class fcmodeler.pathbinder.PathBinder
searchFromService(JList, JCheckBox) - Method in class fcmodeler.pathbinder.gui.EntityPanel: Added by Mohammed ALabsi - To perform search from service.
searchGene(Gene) - Method in class edu.iastate.metnet.hivemindService.SearchByPubMed: Searches for publications using Gene object
searchGeneById(String) - Method in class edu.iastate.metnet.hivemindService.SearchByPubMed: searches for publications using gene id
searchInteractionType(String) - Method in class edu.iastate.metnet.ui.PathwayEditor: search interaction type
SearchInteractionTypeMetaphor - Class in edu.iastate.metnet.graphmodel
SearchInteractionTypeMetaphor() - Constructor for class edu.iastate.metnet.graphmodel.SearchInteractionTypeMetaphor
SearchInteractionTypeMetaphor(String) - Constructor for class edu.iastate.metnet.graphmodel.SearchInteractionTypeMetaphor
searchName() - Method in class edu.iastate.metnet.controller.NodeSelectionController
SearchNameMetaphor - Class in edu.iastate.metnet.graphmodel
SearchNameMetaphor() - Constructor for class edu.iastate.metnet.graphmodel.SearchNameMetaphor
SearchNameMetaphor(String) - Constructor for class edu.iastate.metnet.graphmodel.SearchNameMetaphor
searchNodeName(String) - Method in class edu.iastate.metnet.ui.PathwayEditor: search node name in the graph
SearchPanel - Class in fcmodeler.pathbinder.gui
SearchPanel(EntityPanel, int) - Constructor for class fcmodeler.pathbinder.gui.SearchPanel
SearchPanel(TaxonomyPanel, int) - Constructor for class fcmodeler.pathbinder.gui.SearchPanel
searchService(String) - Method in class edu.iastate.jtm.assistant.PubMedAssistant
SECONDARY1 - Static variable in class edu.iastate.reload.skin.OceanThemeX: The OceanTheme value for secondary1.
SECONDARY1 - Static variable in class javax.swing.plaf.metal.OceanTheme: The OceanTheme value for secondary1.
SECONDARY2 - Static variable in class edu.iastate.reload.skin.OceanThemeX: The OceanTheme value for secondary2.
SECONDARY2 - Static variable in class javax.swing.plaf.metal.OceanTheme: The OceanTheme value for secondary2.
SECONDARY3 - Static variable in class edu.iastate.reload.skin.OceanThemeX: The OceanTheme value for secondary3.
SECONDARY3 - Static variable in class javax.swing.plaf.metal.OceanTheme: The OceanTheme value for secondary3.
seek(long) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile: Set the position in the file for the next read or write.
seek(long) - Method in class edu.iastate.metnet.soft.RandomAccessFile: Set the position in the file for the next read or write.
seekAndRead(long, char) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile
select(Object) - Static method in class edu.iastate.metnet.db.ReturnCode
SelectAllButton - Class in edu.iastate.metnet.mapbuilder
SelectAllButton(JCheckBox[]) - Constructor for class edu.iastate.metnet.mapbuilder.SelectAllButton: Creates the SelectAllButton
selected - Variable in class edu.iastate.metnet.model.PathwayObjectChoice: if selected
selected - Variable in class edu.iastate.metnet.model.SpeciesChoice: selected or not
selectedAnnotation - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
SelectedBlockunit - Class in edu.iastate.metnet.model
SelectedBlockunit() - Constructor for class edu.iastate.metnet.model.SelectedBlockunit
selectedBlockunits - Variable in class edu.iastate.metnet.model.NodeSelectionModel
selectedBorder - Variable in class edu.iastate.metnet.StripedTable.ColorRenderer
selectedItem(double, double) - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet
selectedItem(double, double) - Method in class edu.iastate.metnet.analysis.DefaultJExcelClient
selectedItem(List) - Method in class edu.iastate.metnet.analysis.DefaultJExcelClient
selectedItem(double, double) - Method in class edu.iastate.metnet.model.AbstractPlotData
selectedList - Static variable in class edu.iastate.metnet.birdseyeview.ExploRaseExpFrame
selectedList - Static variable in class edu.iastate.metnet.metaomgraph.ExploRaseFrame
selectedObject - Variable in class edu.iastate.metnet.model.JDBCComboModel: Creates a new instance of JDBCComboModel
selectedSeries(double, double) - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet: given the point (x0, y0) and the line segment (x1, y1) -- (x2, y2), the distance d = |(x2-x1)(y1-y0)-(x1-x0)(y2-y1)| / sqrt((x2-x1)^2+(y2-y1)^2)
selectedSeries(double, double) - Method in interface edu.iastate.metnet.analysis.IExcelSheet
selectedSeries(double, double) - Method in class edu.iastate.metnet.model.AbstractPlotData: given the point (x0, y0) and the line segment (x1, y1) -- (x2, y2), the distance d = |(x2-x1)(y1-y0)-(x1-x0)(y2-y1)| / sqrt((x2-x1)^2+(y2-y1)^2)
SelectionListener - Class in edu.iastate.metnet.ui: the selection listener of the graph
SelectionListener(PathwayEditor) - Constructor for class edu.iastate.metnet.ui.SelectionListener
SelectionListener - Class in edu.iastate.reload.ui: the selection listener of the graph
SelectionListener(NetworkEditForm) - Constructor for class edu.iastate.reload.ui.SelectionListener: default constructor
selectList(String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel: Selects the given gene list, if it exists.
selectNode(String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
SelectPathwayPanel - Class in edu.iastate.metnet.mapbuilder
SelectPathwayPanel() - Constructor for class edu.iastate.metnet.mapbuilder.SelectPathwayPanel
SelectPathwayPanel.UpdateListingListener - Class in edu.iastate.metnet.mapbuilder: Implementation of the "Retrieve Pathway Information" button.
SelectPathwayPanel.UpdateListingListener() - Constructor for class edu.iastate.metnet.mapbuilder.SelectPathwayPanel.UpdateListingListener
selectRows(Collection<Integer>) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
selectValues(String[]) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
sendQuery(String) - Method in class edu.iastate.jtm.assistant.GoogleScholar
sendQuery(String, Limits) - Method in class edu.iastate.jtm.jmed.ESearch
sendQuery(String, Limits, boolean) - Method in class edu.iastate.jtm.jmed.ESearch: Send a query to PubMed.
sendQuery(String) - Method in class edu.iastate.jtm.jmed.ESearch
sendQuery(String, boolean) - Method in class edu.iastate.jtm.jmed.ESearch
sendQuery(String, Limits) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
sendQuery(String, Limits, boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier: Send a query to PubMed.
sendQuery(String) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
sendQuery(String, boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
sendQuery(String[]) - Method in class edu.iastate.jtm.jmed.UmlsSocketClient: Send a query to the server.
sendQuery(boolean, boolean, Set, Set) - Method in class fcmodeler.pathbinder.PathBinder
SentencePane - Class in fcmodeler.pathbinder.gui
SentencePane() - Constructor for class fcmodeler.pathbinder.gui.SentencePane
SentencePane(PathBinder) - Constructor for class fcmodeler.pathbinder.gui.SentencePane
SentenceParser - Class in edu.iastate.jtm: Parse a paragraph into single sentences.
SentenceParser() - Constructor for class edu.iastate.jtm.SentenceParser
SentenceScorer - Class in fcmodeler.pathbinder
SentenceScorer() - Constructor for class fcmodeler.pathbinder.SentenceScorer
SentenceService - Class in fcmodeler.pathbinder
SentenceService() - Constructor for class fcmodeler.pathbinder.SentenceService
SEPARATOR - Static variable in class edu.iastate.jtm.util.NameCharType
seq - Variable in class edu.iastate.metnet.birdseyeview.ColorPanel
seq - Variable in class edu.iastate.metnet.birdseyeview.LegendPanel.spinnerListener
SEQID - Static variable in class edu.iastate.jtm.jmed.Limits
sequence - Static variable in class edu.iastate.biocyc.utils.BiocycUtils: start point of the unique id
Series - Class in edu.iastate.metnet.soft
Series(String) - Constructor for class edu.iastate.metnet.soft.Series
SERVER_KEY - Variable in class edu.iastate.metnet.aracyc.ConsoleApplication: server node in the configure file
service() - Method in class edu.iastate.metnet.ui.PlatformService
ServiceTest - Class in edu.iastate.metnet.metaomgraph
ServiceTest() - Constructor for class edu.iastate.metnet.metaomgraph.ServiceTest
sessionFile - Variable in class edu.iastate.metnet.launch.RunCytoscape
sessionOrganism - Static variable in class edu.iastate.metnet.ui.MainWindow2: organism that the curator can edit
sessionUserLevel - Static variable in class edu.iastate.metnet.ui.MainWindow2: user level: 0 - guest, browse only, 1 - normal, browse only, 2 - expert user, can edit all data, 3 - administrator, can edit all data.
sessionUsername - Static variable in class edu.iastate.metnet.ui.MainWindow2: user name to login
setAbbreviation(String) - Method in class edu.iastate.metnet.dao.AbbreviationObject
setAbbreviation(String) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitabbreviation: Set the value of the Abbreviation column.
setAbbreviation(String) - Method in class edu.iastate.metnet.hibernate.EntityabbreviationKey: Sets the value of the abbreviation property.
setAbstract_(String) - Method in class edu.iastate.metnet.dao.TairReferenceObject
setAc(String) - Method in class edu.iastate.metnet.hibernate.Externaldb
setAc(String) - Method in class edu.iastate.metnet.hibernate.ExternaldbKey: Sets the value of the ac property.
setAccessionInt(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession: Set the value of the accession_int column.
setActionState(boolean) - Method in class edu.iastate.metnet.birdseyeview.MainExperimentComboBoxListener: This method changes the action state.
setActionTime(Date) - Method in class edu.iastate.metnet.dao.HistoryInformation
setActionType(String) - Method in class edu.iastate.metnet.dao.HistoryInformation
setActivatingcompound(String) - Method in class edu.iastate.metnet.hibernate.BrendaactivatingcompoundKey: Sets the value of the activatingcompound property.
setActiveColumn(int) - Method in class fcmodeler.pathbinder.gui.EntityPanel
setActiveLabel(String) - Method in class edu.iastate.metnet.metaomgraph.DualListPanel: Sets the label that appears above the active list.
setActiveLabel(String) - Method in class edu.iastate.metnet.metaomgraph.DualTablePanel: Sets the label that appears above the active list.
setAddPathwayController(AddPathwayController) - Method in class edu.iastate.metnet.ui.AddPathwayForm
setAddPathwayForm(AddPathwayForm) - Method in class edu.iastate.metnet.controller.AddPathwayController
setAddPathwayModel(AddPathwayModel) - Method in class edu.iastate.metnet.controller.AddPathwayController
setAffiliation(String) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the value of the Affiliation column.
setAffy25kID(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setAffy25kID(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setAffy8kID(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setAffy8kID(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setAfgcID(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setAfgcID(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setAlignMap(Map) - Method in class edu.iastate.metnet.dao.AlignmentObject
setAlignment(PathwayAlignment) - Method in class edu.iastate.metnet.dao.MultiPathwayGraphImpl
setAlignment(Integer, Integer) - Method in interface edu.iastate.metnet.dao.PathwayAlignment: put the alignment relation
setAlignment(Integer, Integer) - Method in class edu.iastate.metnet.dao.PathwayAlignmentImpl: put the alignment relation
setAlignment(int) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: set alignment as SwingConstants.TOP SwingConstants.CENTER SwingConstants.BOTTOM
setAlignmentIndex(int) - Method in class edu.iastate.metnet.ui.PathwayEditor
setAllGenesLocusID(ArrayList<String>) - Static method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame
setAllGenesLocusID(ArrayList<String>) - Static method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame
setAllGenesLocusID(ArrayList<String>) - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
setAllLocationMap(HashMap) - Static method in class edu.iastate.metnet.hivemindService.AnnotationService
setAllPathwayList(ArrayList<Integer>) - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
setAllPathwayNameList(ArrayList<String>) - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
setAndRelation(boolean) - Method in class edu.iastate.metnet.graphmodel.RelationObject
setAnnotationDatabase(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the annotation_database column.
setAnnotations(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: This method sets the annotations list.
setAnnotations(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.TextPanel: This method displays the given list of annotations.
setAnnotationTable(Hashtable) - Static method in class edu.iastate.metnet.hivemindService.AnnotationService
setAnnotationText(String) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
setAnnotationtoLocation(String, Annotation) - Method in class edu.iastate.metnet.birdseyeview.cellview.PanelLocationsFactory
setApproved(boolean) - Method in class edu.iastate.metnet.model.CheckCandidate
setAracycid(String) - Method in class edu.iastate.metnet.aracyc.AracycEntity: set the aracyc id
setAracycid(String) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the value of the AracycID column.
setAracycId(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setAracycId(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setAracycId(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setAracycPathway(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setAracycPathway(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setAracycUpdate(boolean) - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph
setAracycUpdate(boolean) - Method in class edu.iastate.reload.ui.NetworkEditForm
setArrayElementName(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the array_element_name column.
setArrayElementName(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the array_element_name column.
setArrayElementName(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the array_element_name column.
setArrayElementType(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the array_element_type column.
setArrayElementType(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the array_element_type column.
setArrayElementType(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the array_element_type column.
setAscending(boolean) - Method in class edu.iastate.metnet.metaomgraph.SortableData: Determines whether to sort in ascending or descending order
setAspect(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the aspect column.
setAthLocus(String) - Method in class edu.iastate.metnet.dao.SoybeanHomology
setAttr(Class<A>, V) - Method in interface edu.iastate.metnet.datamodel.Entity
setAttr(Class<A>, V) - Method in class edu.iastate.metnet.datamodel.EntityImpl
setAttribute(int, String) - Method in class edu.iastate.jtm.assistant.GoogleScholar
setAuthors(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the AUTHORS column.
setAutoAdjustMode(boolean) - Method in class edu.iastate.jtm.jmed.MedlineParser
setAutoDetach(boolean) - Method in class edu.iastate.jtm.gui.StatusBar
setAutosort(boolean) - Method in class edu.iastate.metnet.metaomgraph.ListTree
setAvgIntensity(Double) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the avg_intensity column.
setAvgIntensityStdErr(Double) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the avg_intensity_std_err column.
setAvgLogRatio(Double) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the avg_log_ratio column.
setAvgLogRatioStdErr(Double) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the avg_log_ratio_std_err column.
setBatchSize(int) - Method in class edu.iastate.jtm.jmed.ESearch
setBatchSize(int) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
setBatchSize(int) - Method in class edu.iastate.jtm.util.MySqlConnector
setBiocycId(String) - Method in class edu.iastate.biocyc.dao.rdb.ClassName
setBiocycId(String) - Method in class edu.iastate.metnet.hibernate.AbstractClassName
setBiologicalType(String) - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
setBiologicalType(String) - Method in class edu.iastate.metnet.dao.HistoryInformation
setBirdsEyeView(BirdsEyeView) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setBirdsEyeViewFrame(JFrame) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setBlockId(Integer) - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
setBlockid(Integer) - Method in class edu.iastate.metnet.dao.Candidate
setBlockId(Integer) - Method in class edu.iastate.metnet.dao.HistoryBlockunitImpl
setBlockId(Integer) - Method in class edu.iastate.metnet.dao.HistoryInformation
setBlockid(Integer) - Method in class edu.iastate.metnet.dao.InteractionInformation
setBlockId(Integer) - Method in class edu.iastate.metnet.dao.MyVersionNode
setBlockid(Integer) - Method in class edu.iastate.metnet.dao.PathwayA
setBlockId(Integer) - Method in interface edu.iastate.metnet.dao.PathwayElementNode: set the blockid of the blockunit (version)
setBlockid(String) - Method in class edu.iastate.metnet.dao.ZVertex
setBlockid(Integer) - Method in class edu.iastate.metnet.graphmodel.MetaphorTypeInformation
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the simple primary key value that identifies this object.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitabbreviation: Set the simple primary key value that identifies this object.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitconfidence: Set the simple primary key value that identifies this object.
setBlockId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setBlockId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setBlockId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Set the simple primary key value that identifies this object.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Set the simple primary key value that identifies this object.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.BlockunitcommentKey: Sets the value of the blockid property.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.BlockunitrefKey: Sets the value of the blockid property.
setBlockID(Integer) - Method in class edu.iastate.metnet.hibernate.BlockunitSynonymCandidate
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.BlockunitsynonymKey: Sets the value of the blockid property.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.EntitywithcontextKey: Sets the value of the blockid property.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.GroupShareKey: Sets the value of the blockid property.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.InteractionpartsKey: Sets the value of the blockid property.
setBlockid(Integer) - Method in class edu.iastate.metnet.hibernate.PathwaypartsKey: Sets the value of the blockid property.
setBlockID(int) - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
setBlockID(String) - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
setBlockid(Integer) - Method in class edu.iastate.metnet.model.GroupShareTableModel
setBlockid(Integer) - Method in class edu.iastate.metnet.model.IntermediumEntityInformation
setBlockunit(Blockunit) - Method in class edu.iastate.biocyc.dao.rdb.BlockunitChoice
setBlockunit(Blockunit) - Method in interface edu.iastate.metnet.dao.IMetnetBlockUnit: set the blockunit
setBlockunit(Blockunit) - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
setBlockunit(Blockunit) - Method in class edu.iastate.metnet.model.AbstractBlockunitDecorator
setBlockunit(Blockunit) - Method in class edu.iastate.metnet.model.CompositionBlockunit
setBlockunit(Blockunit) - Method in class edu.iastate.metnet.model.SelectedBlockunit
setBlockunitabbreviationSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Blockunit
setBlockunitcommentSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Blockunit
setBlockunitconfidence(Blockunitconfidence) - Method in class edu.iastate.metnet.hibernate.Blockunit
setBlockUnitConfidence() - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
setBlockUnitConfidence(int) - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
setBlockunitrefSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Blockunit
setBlockunitsynonymSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Blockunit
setBmid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the value of the BMID column.
setBounds(int, int, int, int) - Method in class edu.iastate.metnet.metaomgraph.PolygonPanel.BouncingPolygon
setButtonIcons() - Method in class edu.iastate.metnet.MetNetTitlePane
setCandidate(String) - Method in class edu.iastate.metnet.dao.Candidate
setCandy(Candidate) - Method in class edu.iastate.metnet.model.CheckCandidate
setCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: set the capacity to current info
setCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.ViewInfo
setCenterRoot(boolean) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: if put the root in the center of the screen border
setCharType(CharType) - Method in class edu.iastate.jtm.util.SlidingWindow
setCharType(CharType) - Method in class edu.iastate.jtm.util.TokenProcessor
setChebiAccession(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Set the value of the chebi_accession column.
setChebiDbAccession(String) - Method in class edu.iastate.metnet.dao.ChebiObject
setChebiFormula(String) - Method in class edu.iastate.metnet.dao.ChebiObject
setChebiid(Integer) - Method in class edu.iastate.metnet.dao.ChebiOntologyName
setChebiInChI(String) - Method in class edu.iastate.metnet.dao.ChebiObject
setChebiName(String) - Method in class edu.iastate.metnet.dao.ChebiObject
setChebiSmiles(String) - Method in class edu.iastate.metnet.dao.ChebiObject
setCheckAbb(boolean) - Method in class edu.iastate.jtm.PluralDetector
setCheckBoxList(ArrayList<JCheckBox>) - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
setChild(boolean) - Method in class edu.iastate.metnet.model.CompositionBlockunit
setChildToParentMap(HashMap) - Method in class edu.iastate.metnet.dao.RelationMap
setChloroplastTransitPeptideScore(Double) - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Set the value of the chloroplast_transit_peptide_score column.
setChromosome(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the chromosome column.
setChromosome(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the chromosome column.
setChromosome(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the chromosome column.
setChromosome(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Set the value of the chromosome column.
setCitations(ArrayList) - Method in class edu.iastate.metnet.aracyc.AracycEntity: set citations
setClassId(Integer) - Method in class edu.iastate.biocyc.dao.rdb.ClassName
setClassId(Integer) - Method in class edu.iastate.metnet.dao.CategoryNode
setClassId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractClassName
setClassification(String) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the value of the Classification column.
setCmdline(String) - Method in class edu.iastate.jtm.util.ProcessWrapper
setCode(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractCodeconfidence: Set the simple primary key value that identifies this object.
setCode(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractCodedatasource: Set the simple primary key value that identifies this object.
setCode(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractCodeentitytype: Set the simple primary key value that identifies this object.
setCode(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractCodeinteractiontype: Set the simple primary key value that identifies this object.
setCode(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractCodelocation: Set the simple primary key value that identifies this object.
setCode(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractCodeorganism: Set the simple primary key value that identifies this object.
setCode(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractCodereferencetype: Set the simple primary key value that identifies this object.
setCoderule(Coderule) - Method in class edu.iastate.metnet.hibernate.Abbreviationrules
setCoefficient(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionparts: Set the value of the Coefficient column.
setCoefficient(Integer) - Method in class edu.iastate.metnet.model.EntityPart
setCofactor(String) - Method in class edu.iastate.metnet.hibernate.BrendacofactorKey: Sets the value of the cofactor property.
setColor(Color) - Method in class edu.iastate.metnet.metaomgraph.chart.RangeMarker
setColor1(Color) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.
setColor2(Color) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.
setColumnComparator(Class, Comparator) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
setColumnEditable(int, boolean) - Method in class edu.iastate.metnet.NoneditableTableModel: Determines whether the given column should be editable.
setColumnEditorModel(ColumnEditorModel) - Method in class edu.iastate.metnet.ui.MyJTableEx
setColumnName(int, String) - Method in class edu.iastate.metnet.dataManager.TableDataModel
setColumnName(int, String) - Method in class edu.iastate.metnet.NoneditableTableModel
setColumns(String[]) - Method in class edu.iastate.metnet.dataManager.FileData
setCombineLevelNodes(boolean) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm
setComment(String) - Method in class edu.iastate.metnet.dao.CommentObject
setComment(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setComment(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setComment(String) - Method in class edu.iastate.metnet.hibernate.BlockunitcommentKey: Sets the value of the comment property.
setComment(String) - Method in class edu.iastate.metnet.hibernate.EntitycommentKey: Sets the value of the comment property.
setCommentOrigin(Blockunitcomment) - Method in class edu.iastate.reload.ui.CommentEditForm
setComments(ArrayList) - Method in class edu.iastate.metnet.aracyc.AracycEntity: set comment
setCompareType(String) - Method in class edu.iastate.metnet.hibernate.Abbreviationrules
setComplexID(Integer) - Method in class edu.iastate.metnet.graphmodel.RelationObject
setComplexity(int) - Method in class edu.iastate.jtm.jmed.Limits: Gi is often a part of a biological blob, containing other gis.
setComponentCoefficient(Integer) - Method in class edu.iastate.metnet.graphmodel.RelationObject
setComponentID(Integer) - Method in class edu.iastate.metnet.graphmodel.RelationObject
setCompoundChildId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiVertices: Set the value of the compound_child_id column.
setCompoundFilename(String) - Method in class edu.iastate.metnet.aracyc.ChangeName
setCompoundID(Integer) - Method in class edu.iastate.metnet.dao.ChebiObject
setCompoundId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiChemicalData: Set the value of the compound_id column.
setCompoundId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Set the value of the compound_id column.
setCompoundId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession: Set the value of the compound_id column.
setCompoundId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames: Set the value of the compound_id column.
setCompoundId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference: Set the value of the compound_id column.
setConfidence(String) - Method in class edu.iastate.metnet.dao.InteractionObject
setConfidence(double) - Method in class edu.iastate.metnet.graphmodel.MetaphorTypeInformation
setConfidence(Double) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setConfidence(Double) - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Set the value of the Confidence column.
setConstraints(GridBagConstraints, int, int, int, int, double, double) - Method in class edu.iastate.metnet.utils.Utils: set the value of the GridBagConstraints and reuse it
setContainer(Container) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setControlEbid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setControlInteraction(boolean) - Method in class edu.iastate.metnet.dao.InteractionStructure
setCost(double) - Method in class edu.iastate.metnet.dao.AlignmentObject
setCreatedOn(Date) - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Set the value of the created_on column.
setCuratorToolWindow(MainWindow2) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setCurrentBlockID(Integer) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
setCurrentBlockIDSubSystemMap(MultiKeyMap) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
setCurrentInteraction(MetnetInteraction) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
setCurrentLiveEntity(MetnetLiveEntity) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
setCurrentNodeSubSystemMap(Map) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
setCurrentPathway(MetnetPathway) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
setCurrentValidEdgeMap(Map) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
setCurrentValidity(GraphValidity) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
setCurrentValidNodeMap(Map) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
setCytoscape(boolean) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setData(int, int, String) - Method in class edu.iastate.metnet.dataManager.TableDataModel
setData(Object[][]) - Method in class edu.iastate.metnet.NoneditableTableModel
setDatabase(int) - Method in class edu.iastate.jtm.jmed.EUtility
setDatabase(int) - Method in class edu.iastate.jtm.jmed.PubMedFetcher
setDatabase(MySqlConnector) - Method in class fcmodeler.pathbinder.updater.DictionaryPanel
setDatabase(MySqlConnector) - Method in class fcmodeler.pathbinder.updater.FilterPanel
setDatabase(MySqlConnector) - Method in class fcmodeler.pathbinder.updater.InteractionUpdatePanel
setDatabase(MySqlConnector) - Method in class fcmodeler.pathbinder.updater.MedCrawlerPanel
setDataColumnHeaders(Object[][]) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the data column headers to the values in headers[x][0].
setDataColumnHeaders(Object[]) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the data column headers to the given values.
setDataManager(DataManager) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setDataMap(Map) - Method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement: set the data map
setDataMap(Map) - Method in interface edu.iastate.biocyc.dao.txt.BiocycElement: set the data map for all attributes
setDataObject(HistoryBlockunit) - Method in class edu.iastate.metnet.dao.MyVersionNode: constructor for metnet interaction structure
setDataObject(Object) - Method in class edu.iastate.metnet.dao.MyVersionNode
setDataSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setDataSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setDataSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setDataTable(Hashtable) - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
setDatatype(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Set the value of the datatype column.
setDatatypeId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Set the value of the datatype_id column.
setDate(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setDate(Date) - Method in class edu.iastate.metnet.dataManager.Properties
setDate(Date) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the value of the Date column.
setDate(Date) - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Set the value of the Date column.
setDate(Date) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the value of the Date column.
setDateAnnotated(Date) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the date_annotated column.
setDateType(int) - Method in class edu.iastate.jtm.jmed.Limits
setDb(String) - Method in class edu.iastate.metnet.hibernate.Externaldb
setDb(String) - Method in class edu.iastate.metnet.hibernate.ExternaldbKey: Sets the value of the db property.
setDefaultColumn(int) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the index of the "default" info column.
setDefaultTitle(String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the title used on all new MetaOmChartPanels.
setDefaultXAxis(String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the label used for the x-axis of all new MetaOmChartPanels.
setDefaultYAxis(String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Retrieves the label used for the y-axis of all new MetaOmChartPanels.
setDefinition(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds
setDegree(Integer) - Method in class edu.iastate.metnet.dao.TrivialMetabolite
setDegree(int) - Method in class edu.iastate.metnet.dao.TrivialMetabolite
setDelay(int) - Method in class edu.iastate.metnet.metaomgraph.throbber.Throbber
setDelegate(TableModel) - Method in class com.jgoodies.binding.extras.DelegatingTableModel: Sets a new TableModel delegate.
setDescription(String) - Method in class edu.iastate.metnet.dao.HistoryInformation
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeconfidence: Set the value of the Description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodedatasource: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeentitytype: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeinteractiontype: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodelocation: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeorganism: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodereferencetype: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractCoderule: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Set the value of the description column.
setDescription(String) - Method in class edu.iastate.metnet.hibernate.BackgroundTask
setDirectory(String) - Method in class edu.iastate.biocyc.io.BiocycImporter
setDisplay(Object) - Method in class edu.iastate.metnet.model.DisplayObject
setDocBevItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setDocCytoItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setDocMenu(JMenu) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setDocMogItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setDocPbItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setDocPumaItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setEc(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setEc(String) - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Set the value of the EC column.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendarecommendname: Set the simple primary key value that identifies this object.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the ECID column.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.BrendaactivatingcompoundKey: Sets the value of the ecid property.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.BrendacofactorKey: Sets the value of the ecid property.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.BrendainhibitorKey: Sets the value of the ecid property.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.BrendametalionKey: Sets the value of the ecid property.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.BrendaproductKey: Sets the value of the ecid property.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.BrendasubstrateKey: Sets the value of the ecid property.
setEcid(String) - Method in class edu.iastate.metnet.hibernate.BrendasynonymsKey: Sets the value of the ecid property.
setEdgeSeparation(double) - Method in class edu.iastate.reload.ui.JGraphParallelEdgeRouter
setEmail(String) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the value of the Email column.
setEnabled(boolean) - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager
setEnabled(boolean) - Method in class fcmodeler.pathbinder.gui.SearchPanel
setEnableModelListener(boolean) - Method in class edu.iastate.reload.ui.NetworkEditForm
setEnd(int) - Method in class edu.iastate.jtm.util.SlidingWindow.Stride
setEnd(int) - Method in class edu.iastate.metnet.metaomgraph.chart.RangeMarker
setEntites(ArrayList<String>) - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
setEntity(boolean) - Method in class edu.iastate.metnet.dao.AbbreviationObject
setEntity(boolean) - Method in class edu.iastate.metnet.dao.CommentObject
setEntity(boolean) - Method in class edu.iastate.metnet.dao.ReferenceObject
setEntity(boolean) - Method in class edu.iastate.metnet.dao.SynonymObject
setEntity(Entity) - Method in class edu.iastate.metnet.hibernate.Blockunit
setEntity(int, Entity[]) - Method in class fcmodeler.pathbinder.PathBinder
setEntityabbreviationSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Entity
setEntitycommentSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Entity
setEntityexternaldbSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Entity
setEntityID(Integer) - Method in class edu.iastate.metnet.dao.ChebiObject
setEntityId(Integer) - Method in class edu.iastate.metnet.dao.EntityNode
setEntityId(Integer) - Method in class edu.iastate.metnet.dao.TrivialMetabolite
setEntityId(int) - Method in class edu.iastate.metnet.dao.TrivialMetabolite
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Set the simple primary key value that identifies this object.
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityOntology: Set the value of the entityid column.
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchem: Set the value of the entityid column.
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchemName: Set the value of the entityid column.
setEntityId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.EntityabbreviationKey: Sets the value of the entityid property.
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.EntitycommentKey: Sets the value of the entityid property.
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.EntityrefKey: Sets the value of the entityid property.
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.EntitysynonymKey: Sets the value of the entityid property.
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.EntitywithcontextKey: Sets the value of the entityid property.
setEntityid(Integer) - Method in class edu.iastate.metnet.hibernate.ExternaldbKey: Sets the value of the entityid property.
setEntityOntologySet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Entity
setEntityPanel(EntityPanel) - Method in class fcmodeler.pathbinder.gui.PbFrame
setEntityrefSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Entity
setEntitysynonymSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Entity
setEntitytype(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeentitytype: Set the value of the entitytype column.
setEntityType(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setEntityType(String) - Method in class edu.iastate.metnet.model.EntityPart
setEnzyme(String) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Set the value of the Enzyme column.
setEnzymeName(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAracycDump: Set the value of the enzyme_name column.
setEnzymes(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setEsAlignmentList(List) - Method in class edu.iastate.metnet.ui.PathwayEditor
setEValue(String) - Method in class edu.iastate.metnet.dao.SoybeanHomology
setEvidenceCode(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the evidence_code column.
setExperiment(String) - Method in class edu.iastate.metnet.birdseyeview.LoadController: This method sets the name of the experiment which will be analyzed.
setExperiments(ArrayList, String) - Method in class edu.iastate.metnet.birdseyeview.ButtonPanel: This method populates the experiment combo box and selects the correct item.
setExperiments(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.ExperimentChooserPanel: This method populates the experiment list so the user can choose which experiment to analyze.
setExperiments(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.LoadWindow: This method calls the experiment chooser panel to populate the experiment list.
setExperiments(String, ArrayList) - Method in class edu.iastate.metnet.birdseyeview.RootPanel: This method informs the button panel that there are new experiments to display.
setExperiments(ArrayList<String>) - Method in class edu.iastate.metnet.hivemindService.ExploRaseExportObj
setExperimentsTable(Hashtable) - Method in class edu.iastate.metnet.birdseyeview.LoadController
setExtendedInfoEnabled(boolean) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartToolBar
setExtendedInfoEnabled(boolean) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
setExtInfoDividerPos(double) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
setFcmlFile(String) - Method in class edu.iastate.metnet.ui.SBMLExporter
setField(int) - Method in class edu.iastate.jtm.jmed.Limits
setFileData(FileData) - Method in class edu.iastate.metnet.dataManager.DataManager
setFileExitItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setFileField(String) - Method in class edu.iastate.metnet.birdseyeview.LoadPanel: This method sets the file field with the given text.
setFileName(String) - Method in class edu.iastate.metnet.dataManager.Properties
setFilterTaxonomy(boolean) - Method in class fcmodeler.pathbinder.PmidFilter
setFinalId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiRelation: Set the value of the final_id column.
setFinishTime(Date) - Method in class edu.iastate.metnet.hibernate.BackgroundTask
setFirstname(String) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the value of the Firstname column.
setFirstSize(int) - Method in class edu.iastate.jtm.jmed.ESearch
setFirstSize(int) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
setFormula(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiChemicalData: Set the value of the formula column.
setFrame(int) - Method in class edu.iastate.metnet.metaomgraph.throbber.MetaOmThrobber
setFromDate(String) - Method in class edu.iastate.jtm.jmed.Limits
setFunctionCategory(String) - Method in class edu.iastate.metnet.dao.SoybeanHomology
setFunctionconfidence(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitconfidence: Set the value of the FunctionConfidence column.
setFunctionConfidence(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setFunctionconfidence(Integer) - Method in class edu.iastate.metnet.hibernate.Blockunit
setFunctionConfidence(int) - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
setGenbankAccession(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the genbank_accession column.
setGenebankAccess(String) - Method in class edu.iastate.metnet.dao.SoybeanHomology
setGeneFamily(String) - Method in class edu.iastate.metnet.dao.SoybeanHomology
setGeneFilename(String) - Method in class edu.iastate.metnet.aracyc.ChangeName
setGeneId(String) - Method in class edu.iastate.metnet.hivemindService.SimpleGeneObj
setGeneName(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setGeneName(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setGeneName(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Set the value of the gene_name column.
setGenes(int) - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway: This method adds the gene panels to the panel.
setGobiNodeList(ArrayList<GobiNode>) - Static method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame
setGobiNodeList(ArrayList<GobiNode>) - Static method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame
setGobiNodeList(ArrayList<GobiNode>) - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
setGoBiologicalProcess(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setGoBiologicalProcess(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setGoBioProcesses(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.Annotation: This method sets the the node IDs of the GO biological processes in which this gene product participates.
setGoCellularComponent(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setGoCellularComponent(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setGoFunctions(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.Annotation: This method sets the node IDs of the GO molecular functions of this gene product.
setGoGeneProductID(int) - Method in class edu.iastate.metnet.birdseyeview.Annotation: Returns the gene ontology gene product ID.
setGoId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the go_id column.
setGoMolecularFunction(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setGoMolecularFunction(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setGoslimTerm(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the goslim_term column.
setGoTerm(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the go_term column.
setGraphValidity(GraphValidity) - Method in class edu.iastate.metnet.graphmodel.ValidityMetaphor
setGroupid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractGroupList: Set the simple primary key value that identifies this object.
setGroupid(Integer) - Method in class edu.iastate.metnet.hibernate.GroupMemberKey: Sets the value of the groupid property.
setGroupid(Integer) - Method in class edu.iastate.metnet.hibernate.GroupShareKey: Sets the value of the groupid property.
setGroupid(Integer) - Method in class edu.iastate.metnet.ui.MemberManagerForm
setGroupList(GroupList) - Method in class edu.iastate.metnet.dao.GroupObject
setGroupMemberList(Vector) - Method in class edu.iastate.metnet.dao.GroupObject
setGroupname(String) - Method in class edu.iastate.metnet.hibernate.AbstractGroupList: Set the value of the groupname column.
setGroupName(String) - Method in class edu.iastate.metnet.ui.MemberManagerForm
setGroupShareList(Vector) - Method in class edu.iastate.metnet.dao.GroupObject
setHasAbstract(boolean) - Method in class edu.iastate.jtm.jmed.ESearch
setHasAbstract(boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
setHeight(double) - Method in class edu.iastate.metnet.dao.ZVertex
setHelpAboutItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setHighlightQueryKeyword(boolean) - Method in class edu.iastate.jtm.assistant.Highlighter
setHighlightUserKeyword(boolean) - Method in class edu.iastate.jtm.assistant.Highlighter
setHitsThreshold(int) - Method in class edu.iastate.jtm.EntityFinder
setHost(String) - Method in class edu.iastate.jtm.util.RemoteControl
setHtmlMode(boolean) - Static method in class edu.iastate.jtm.jmed.MeshDescriptor
setIbid(Integer) - Method in class edu.iastate.metnet.dao.InteractionStructure
setId(Integer) - Method in class edu.iastate.metnet.dao.AbbreviationObject
setId(Integer) - Method in class edu.iastate.metnet.dao.Candidate
setId(Integer) - Method in class edu.iastate.metnet.dao.CommentObject
setId(String) - Method in class edu.iastate.metnet.dao.GoTermID
setID(int) - Method in interface edu.iastate.metnet.dao.IMetnetBlockUnit: set the identity
setID(int) - Method in class edu.iastate.metnet.dao.MetnetBlockUnit
setId(Integer) - Method in class edu.iastate.metnet.dao.ReferenceObject
setId(Integer) - Method in class edu.iastate.metnet.dao.SynonymObject
setId(String) - Method in class edu.iastate.metnet.export.GoTermID
setId(BlockunitcommentKey) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitcomment: Set the composite id instance that identifies this object.
setId(BlockunitrefKey) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitref: Set the composite id instance that identifies this object.
setId(BlockunitsynonymKey) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitsynonym: Set the composite id instance that identifies this object.
setId(BrendaactivatingcompoundKey) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaactivatingcompound: Set the composite id instance that identifies this object.
setId(BrendacofactorKey) - Method in class edu.iastate.metnet.hibernate.AbstractBrendacofactor: Set the composite id instance that identifies this object.
setId(BrendainhibitorKey) - Method in class edu.iastate.metnet.hibernate.AbstractBrendainhibitor: Set the composite id instance that identifies this object.
setId(BrendametalionKey) - Method in class edu.iastate.metnet.hibernate.AbstractBrendametalion: Set the composite id instance that identifies this object.
setId(BrendaproductKey) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaproduct: Set the composite id instance that identifies this object.
setId(BrendasubstrateKey) - Method in class edu.iastate.metnet.hibernate.AbstractBrendasubstrate: Set the composite id instance that identifies this object.
setId(BrendasynonymsKey) - Method in class edu.iastate.metnet.hibernate.AbstractBrendasynonyms: Set the composite id instance that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiChemicalData: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiOntology: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiRelation: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiVertices: Set the simple primary key value that identifies this object.
setId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractCoderule: Set the simple primary key value that identifies this object.
setId(EntityabbreviationKey) - Method in class edu.iastate.metnet.hibernate.AbstractEntityabbreviation: Set the composite id instance that identifies this object.
setId(EntitycommentKey) - Method in class edu.iastate.metnet.hibernate.AbstractEntitycomment: Set the composite id instance that identifies this object.
setId(EntityrefKey) - Method in class edu.iastate.metnet.hibernate.AbstractEntityref: Set the composite id instance that identifies this object.
setId(EntitysynonymKey) - Method in class edu.iastate.metnet.hibernate.AbstractEntitysynonym: Set the composite id instance that identifies this object.
setId(EntitywithcontextKey) - Method in class edu.iastate.metnet.hibernate.AbstractEntitywithcontext: Set the composite id instance that identifies this object.
setId(ExternaldbKey) - Method in class edu.iastate.metnet.hibernate.AbstractExternaldb: Set the composite id instance that identifies this object.
setId(GroupMemberKey) - Method in class edu.iastate.metnet.hibernate.AbstractGroupMember: Set the composite id instance that identifies this object.
setId(GroupShareKey) - Method in class edu.iastate.metnet.hibernate.AbstractGroupShare: Set the composite id instance that identifies this object.
setId(InteractionpartsKey) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionparts: Set the composite id instance that identifies this object.
setId(PathwaypartsKey) - Method in class edu.iastate.metnet.hibernate.AbstractPathwayparts: Set the composite id instance that identifies this object.
setID(Integer) - Method in class edu.iastate.metnet.hibernate.BlockunitSynonymCandidate
setIdColumn(int) - Method in class edu.iastate.metnet.dataManager.FileData
setIdType(int) - Method in class edu.iastate.metnet.dataManager.FileData
setIdType(int) - Method in class edu.iastate.metnet.hivemindService.SimpleGeneObj
setIgnoreError(boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
setIgnoreWarning(boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
setIgnoreXmlError(boolean) - Method in class edu.iastate.jtm.jmed.StreamXMLParser
setImportDate(Date) - Method in class edu.iastate.metnet.dao.MyVersionNode
setImported(boolean) - Method in class edu.iastate.metnet.birdseyeview.LoadController
setInactiveLabel(String) - Method in class edu.iastate.metnet.metaomgraph.DualListPanel: Sets the label that appears above the inactive list.
setInactiveLabel(String) - Method in class edu.iastate.metnet.metaomgraph.DualTablePanel: Sets the label that appears above the inactive list.
setIncomingBlockunitSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Blockunit
setIndex(int) - Method in class edu.iastate.metnet.metaomgraph.SortableData: Sets this object's index
setInformation(String) - Method in class edu.iastate.metnet.dao.MyVersionNode
setInhibitor(String) - Method in class edu.iastate.metnet.hibernate.BrendainhibitorKey: Sets the value of the inhibitor property.
setInitId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiRelation: Set the value of the init_id column.
setInPlatform(boolean) - Static method in class edu.iastate.metnet.ui.MainWindow2
setInput(DirectedGraph) - Method in class edu.iastate.metnet.dao.AlignmentObject
setInputUsed(DirectedGraph) - Method in class edu.iastate.metnet.dao.AlignmentObject
setInsertTime(Date) - Method in class edu.iastate.biocyc.dao.rdb.ClassName
setInsertTime(Date) - Method in class edu.iastate.metnet.dao.HistoryBlockunitImpl
setInsertTime(Date) - Method in class edu.iastate.metnet.hibernate.AbstractClassName
setInsertTime(Date) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setInsertTime(Date) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setInsertTime(Date) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setInsets(Insets) - Static method in class edu.iastate.jtm.gui.FileBar
setInteraction(Interaction) - Method in class edu.iastate.metnet.hibernate.Blockunit
setInteractionList(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setInteractionSet() - Method in class edu.iastate.metnet.dao.MetnetPathway
setInteractionType(String) - Method in class edu.iastate.metnet.graphmodel.MetaphorTypeInformation
setInteractionType(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setInterval(long) - Method in class edu.iastate.jtm.jmed.PubMedTimer: Set min interval between 2 consective queries.
setIsAmbiguous(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the is_ambiguous column.
setIsAmbiguous(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the is_ambiguous column.
setIsAmbiguous(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the is_ambiguous column.
setIsControl(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the is_control column.
setIsControl(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the is_control column.
setIsControl(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the is_control column.
setJGraph(JGraph) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
setJournal(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the JOURNAL column.
setJustified(boolean) - Method in class edu.iastate.metnet.dataManager.JMultilineLabel
setKey(char[]) - Method in class edu.iastate.jtm.dic.AbstractTrieNode: Set a node's key.
setKey(char[]) - Method in interface edu.iastate.jtm.dic.TrieNode: Set a node's key.
setKey(String) - Method in class edu.iastate.metnet.soft.Attribute
setKi(Double) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Set the value of the Ki column.
setKm(Double) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Set the value of the Km column.
setLabel(String) - Method in class edu.iastate.metnet.dao.ZVertex
setLabel(String) - Method in class edu.iastate.metnet.metaomgraph.chart.RangeMarker
setLast(boolean) - Method in class edu.iastate.metnet.newgui.oldWizardPanel
setLastCorrelation(CorrelationValue[], String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
setLastCorrelation(CorrelationValue[]) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
setLastDir(File) - Static method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
setLastDir(File) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils: Sets the directory last accessed by the user.
setLastDir(File) - Method in class edu.iastate.metnet.soft.SOFTParser
setLastModifiedDate(String) - Method in class edu.iastate.metnet.dao.PathwayObject
setLastname(String) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the value of the Lastname column.
setLastQueryTime(long) - Method in class edu.iastate.jtm.jmed.PubMedTimer: Set the time of last successful query.
setLeft(int) - Method in class edu.iastate.jtm.EntityFinder.Hit: Setter for property left.
setLeftNode(PathwayElementNode) - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode
setLeftNode(PathwayElementNode) - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode
setLeftPart() - Method in class edu.iastate.metnet.dao.MetnetInteraction
setLeftPart(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setLeftPart(Vector) - Method in class edu.iastate.metnet.hibernate.Interaction
setLeftToRightMap(MultiHashMap) - Method in class edu.iastate.metnet.dao.BidiMultiHashMap
setLeftUnit(Blockunit) - Method in class edu.iastate.metnet.model.AbstractMultiBlockunitDecorator
setLegendVisible(boolean) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
setlevelCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.AbstractView
setlevelCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.cellview.CellView
setlevelCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.goview.GoLevel: This method set the current level's capacity
setlevelCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.goview.GoView
setlevelCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.pathwayview.PathwayView
setlevelCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.RootPanel: this method set the GO VIEW's current level's capacity
setlevelCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.ViewPanel: this method set the GO views' current level's gene capacity
setLevelDistance(int) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: set distance between the tree level
setLevelHeights(List) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: change the level height to make it more compact.
setList(List) - Method in class edu.iastate.metnet.model.DomainObjectListModel
setListModel(ListModel) - Method in class com.jgoodies.binding.extras.ListModelHolder: Sets a new list model and notifies any registered value listeners if it has changed.
setListModel(ArrayListModel) - Method in class edu.iastate.reload.ui.CommentEditForm
setListModel(ArrayListModel) - Method in class edu.iastate.reload.ui.ReferenceEditForm
setListModel(ArrayListModel) - Method in class edu.iastate.reload.ui.SynonymEditForm
setLiveEntity(Blockunit) - Method in class edu.iastate.metnet.dao.InputNode
setLoadController(LoadController) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
setLocation(String) - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
setLocation(String) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the value of the Location column.
setLocation(String) - Method in class edu.iastate.metnet.hibernate.AbstractGtairProperty: Set the value of the Location column.
setLocation(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setLocation(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setLocation(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setLocation(String) - Method in class edu.iastate.metnet.model.EntityPart
setLocationconfidence(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitconfidence: Set the value of the LocationConfidence column.
setLocationConfidence(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setLocationconfidence(Integer) - Method in class edu.iastate.metnet.hibernate.Blockunit
setLocationConfidence(int) - Method in class edu.iastate.metnet.model.EntityConfidenceObservable
setLocationInRef(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference: Set the value of the location_in_ref column.
setLocations(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.Annotation: Sets the locations and the location string.
setLocusID(String) - Method in class edu.iastate.metnet.birdseyeview.Annotation: Sets the locus ID.
setLocusid(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: set the locus id
setLocusid(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setLocusid(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setLocusid(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
setLocusId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the locus_id column.
setLocusId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the locus_id column.
setLocusId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the locus_id column.
setLocusId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAgiToUniprot: Set the value of the locus_id column.
setLocusId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAracycDump: Set the value of the locus_id column.
setLocusId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the locus_id column.
setLocusId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Set the value of the locus_id column.
setLocusId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Set the value of the locus_id column.
setLongterm(String) - Method in class edu.iastate.metnet.hibernate.AbstractAbbreviationrules: Set the value of the longterm column.
setMaximumsize(int, int) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode: This method transfer the size information to node
setMaxSentenceLength(int) - Method in class edu.iastate.jtm.EntityFinder
setMaxWidth(int) - Method in class edu.iastate.metnet.dataManager.JMultilineLabel
setMedParser(MedlineParser) - Method in class edu.iastate.jtm.jmed.EFetch: Set the fetcher's parser.
setMember(String) - Method in class edu.iastate.metnet.hibernate.GroupMemberKey: Sets the value of the member property.
setMenu(JPopupMenu) - Method in class edu.iastate.metnet.metaomgraph.MenuButton: Sets the menu displayed by this MenuButton.
setMessage(String) - Method in class edu.iastate.jtm.assistant.CitationPool
setMessage(String) - Method in class edu.iastate.jtm.gui.DefaultMonitorable
setMetalion(String) - Method in class edu.iastate.metnet.hibernate.BrendametalionKey: Sets the value of the metalion property.
setMetaOmGraph(MetaOmGraph) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setMetnetEntityID(int) - Method in class edu.iastate.metnet.birdseyeview.Annotation: Returns the metnet entity ID.
setMetnetLocation(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setMetnetLocation(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setMetnetPathway(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setMetnetPathway(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setMinCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.goview.GoLevel: This method set the current level's capacity
setminCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.ViewInfo
setMinRows(int) - Method in class edu.iastate.jtm.gui.RowHeaderTable
setMinX(double) - Method in class edu.iastate.metnet.dao.ZVertex
setMinY(double) - Method in class edu.iastate.metnet.dao.ZVertex
setMitochondrialTargetingPeptideScore(Double) - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Set the value of the mitochondrial_targeting_peptide_score column.
setMode(int) - Method in class edu.iastate.metnet.metaomgraph.GraphFileFilter: Changes which files will be accepted by this filter.
setModel(DefaultTreeModel) - Method in class edu.iastate.jtm.gui.DnDTree
setModel(TableModel) - Method in class edu.iastate.jtm.gui.RowHeaderTable
setModel(TableModel) - Method in class edu.iastate.jtm.gui.TableMap
setModel(TableModel) - Method in class edu.iastate.jtm.gui.TableSorter
setModel(DirectedGraph) - Method in class edu.iastate.metnet.dao.AlignmentObject
setModel(TableModel) - Method in class edu.iastate.metnet.metaomgraph.chart.OrderableTable
setModel(TableModel) - Method in class edu.iastate.metnet.model.TableMap
setModel(TableModel) - Method in class edu.iastate.metnet.model.TableSorter
setModelIdCellMap(Map) - Method in class edu.iastate.metnet.graphmodel.ValidityMetaphor
setModelUsed(DirectedGraph) - Method in class edu.iastate.metnet.dao.AlignmentObject
setMonitorable(boolean) - Method in class edu.iastate.jtm.assistant.CitationPool
setMonitorable(boolean) - Method in class edu.iastate.jtm.gui.DefaultMonitorable
setMonitorable(boolean) - Method in interface edu.iastate.jtm.gui.Monitorable
setMonitorable(boolean) - Method in class fcmodeler.pathbinder.MedLeaseClient
setMultiNodeFlag(int) - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph
setMyVersionGraph(MyVersionGraph) - Method in class edu.iastate.metnet.graphmodel.VersionGraphModel: set the version graph structure
setMyVersionGraph(MyVersionGraph) - Method in class edu.iastate.metnet.ui.VersionEditor
setName(String) - Method in class edu.iastate.biocyc.dao.rdb.ClassName
setName(String) - Method in class edu.iastate.metnet.aracyc.AracycEntity: set the name
setName() - Method in class edu.iastate.metnet.birdseyeview.Annotation: Sets the name.
setName(String) - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode
setName(String) - Method in class edu.iastate.metnet.dao.CategoryNode
setName(String) - Method in class edu.iastate.metnet.dao.HistoryBlockunitImpl
setName(String) - Method in class edu.iastate.metnet.dao.HistoryInformation
setName(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setName(String) - Method in class edu.iastate.metnet.dao.NameSource
setName(String) - Method in class edu.iastate.metnet.dao.PathwayObject
setName(String) - Method in class edu.iastate.metnet.dao.TrivialMetabolite
setName(String) - Method in class edu.iastate.metnet.graphmodel.SearchNameMetaphor
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the value of the Name column.
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Set the value of the name column.
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames: Set the value of the name column.
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractClassName
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodedatasource: Set the value of the name column.
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeinteractiontype: Set the value of the name column.
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodelocation: Set the value of the name column.
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodereferencetype: Set the value of the name column.
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Set the value of the Name column.
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setName(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setName(String) - Method in class edu.iastate.metnet.metaomgraph.GeneList
setName(String) - Method in class edu.iastate.metnet.model.EntityPart
setName(ValueHolder) - Method in class edu.iastate.metnet.model.NodeSelectionModel
setNames(Vector) - Method in class edu.iastate.metnet.dao.Candidate
setNameSource(NameSource) - Method in class edu.iastate.metnet.dao.ChebiOntologyName
setNewBlockunit(boolean) - Method in class edu.iastate.metnet.model.SelectedBlockunit
setNo(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the NO column.
setNodeDistance(int) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: set distance between the nodes
setNodeSelectionController(NodeSelectionController) - Method in class edu.iastate.metnet.ui.NodeSelectionForm
setNodeSelectionForm(NodeSelectionForm) - Method in class edu.iastate.metnet.controller.NodeSelectionController
setNodeSelectionModel(NodeSelectionModel) - Method in class edu.iastate.metnet.controller.NodeSelectionController
setNumOfColumns(int) - Method in class edu.iastate.metnet.dataManager.Properties
setNumOfRows(int) - Method in class edu.iastate.metnet.dataManager.Properties
setObjectName(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the object_name column.
setOldBlockunit(boolean) - Method in class edu.iastate.metnet.model.SelectedBlockunit
setOntologyId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiVertices: Set the value of the ontology_id column.
setOntologyId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityOntology: Set the value of the ontology_id column.
setOntologyType(String) - Method in class edu.iastate.metnet.hibernate.AbstractEntityOntology: Set the value of the ontology_type column.
setOpenBevItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setOpenCytoItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setOpenMogItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setOpenPbItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setOpenPumaItem(JMenuItem) - Method in class edu.iastate.metnet.launch.LaunchMetNet
setOrganism(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setOrganism(String) - Method in class edu.iastate.metnet.dao.PathwayObject
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the value of the Organism column.
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the ORGANISM column.
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeorganism: Set the value of the organism column.
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Set the value of the Organism column.
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the organism column.
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the organism column.
setOrganism(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the organism column.
setOrientation(int) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: SwingConstants.NORTH SwingConstants.EAST SwingConstants.SOUTH SwingConstants.WEST
setOtherScore(Double) - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Set the value of the other_score column.
setOutgoingBlockunitSet(ArrayList) - Method in class edu.iastate.metnet.hibernate.Blockunit
setOutputOriginal(boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
setOutputPlain(boolean) - Method in class edu.iastate.jtm.jmed.StreamXMLParser
setOwner(String) - Method in class edu.iastate.metnet.hibernate.AbstractGroupList: Set the value of the owner column.
setPages(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the PAGES column.
setPaint(TexturePaint) - Method in class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel
setPanel(Rectangle) - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Compartment: This method sets the dimensions of the panel.
setPanel(Rectangle) - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway: This method sets the dimensions of the panel and sets up the gene panel.
setPanelEnabled(boolean) - Method in class fcmodeler.pathbinder.updater.MedCrawlerPanel
setParam(Object) - Method in class edu.iastate.metnet.utils.SwingWorker
setParenChar(char, char) - Method in class edu.iastate.jtm.util.ParenFinder
setParent(TrieNode) - Method in class edu.iastate.jtm.dic.AbstractTrieNode
setParent(TrieNode) - Method in interface edu.iastate.jtm.dic.TrieNode
setParent(boolean) - Method in class edu.iastate.metnet.model.CompositionBlockunit
setParent(MutableTreeNode) - Method in class fcmodeler.pathbinder.gui.VerbNode
setParentId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Set the value of the parent_id column.
setParentToChildMap(MultiHashMap) - Method in class edu.iastate.metnet.dao.RelationMap
setParenType(CharType) - Method in class edu.iastate.jtm.util.ParenFinder
setParser(MedlineParser) - Method in class edu.iastate.jtm.jmed.PubMedFetcher: Set the fetcher's parser.
setPart(Integer) - Method in class edu.iastate.metnet.hibernate.InteractionpartsKey: Sets the value of the part property.
setPart(Integer) - Method in class edu.iastate.metnet.hibernate.PathwaypartsKey: Sets the value of the part property.
setPartEbidList(String, Vector) - Method in class edu.iastate.metnet.hibernate.HistoryFlatInteraction: get out the left part
setParts(Vector) - Method in class edu.iastate.metnet.dao.PathwayA
setParts(Vector) - Method in class edu.iastate.metnet.hibernate.Interaction
setPass(String) - Method in class edu.iastate.jtm.util.RemoteControl
setPassword(String) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the value of the Password column.
setPath(String) - Method in class edu.iastate.metnet.dao.ZEdge
setPathBinder(PbFrame) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setPathway(PathwayA) - Method in class edu.iastate.metnet.hibernate.Blockunit
setPathwayEditor(PathwayEditor) - Method in class edu.iastate.metnet.ui.NodeSelectionForm
setPathwayGeneTable(Hashtable) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setPathwayId(int) - Method in class edu.iastate.metnet.launch.Pathway
setPathwayInfo(Blockunit) - Method in class edu.iastate.reload.ui.NetworkEditForm: fill in the pathway information in the UI
setPathwayList(ArrayList<Integer>) - Static method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame
setPathwayList(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setPathwayList(ArrayList<Integer>) - Static method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame
setPathwayList(ArrayList<Integer>) - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
setPathwayName(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAracycDump: Set the value of the pathway_name column.
setPathwayName(String) - Method in class edu.iastate.metnet.launch.Pathway
setPathwayNameList(ArrayList<String>) - Static method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame
setPathwayNameList(ArrayList<String>) - Static method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame
setPathwayNameList(ArrayList<String>) - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame
setPathwayObject(PathwayObject) - Method in class edu.iastate.metnet.model.PathwayObjectChoice
setPathwayparts(Vector) - Method in class edu.iastate.metnet.hibernate.Interaction
setPathways(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.Annotation: Sets the pathways and the pathway string.
setPbid(Integer) - Method in class edu.iastate.metnet.dao.CategoryNode
setPbid(Integer) - Method in class edu.iastate.metnet.dao.PathwayObject
setPbidSet(Set) - Method in class edu.iastate.metnet.ui.AddPathwayForm
setPeekNext(boolean) - Method in class edu.iastate.jtm.EntityFinder
setPlatform(Platform) - Method in class edu.iastate.metnet.soft.Series
setPoints(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.cellview.CellularLocation: This method sets the list of points for this location.
setPopupEnabled(boolean) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
setPortObject(int) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper
setPosition(List) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm: set position for a list of trees
setPosition(Point, int) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.TreeNode
setPredictedLocation(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject: set predicted location
setPredictedLocation(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setPredictedLocation(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setPredictedLocation(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl
setPreferredSize(Dimension) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode: This method sets the panel's preferred size to the given size.
setPreMatchedNode(TrieNode) - Method in class edu.iastate.jtm.dic.TrieDictionary
setPresentation(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeconfidence: Set the value of the Presentation column.
setPresentation(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeentitytype: Set the value of the presentation column.
setPresentation(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeinteractiontype: Set the value of the presentation column.
setPresentation(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodelocation: Set the value of the presentation column.
setPresentation(String) - Method in class edu.iastate.metnet.hibernate.AbstractCodeorganism: Set the value of the presentation column.
setPresentation(String) - Method in class edu.iastate.metnet.hibernate.AbstractCoderule: Set the value of the presentation column.
setProcessedSet(Set) - Method in class fcmodeler.pathbinder.updater.MedCrawlerPanel
setProduct(String) - Method in class edu.iastate.metnet.hibernate.BrendaproductKey: Sets the value of the product property.
setProducts(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setProgress(double) - Method in class edu.iastate.jtm.assistant.CitationPool
setProgress(double) - Method in class edu.iastate.jtm.gui.DefaultMonitorable
setProperties() - Method in class edu.iastate.metnet.dataManager.JMultilineLabel
setProperties(Interactionproperties) - Method in class edu.iastate.metnet.hibernate.Interaction
setProreversal(Double) - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Set the value of the ProReversal column.
setProteinFilename(String) - Method in class edu.iastate.metnet.aracyc.ChangeName
setPubchemid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchem: Set the value of the pubchemid column.
setPubchemid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchemName: Set the value of the pubchemid column.
setPublicationId(Integer) - Method in class edu.iastate.metnet.dao.TairReferenceObject
setPubMed(PubMedAssistant) - Static method in class edu.iastate.metnet.launch.LaunchMetNet
setPubmedId(Integer) - Method in class edu.iastate.metnet.dao.TairReferenceObject
setPubMode(boolean) - Method in class edu.iastate.jtm.jmed.MedlineParser
setQueryKey(String) - Method in class edu.iastate.jtm.jmed.Limits
setQuotedQuery(boolean) - Method in class edu.iastate.jtm.jmed.ESearch
setQuotedQuery(boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier
setRandomize(boolean) - Method in class edu.iastate.jtm.jmed.PubMedSampler
setRangeMarkers(Vector<RangeMarker>) - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog.CustomSortObject
setRangeMarkers(Vector<RangeMarker>) - Method in class edu.iastate.metnet.metaomgraph.chart.DataSorter
setReactionName(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAracycDump: Set the value of the reaction_name column.
setReactionRateMap(Map) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
setRecommendname(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendarecommendname: Set the value of the RECOMMENDNAME column.
setRecordId(Integer) - Method in class edu.iastate.metnet.dao.CategoryNode
setRecordId(Integer) - Method in class edu.iastate.metnet.dao.HistoryBlockunitImpl
setRecordId(Integer) - Method in class edu.iastate.metnet.dao.HistoryInformation
setRecordId(Integer) - Method in class edu.iastate.metnet.dao.MyVersionNode
setRecordId(Integer) - Method in class edu.iastate.metnet.dao.SoybeanHomology
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the simple primary key value that identifies this object.
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the simple primary key value that identifies this object.
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the simple primary key value that identifies this object.
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairAgiToUniprot: Set the simple primary key value that identifies this object.
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairAracycDump: Set the simple primary key value that identifies this object.
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the simple primary key value that identifies this object.
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes: Set the simple primary key value that identifies this object.
setRecordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Set the simple primary key value that identifies this object.
setReference(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the reference column.
setReferenceDbName(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference: Set the value of the reference_db_name column.
setReferenceId(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference: Set the value of the reference_id column.
setReferenceList(ArrayList<TairReference>) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setReferenceList(ArrayList<TairReference>) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setReferenceOrigin(Blockunitref) - Method in class edu.iastate.reload.ui.ReferenceEditForm
setRefillZone(int) - Method in class edu.iastate.jtm.jmed.StreamXMLParser: Set buffer refill size.
setRefType(String) - Method in class edu.iastate.metnet.dao.ReferenceObject
setReftype(String) - Method in class edu.iastate.metnet.hibernate.BlockunitrefKey: Sets the value of the reftype property.
setReftype(String) - Method in class edu.iastate.metnet.hibernate.EntityrefKey: Sets the value of the reftype property.
setRefValue(String) - Method in class edu.iastate.metnet.dao.ReferenceObject
setRefvalue(String) - Method in class edu.iastate.metnet.hibernate.BlockunitrefKey: Sets the value of the refvalue property.
setRefvalue(String) - Method in class edu.iastate.metnet.hibernate.EntityrefKey: Sets the value of the refvalue property.
setRejectHits(boolean) - Method in class edu.iastate.jtm.EntityFinder
setRejectLong(boolean) - Method in class edu.iastate.jtm.EntityFinder
setRelativeDate(int) - Method in class edu.iastate.jtm.jmed.Limits
setRescanTitle(boolean) - Method in class fcmodeler.pathbinder.MedCrawler
setRetrieveCount(int) - Method in class edu.iastate.jtm.jmed.Limits
setRetrieveMode(int) - Method in class edu.iastate.jtm.jmed.Limits
setRetrieveStartNum(int) - Method in class edu.iastate.jtm.jmed.Limits
setRetrieveType(int) - Method in class edu.iastate.jtm.jmed.Limits
setReversal(Double) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setReversible(String) - Method in class edu.iastate.metnet.dao.InteractionObject
setReversible(boolean) - Method in class edu.iastate.metnet.graphmodel.MetaphorTypeInformation
setRight(int) - Method in class edu.iastate.jtm.EntityFinder.Hit: Setter for property right.
setRightNode(PathwayElementNode) - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode
setRightNode(PathwayElementNode) - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode
setRightPart() - Method in class edu.iastate.metnet.dao.MetnetInteraction
setRightPart(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setRightPart(Vector) - Method in class edu.iastate.metnet.hibernate.Interaction
setRightToLeftMap(MultiHashMap) - Method in class edu.iastate.metnet.dao.BidiMultiHashMap
setRightUnit(Blockunit) - Method in class edu.iastate.metnet.model.AbstractMultiBlockunitDecorator
setRNodeName(String) - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo
setRole(String) - Method in class edu.iastate.metnet.hibernate.InteractionpartsKey: Sets the value of the role property.
setRootMatcher(Matcher) - Method in class edu.iastate.jtm.jmed.StreamXMLParser
setRootPanel(RootPanel) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
setRowEditorModel(RowEditorModel) - Method in class edu.iastate.metnet.ui.MyJTableEx
setRowHeaderWidth(int) - Method in class edu.iastate.jtm.gui.RowHeaderTable
setRowid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the simple primary key value that identifies this object.
setRowid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityOntology: Set the simple primary key value that identifies this object.
setRowid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchem: Set the simple primary key value that identifies this object.
setRowid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchemName: Set the simple primary key value that identifies this object.
setRowNames(Object[][], String[]) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the row names and info column headers to the given values.
setRowNames(Object[][]) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject: Sets the row names and info column headers to the given values.
setRowPointers(List<Long>) - Method in class edu.iastate.metnet.soft.Entity
setRows(String[][]) - Method in class edu.iastate.metnet.dataManager.FileData
setRuleid(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractAbbreviationrules: Set the simple primary key value that identifies this object.
setSamples(List<Sample>) - Method in class edu.iastate.metnet.soft.Series
setSaxParser(SAXReader) - Method in class edu.iastate.jtm.jmed.StreamXMLParser
setSbmlFile(String) - Method in class edu.iastate.metnet.ui.SBMLExporter
setScore(double) - Method in class fcmodeler.pathbinder.PbSentence
setSearchFieldColors(JTextField, boolean) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils: Used for setting the colors of a JTextField based on the results of a search.
setSearchPanel1(SearchPanel) - Method in class fcmodeler.pathbinder.gui.EntityPanel
setSearchPanel2(SearchPanel) - Method in class fcmodeler.pathbinder.gui.EntityPanel
setSearchText(String) - Method in class fcmodeler.pathbinder.gui.SearchPanel: added by Mohammed Alabsi -- used to set the fieldtext with the entity name June 16th, 2006
setSelected(boolean) - Method in class edu.iastate.biocyc.dao.rdb.BlockunitChoice
setSelected(boolean) - Method in class edu.iastate.metnet.model.PathwayObjectChoice
setSelected(boolean) - Method in class edu.iastate.metnet.model.SpeciesChoice
setSelectedBlockunits(SelectionInList) - Method in class edu.iastate.metnet.model.NodeSelectionModel
setSelectedFile(File) - Method in class edu.iastate.jtm.gui.FileBar
setSelectedItem(Object) - Method in class edu.iastate.metnet.model.JDBCComboModel: set the selected item to the specified value object
setSelectedNodes(Object[]) - Method in class edu.iastate.metnet.graphmodel.RemoveSelectedNodes
setSelectedPoint(Point2D) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
setSelectedRows(int[]) - Static method in class edu.iastate.metnet.hivemindService.CytoscapeHMService
setSelectedSeries(int) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
setSelection(List) - Method in class edu.iastate.metnet.controller.NodeSelectionController
setSelectionMode(int) - Method in class edu.iastate.metnet.metaomgraph.chart.OrderableTable
setSentence(int) - Method in class fcmodeler.pathbinder.InteractUpdate
setSentences(PbSentence[], Set, Set, Set, Set, Set, Set, Object[], Object[]) - Method in class fcmodeler.pathbinder.gui.PbViewer
setSentences(PbSentence[], List) - Method in class fcmodeler.pathbinder.gui.SentencePane
setSeqStart(int) - Method in class edu.iastate.jtm.jmed.Limits: Show sequence starting from this base number.
setSeqStop(int) - Method in class edu.iastate.jtm.jmed.Limits: Show sequence ending on this base number.
setSharedUserList(ArrayList) - Method in class edu.iastate.metnet.hibernate.Blockunit
setShortterm(String) - Method in class edu.iastate.metnet.hibernate.AbstractAbbreviationrules: Set the value of the shortterm column.
setShowingOnStartup(boolean) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTips.MetaOmShowTipsChoice
setShowOriginal(boolean) - Method in class edu.iastate.jtm.jmed.EUtility
setSignalPeptideScore(Double) - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Set the value of the signal_peptide_score column.
setSignature(String) - Method in class edu.iastate.metnet.dao.InteractionStructure
setSkipTo(int) - Method in class edu.iastate.jtm.util.SlidingWindow.Stride
setSortByData(boolean) - Method in class edu.iastate.metnet.metaomgraph.SortableData: Sets whether to sort by data or by index.
setSortByScore(boolean) - Static method in class fcmodeler.pathbinder.PbSentence
setSortingStatus(int, int) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
setSortOrder(int[]) - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog.CustomSortObject
setSortOrder(int[]) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel
setSource(String) - Method in class edu.iastate.biocyc.dao.rdb.ClassName
setSource(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setSource(String) - Method in class edu.iastate.metnet.dao.NameSource
setSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the value of the Source column.
setSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiChemicalData: Set the value of the source column.
setSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Set the value of the source column.
setSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession: Set the value of the source column.
setSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames: Set the value of the source column.
setSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractClassName
setSource(String) - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Set the value of the Source column.
setSourceId(String) - Method in class edu.iastate.metnet.dao.ZEdge
setSoybeanProbeId(String) - Method in class edu.iastate.metnet.dao.SoybeanHomology
setSpecies(String) - Method in class edu.iastate.metnet.model.SpeciesChoice
setSplitDigit(boolean) - Method in class edu.iastate.jtm.util.SlidingWindow
setSplitWithinParen(boolean) - Method in class fcmodeler.pathbinder.MedCrawler
setStart(int) - Method in class edu.iastate.jtm.util.SlidingWindow.Stride
setStart(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the start column.
setStart(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the start column.
setStart(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the start column.
setStart(int) - Method in class edu.iastate.metnet.metaomgraph.chart.RangeMarker
setStatus(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds: Set the value of the status column.
setStatus(String) - Method in class edu.iastate.metnet.hibernate.BackgroundTask
setStop(boolean) - Method in class edu.iastate.jtm.assistant.CitationPool
setStop(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements: Set the value of the stop column.
setStop(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements: Set the value of the stop column.
setStop(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the stop column.
setStoreInteraction(boolean) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter
setStoreInteraction(boolean) - Method in class edu.iastate.metnet.graphmodel.RemoveBridgeNodes
setStrand(int) - Method in class edu.iastate.jtm.jmed.Limits: What strand of DNA to show (1=plus or 2=minus).
setStrength(Double) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setStrength(Double) - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Set the value of the Strength column.
setStyle(int) - Method in class edu.iastate.metnet.metaomgraph.chart.RangeMarker
setStylesheet(Map) - Method in class edu.iastate.jtm.gui.HighlightableTextPane
setSubFamily(String) - Method in class edu.iastate.metnet.dao.SoybeanHomology
setSubmitTime(Date) - Method in class edu.iastate.metnet.hibernate.BackgroundTask
setSubstrate(String) - Method in class edu.iastate.metnet.hibernate.BrendasubstrateKey: Sets the value of the substrate property.
setSubstrates(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setSubSystem(int) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor
setSubSystem(Integer) - Method in class edu.iastate.metnet.model.IntermediumEntityInformation
setSubtype(String) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Set the value of the Subtype column.
setSuid(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements: Set the value of the suid column.
setSwingValue(String, String) - Method in class edu.iastate.metnet.ui.AddPathwayForm
setSynonym(String) - Method in class edu.iastate.metnet.dao.SynonymObject
setSynonym(String) - Method in class edu.iastate.metnet.hibernate.BlockunitSynonymCandidate
setSynonym(String) - Method in class edu.iastate.metnet.hibernate.BlockunitsynonymKey: Sets the value of the synonym property.
setSynonym(String) - Method in class edu.iastate.metnet.hibernate.EntitysynonymKey: Sets the value of the synonym property.
setSynonymOrigin(Blockunitsynonym) - Method in class edu.iastate.reload.ui.SynonymEditForm
setSynonyms(ArrayList) - Method in class edu.iastate.metnet.aracyc.AracycEntity: set the synonym
setSynonyms(String) - Method in class edu.iastate.metnet.hibernate.BrendasynonymsKey: Sets the value of the synonyms property.
setSynonymSources(Vector) - Method in class edu.iastate.metnet.dao.ChebiOntologyName
setTableData(Object[][]) - Method in class edu.iastate.metnet.soft.Entity
setTableHeader(JTableHeader) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
setTableHeaders(String[]) - Method in class edu.iastate.metnet.soft.Entity
setTableModel(TableModel) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
setTairAccession(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the tair_accession column.
setTairid(String) - Method in class edu.iastate.metnet.hibernate.AbstractGtairProperty: Set the simple primary key value that identifies this object.
setTairKeywordId(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim: Set the value of the tair_keyword_id column.
setTargetId(String) - Method in class edu.iastate.metnet.dao.ZEdge
setTargetLocation(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis: Set the value of the target_location column.
setTaskID(Integer) - Method in class edu.iastate.metnet.hibernate.BackgroundTask
setTaskResult(String) - Method in class edu.iastate.metnet.hibernate.BackgroundTask
setTemplateRecordId(Integer) - Method in class edu.iastate.metnet.ui.AddPathwayForm
setTerm(String) - Method in class edu.iastate.metnet.dao.GoTermID
setTerm(String) - Method in class edu.iastate.metnet.export.GoTermID
setText(String) - Method in class edu.iastate.jtm.gui.HighlightableTextPane
setText(String) - Method in class edu.iastate.metnet.dataManager.JMultilineLabel
setText(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments: Set the value of the text column.
setTextpanelCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.ViewInfo
setTimeScale(Double) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setTimescale(Double) - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Set the value of the TimeScale column.
setTiming(boolean) - Method in class edu.iastate.jtm.jmed.UmlsQueryClient: Time the query if true.
setTitle(String) - Method in class edu.iastate.metnet.dao.TairReferenceObject
setTitle(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the TITLE column.
setTitle(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiOntology: Set the value of the title column.
setToDate(String) - Method in class edu.iastate.jtm.jmed.Limits
setTokenProcessor(TokenProcessor) - Method in class edu.iastate.jtm.dic.AbstractDictionary
setTooltipTemplate(String) - Method in class edu.iastate.metnet.model.AbstractBlockunitDecorator
setType(char, int) - Method in class edu.iastate.jtm.util.CharType
setType(String) - Method in class edu.iastate.metnet.dao.CategoryNode
setType(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setType(Integer) - Method in class edu.iastate.metnet.hibernate.AbstractAbbreviationrules: Set the value of the type column.
setType(String) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the value of the Type column.
setType(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession: Set the value of the type column.
setType(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames: Set the value of the type column.
setType(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiRelation: Set the value of the type column.
setType(String) - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Set the value of the Type column.
setType(String) - Method in class edu.iastate.metnet.hibernate.AbstractInteraction: Set the value of the Type column.
setUniprotID(String) - Method in interface edu.iastate.metnet.datamodel.db.Gene
setUniprotID(String) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl
setUniprotId(String) - Method in class edu.iastate.metnet.hibernate.AbstractTairAgiToUniprot: Set the value of the uniprot_id column.
setUnitMatcher(Matcher, Matcher) - Method in class edu.iastate.jtm.jmed.StreamXMLParser
setUnsortable(int) - Method in class edu.iastate.jtm.gui.TableSorter
setUp() - Method in class edu.iastate.biocyc.test.ArabReaderTest
setUp() - Method in class edu.iastate.biocyc.test.BlockunitTest
setUp() - Method in class edu.iastate.biocyc.test.RiceReaderTest
setup() - Method in class edu.iastate.metnet.aracyc.ConsoleApplication: set up the system wide property setting
setUp() - Method in class edu.iastate.metnet.test.BlockunitFinderTest
setUp() - Method in class edu.iastate.metnet.test.MD5DigestTest
setUp() - Method in class edu.iastate.metnet.test.MyFacadeTest
setUp() - Method in class edu.iastate.metnet.test.MyPaperTest
setUp() - Method in class edu.iastate.metnet.test.MySolverTest
setUp() - Method in class edu.iastate.metnet.test.UtilsTest
setupLookAndFeel() - Method in class edu.iastate.metnet.launch.RunCytoscape
setupStatement() - Method in class edu.iastate.metnet.aracyc.ConsoleApplication: set up the SQL statement from the server and db configuration
setupTableHeader(JTable) - Method in class edu.iastate.jtm.gui.TableSorter
setURL(URL) - Method in class edu.iastate.jtm.gui.HyperlinkLabel
setUseHistory(boolean) - Method in class edu.iastate.jtm.jmed.Limits
setUser(String) - Method in class edu.iastate.jtm.util.RemoteControl
setUser(String) - Method in class edu.iastate.metnet.dao.InteractionInformation
setUsername(String) - Method in class edu.iastate.biocyc.dao.rdb.ClassName
setUsername(String) - Method in class edu.iastate.metnet.dao.CommentObject
setUsername(String) - Method in class edu.iastate.metnet.dao.HistoryBlockunitImpl
setUsername(String) - Method in class edu.iastate.metnet.dao.HistoryInformation
setUsername(String) - Method in class edu.iastate.metnet.dao.MyVersionNode
setUsername(String) - Method in class edu.iastate.metnet.dao.ReferenceObject
setUsername(String) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit: Set the value of the Username column.
setUsername(String) - Method in class edu.iastate.metnet.hibernate.AbstractClassName
setUsername(String) - Method in class edu.iastate.metnet.hibernate.AbstractEntity: Set the value of the Username column.
setUsername(String) - Method in class edu.iastate.metnet.hibernate.AbstractEntitycomment: Set the value of the Username column.
setUsername(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction
setUsername(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity
setUsername(String) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway
setUsername(String) - Method in class edu.iastate.metnet.hibernate.AbstractUser: Set the simple primary key value that identifies this object.
setUsername(String) - Method in class edu.iastate.metnet.hibernate.BlockunitcommentKey: Sets the value of the username property.
setUsername(String) - Method in class edu.iastate.metnet.hibernate.BlockunitrefKey: Sets the value of the username property.
setUsername(String) - Method in class edu.iastate.metnet.hibernate.EntityrefKey: Sets the value of the username property.
setUserObject(Object) - Method in class edu.iastate.jtm.jmed.Query.CompositeTerm
setUserObject(Object) - Method in class edu.iastate.jtm.jmed.Query.SimpleTerm
setUserObject(Object) - Method in class fcmodeler.pathbinder.gui.VerbNode
setValidSize(int) - Method in class edu.iastate.metnet.dao.AlignmentObject
setValue(Object) - Method in class com.jgoodies.binding.extras.ListModelHolder: Sets a new value and notifies any registered value listeners if the value has changed.
setValue(Object) - Method in class edu.iastate.jtm.dic.AbstractTrieNode: Attach a value to the node.
setValue(Object) - Method in interface edu.iastate.jtm.dic.TrieNode: Attach a value to the node.
setValue(Object) - Method in class edu.iastate.jtm.EntityFinder.Hit: Setter for property value.
setValue(Object) - Method in class edu.iastate.jtm.gui.HyperLinkCellRenderer
setValue(Map) - Method in class edu.iastate.metnet.aracyc.AbstractAracycEntity
setValue(Map) - Method in interface edu.iastate.metnet.aracyc.IAracycEntity
setValue(Double) - Method in class edu.iastate.metnet.hibernate.AbstractCodeconfidence: Set the value of the Value column.
setValue(Object) - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog.ColumnValueRenderer
setValue(double) - Method in class edu.iastate.metnet.metaomgraph.SortableData: Sets a new data value for this object
setValue(Object) - Method in class edu.iastate.metnet.model.DisplayObject
setValue(String) - Method in class edu.iastate.metnet.soft.Attribute
setValueAt(Object, int, int) - Method in class edu.iastate.biocyc.ui.PathwayChoiceModel
setValueAt(Object, int, int) - Method in class edu.iastate.jtm.assistant.CitationPool
setValueAt(Object, int, int) - Method in class edu.iastate.jtm.gui.TableMap
setValueAt(Object, int, int) - Method in class edu.iastate.jtm.gui.TableSorter
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.metaomgraph.TableSorter
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.AbbreviationRulesModel
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.CandidateModel
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.CompositionSelectionModel
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.GroupShareTableModel
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.InteractionPartsModel: set the object value of the cell
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.MultiSelectionModel
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.SpeciesTableModel: set the value
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.TableMap
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.model.TableSorter
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.NoneditableTableModel
setValueAt(Object, int, int) - Method in class edu.iastate.metnet.ui.PathwayChoiceTableModel: set the value
setVariance(double) - Method in class edu.iastate.metnet.birdseyeview.Annotation: Sets the experimental variance.
setVerbose(boolean) - Method in class edu.iastate.jtm.EntityFinder
setVerbose(boolean) - Method in class edu.iastate.jtm.jmed.PubMedFetcher: Set verbose mode.
setVerbose(boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier: Set verbose mode.
setVerbose(boolean) - Method in class edu.iastate.jtm.jmed.PubMedTimer: Set verbose mode.
setVerbose(boolean) - Method in class edu.iastate.jtm.jmed.StreamXMLParser: Set verbose mode.
setVersionEditor(VersionEditor) - Method in class edu.iastate.metnet.ui.VersionSaver
setVersionGraphModel(VersionGraphModel) - Method in class edu.iastate.metnet.ui.VersionEditor: notice to invalidate the graph, set it as null
setVersionListener(VersionListener) - Method in class edu.iastate.metnet.ui.VersionEditor
setVerticeRef(String) - Method in class edu.iastate.metnet.hibernate.AbstractChebiVertices: Set the value of the vertice_ref column.
setVmax(Double) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties: Set the value of the Vmax column.
setVol(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the VOL column.
setWaitTime(long) - Method in class edu.iastate.jtm.util.ProcessWrapper
setWalkType(int) - Method in class edu.iastate.metnet.graphmodel.GraphWalker
setWebEnv(String) - Method in class edu.iastate.jtm.jmed.Limits
setWidth(double) - Method in class edu.iastate.metnet.dao.ZVertex
setWillDeleted(boolean) - Method in class edu.iastate.metnet.model.SelectedBlockunit
setXmlParser(SAXReader) - Method in class edu.iastate.jtm.jmed.EUtility
setXmlWriter(XMLWriter) - Method in class edu.iastate.jtm.jmed.EUtility
setXsltFile(String) - Method in class edu.iastate.metnet.ui.SBMLExporter
setXVel(int, int) - Method in class edu.iastate.metnet.metaomgraph.PolygonPanel.BouncingPolygon
setYear(String) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref: Set the value of the YEAR column.
setYVel(int, int) - Method in class edu.iastate.metnet.metaomgraph.PolygonPanel.BouncingPolygon
SH - Static variable in class edu.iastate.jtm.jmed.Query.Field
sharedInstance - Static variable in class edu.iastate.reload.ui.JGraphParallelEdgeRouter
sheetList - Variable in class edu.iastate.metnet.analysis.DefaultJExcelClient
sheetName - Variable in class edu.iastate.metnet.analysis.AbstractExcelSheet
show - Variable in class edu.iastate.metnet.metaomgraph.MetaOmTips.MetaOmShowTipsChoice
SHOW_TIPS_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmGraph
showActionList() - Method in class edu.iastate.metnet.birdseyeview.ButtonPanel: Added by Mohammed Alabsi - April 13th, 2006 Method to enable metaOmGraphButton button
showDialog() - Method in class edu.iastate.jtm.assistant.Highlighter
showframe(boolean) - Method in class fcmodeler.pathbinder.gui.SentencePane
showhideLegend() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: This method shows or hides the legend pane
showhideLegend() - Method in class edu.iastate.metnet.birdseyeview.RootPanel
showMessage(String) - Method in class edu.iastate.jtm.gui.StatusBar
showMessage(String) - Method in interface edu.iastate.jtm.util.ProgressMonitor
showMessage(String) - Method in class edu.iastate.jtm.util.RemoteControl
showNewData() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView: Cooperate with newVariant() After all variants called newVariant(), call it to display new data
showOriginal - Variable in class edu.iastate.jtm.jmed.EUtility
showPathBinder() - Method in class fcmodeler.pathbinder.gui.PbFrame
showProgress(int) - Method in class edu.iastate.jtm.gui.StatusBar
showSearchDialog() - Method in class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel: Displays a modal dialog that contains a TreeSearchQueryConstructionPanel.
showSortDialog() - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog
shuttlesort(int[], int[], int, int) - Method in class edu.iastate.jtm.gui.TableSorter
shuttlesort(int[], int[], int, int) - Method in class edu.iastate.metnet.model.TableSorter: This is a home-grown implementation which we have not had time to research - it may perform poorly in some circumstances.
SID - Static variable in class edu.iastate.jtm.jmed.Limits
signature - Variable in class edu.iastate.metnet.dao.InteractionStructure: signature
SimpleChipAnimationPanel - Class in edu.iastate.metnet.metaomgraph
SimpleChipAnimationPanel() - Constructor for class edu.iastate.metnet.metaomgraph.SimpleChipAnimationPanel
SimpleGeneObj - Class in edu.iastate.metnet.hivemindService: contains gene id and id type, with no annotation data
SimpleGeneObj(String, int) - Constructor for class edu.iastate.metnet.hivemindService.SimpleGeneObj
SimpleModalMaker - Class in edu.iastate.metnet.metaomgraph: If you make a Dialog or JDialog modal, it will block ALL frames running in the current application context.
SimpleModalMaker() - Constructor for class edu.iastate.metnet.metaomgraph.SimpleModalMaker
SimpleTermPanel - Class in edu.iastate.jtm.assistant
SimpleTermPanel() - Constructor for class edu.iastate.jtm.assistant.SimpleTermPanel
singlize(String) - Method in class edu.iastate.jtm.PluralDetector: Return singular form of a plural.
singlize(CharBuffer) - Method in class edu.iastate.jtm.PluralDetector
size() - Method in class edu.iastate.jtm.dic.AbstractDictionary
size() - Method in class edu.iastate.jtm.dic.Trie: Return the number of entries in this trie.
size - Variable in class edu.iastate.metnet.birdseyeview.AbstractView
size - Variable in class edu.iastate.metnet.birdseyeview.AnnotationTextPanel
size() - Method in class edu.iastate.metnet.dao.MyVersionGraph: get the node size of the version, to handle if there is not any history record.
size() - Method in class edu.iastate.metnet.graphmodel.PathwayModel: return the number of pathway in this model
sizeColumnsToFit() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel: Resizes the columns of the entry table to their initial length.
sizeColumnWidthToFit(JTable) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils
sizeComponent(Component, double, double) - Static method in class edu.iastate.jtm.gui.ScreenUtil
skip(CharBuffer) - Method in class edu.iastate.jtm.util.SlidingWindow
skipBytes(int) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile: Skips exactly n bytes of input.
skipBytes(int) - Method in class edu.iastate.metnet.soft.RandomAccessFile: Skips exactly n bytes of input.
skipSpace - Variable in class edu.iastate.jtm.dic.AbstractDictionary
slideWindow(CharBuffer, boolean, boolean) - Method in class edu.iastate.jtm.util.SlidingWindow
SlidingWindow - Class in edu.iastate.jtm.util
SlidingWindow(boolean) - Constructor for class edu.iastate.jtm.util.SlidingWindow: Creates a new instance of SlidingWindow
SlidingWindow() - Constructor for class edu.iastate.jtm.util.SlidingWindow
SlidingWindow.Stride - Class in edu.iastate.jtm.util
SlidingWindow.Stride() - Constructor for class edu.iastate.jtm.util.SlidingWindow.Stride
SlidingWindow.Stride(int) - Constructor for class edu.iastate.jtm.util.SlidingWindow.Stride
SlidingWindow.Stride(int, int) - Constructor for class edu.iastate.jtm.util.SlidingWindow.Stride
SNP - Static variable in class edu.iastate.jtm.jmed.Entrez
socket - Static variable in class edu.iastate.metnet.utils.Utils: socket for single instance testing
SOFTException - Exception in edu.iastate.metnet.soft
SOFTException() - Constructor for exception edu.iastate.metnet.soft.SOFTException
SOFTException(String) - Constructor for exception edu.iastate.metnet.soft.SOFTException
SOFTFile - Class in edu.iastate.metnet.soft
SOFTFile(File) - Constructor for class edu.iastate.metnet.soft.SOFTFile
SOFTFile(String) - Constructor for class edu.iastate.metnet.soft.SOFTFile
SOFTParser - Class in edu.iastate.metnet.soft
SOFTParser() - Constructor for class edu.iastate.metnet.soft.SOFTParser
SOFTParserOptionPanel - Class in edu.iastate.metnet.soft
SOFTParserOptionPanel() - Constructor for class edu.iastate.metnet.soft.SOFTParserOptionPanel
solve(List, List) - Method in class edu.iastate.metnet.analysis.MySolver: solve the linear equation
solve(float[][], float[]) - Method in class edu.iastate.metnet.analysis.MySolver
solver - Static variable in class edu.iastate.metnet.analysis.MySolver: singleton pattern
SOME - Static variable in interface edu.iastate.jtm.util.Queue
SOME_MARKED - Static variable in interface edu.iastate.jtm.gui.Markable
someIcon - Variable in class edu.iastate.jtm.gui.MarkableHeaderRenderer
sort() - Method in class edu.iastate.jtm.gui.TableSorter
sort(Object) - Method in class edu.iastate.metnet.model.TableSorter
SORTABLE - Static variable in class edu.iastate.jtm.gui.TableSorter
SortableData - Class in edu.iastate.metnet.metaomgraph: Class for sorting data in ascending or descending order while retaining information about the data's original order.
SortableData(double, int) - Constructor for class edu.iastate.metnet.metaomgraph.SortableData: Constructs a new object that sorts by data in ascending order.
SortableData(double, int, boolean) - Constructor for class edu.iastate.metnet.metaomgraph.SortableData: Constructs a new object that sorts by data.
SortableData(double, int, boolean, boolean) - Constructor for class edu.iastate.metnet.metaomgraph.SortableData: Constructor.
SortableHeaderRenderer - Class in edu.iastate.jtm.gui
SortableHeaderRenderer(TableSorter) - Constructor for class edu.iastate.jtm.gui.SortableHeaderRenderer
sortAlignmentList(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacade: sort the alignment list
sortAlignmentList(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal: sort the alignment list
sortByColumn(int) - Method in class edu.iastate.jtm.gui.TableSorter
sortByColumn(int) - Method in class edu.iastate.metnet.model.TableSorter
sortByColumn(int, boolean) - Method in class edu.iastate.metnet.model.TableSorter
sortByColumnName() - Method in class edu.iastate.metnet.metaomgraph.chart.DataSorter: Sorts the data alphabetically by column name.
sortByExtendedInfo() - Method in class edu.iastate.metnet.metaomgraph.chart.DataSorter: Displays a frame that allows the user to construct a query, then searches the active project's extended info tree for hits.
sortByPOs() - Method in class edu.iastate.metnet.metaomgraph.chart.DataSorter: Sorts data by Plant Ontology information.
sortByYValue(double[]) - Method in class edu.iastate.metnet.metaomgraph.chart.DataSorter: Sorts the data according to a second array of values, such that the index of the highest value in the passed array appears in the first cell of the result array.
sortCustom() - Method in class edu.iastate.metnet.metaomgraph.chart.DataSorter
sorter - Variable in class edu.iastate.jtm.gui.SortableHeaderRenderer
sortingColumns - Variable in class edu.iastate.metnet.model.TableSorter
sortKeywords(DefaultComboBoxModel) - Method in class edu.iastate.jtm.assistant.Highlighter
source - Variable in class edu.iastate.biocyc.dao.rdb.ClassName: source
source - Variable in class edu.iastate.metnet.dao.InteractionInformation: data source of the interaction
source - Variable in class edu.iastate.metnet.dao.NameSource
sourceId - Variable in class edu.iastate.metnet.dao.ZEdge: source block id
SoybeanHomology - Class in edu.iastate.metnet.dao: store the soybean homology information
SoybeanHomology() - Constructor for class edu.iastate.metnet.dao.SoybeanHomology: default constructor
SoybeanHomology(Integer) - Constructor for class edu.iastate.metnet.dao.SoybeanHomology: default constructor
soybeanProbeId - Variable in class edu.iastate.metnet.dao.SoybeanHomology: soybean probe ID
SPACE - Static variable in class edu.iastate.jtm.util.SlidingWindow
SPEARMAN - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmAnalyzer
SPEARMAN_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
spearmanCorrelation(double[], boolean, Double) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc
spearmanCorrelation(Object[], boolean, Double) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc: Calculates the Spearman Correlation of this calculator's base data with another set of data.
spearmanCorrelationStandard(double[]) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc: Calculates the Spearman Correlation of this calculator's base data with another set of data.
spearmanCorrelationWithReplacements(double[], Double) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc
spearmanCorrelationWithSkips(double[]) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc
species - Variable in class edu.iastate.metnet.model.SpeciesChoice: species
SpeciesChoice - Class in edu.iastate.metnet.model: species choise
SpeciesChoice(String) - Constructor for class edu.iastate.metnet.model.SpeciesChoice: default constructor
speciesListModel - Variable in class edu.iastate.metnet.ui.SpeciesSelector: species list model
SpeciesSelector - Class in edu.iastate.metnet.ui: select one or more species
SpeciesSelector(Object) - Constructor for class edu.iastate.metnet.ui.SpeciesSelector: Creates new form SpeciesSelector
SpeciesTableModel - Class in edu.iastate.metnet.model
SpeciesTableModel(ListModel) - Constructor for class edu.iastate.metnet.model.SpeciesTableModel: default constructor
SpinnerAdapterFactory - Class in com.jgoodies.binding.extras: A factory that vends SpinnerModel implementations that are bound to a ValueModel Can be used to bind a ValueModel to instances of JSpinner.
SpinningPolygonThrobber - Class in edu.iastate.metnet.metaomgraph.throbber
SpinningPolygonThrobber() - Constructor for class edu.iastate.metnet.metaomgraph.throbber.SpinningPolygonThrobber
splash(Image) - Static method in class edu.iastate.jtm.gui.SplashWindow: Constructs and displays a SplashWindow.
splash - Static variable in class edu.iastate.metnet.ui.MainWindow2: splash window instance
Splash - Class in edu.iastate.metnet.ui: splash screen
Splash() - Constructor for class edu.iastate.metnet.ui.Splash: Creates new form Splash
SplashWindow - Class in edu.iastate.jtm.gui
SplashWindow(Frame, Image) - Constructor for class edu.iastate.jtm.gui.SplashWindow: Constructs a splash window and centers it on the screen.
split(File, int) - Static method in class edu.iastate.jtm.util.FileSplitter: Split a large file into small ones.
splitDelim(String, boolean) - Static method in class edu.iastate.jtm.TokenAnalyzer: Split a token at delimiters - , .
splitEntity(String) - Static method in class edu.iastate.metnet.utils.Utils: to facility input, we use ,, to separate name and return in ()
splitEntityList(String) - Static method in class edu.iastate.metnet.utils.Utils
splitGreekDigit(String) - Static method in class edu.iastate.jtm.TokenAnalyzer: Split Greek letters and numbers at the start or end of a token.
splitKey(String, boolean) - Method in class edu.iastate.jtm.dic.Trie: Split a string into keys in the trie.
splitKey(String) - Method in class edu.iastate.jtm.dic.Trie: Split a string into keys in the trie (greedy).
splitXml(File, String, int, boolean) - Method in class edu.iastate.jtm.jmed.MedlineParser: Split a large XML file into small ones.
splitXml(InputStream, String, int, boolean) - Method in class edu.iastate.jtm.jmed.MedlineParser: Split a large XML stream into small files.
SpringUtilities - Class in edu.iastate.jtm.gui: A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.
SpringUtilities() - Constructor for class edu.iastate.jtm.gui.SpringUtilities
sql - Variable in class edu.iastate.metnet.db.AbstractMetNetTable
sql - Variable in class edu.iastate.metnet.ui.AddInteractionForm: sql string
sql - Variable in class edu.iastate.metnet.ui.AddPathwayForm: SQL statement
srtIcon - Variable in class edu.iastate.jtm.gui.SortableHeaderRenderer
start() - Method in class edu.iastate.jtm.gui.SwingWorker: Start the worker thread.
start(int) - Method in class edu.iastate.jtm.SentenceParser
start() - Method in class edu.iastate.jtm.util.SlidingWindow
start(int) - Method in class edu.iastate.jtm.util.SlidingWindow
start() - Method in class edu.iastate.metnet.metaomgraph.AnimatedSwingWorker: Start the worker thread.
start() - Method in class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel
start() - Method in class edu.iastate.metnet.metaomgraph.SwingWorker: Start the worker thread.
start() - Method in class edu.iastate.metnet.metaomgraph.throbber.Throbber
start() - Method in class edu.iastate.metnet.ui.Blip: Starts the animation timer.
start() - Static method in class edu.iastate.metnet.ui.WaitingDialog: start the running of waiting dialog
start(JFrame) - Static method in class edu.iastate.metnet.ui.WaitingDialog: start the running of waiting dialog
start(JDialog) - Static method in class edu.iastate.metnet.ui.WaitingDialog
start() - Method in class edu.iastate.metnet.utils.SwingWorker: Start the worker thread.
start() - Method in class edu.iastate.metnet.utils.SwingWorker2: Starts the worker thread.
startDocument() - Method in class fcmodeler.pathbinder.echo
startEditing(Object, MouseEvent) - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph.EditorGraphUI: Will start editing for cell if there is a cellEditor and shouldSelectCell returns true.
startElement(String, String, String, Attributes) - Method in class fcmodeler.pathbinder.echo
startLoading() - Method in class edu.iastate.metnet.threads.DataThread
startService() - Static method in class edu.iastate.jtm.jmed.EUtility: Start processing job queue.
stateChanged(ChangeEvent) - Method in class edu.iastate.metnet.birdseyeview.LegendPanel.spinnerListener
stateChanged(ChangeEvent) - Method in class edu.iastate.metnet.metaomgraph.CreateListFrame
stateChanged(ChangeEvent) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel: Called when this table's MetaOmProject changes.
stateChanged(ChangeEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
stateChanged(ChangeEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
statement - Static variable in class edu.iastate.metnet.aracyc.ConsoleApplication: sql statement
statement - Variable in class edu.iastate.metnet.ui.AddInteractionForm: statement for database
statement - Variable in class edu.iastate.metnet.ui.AddPathwayForm: SQL statement
statement - Variable in class edu.iastate.metnet.ui.ChangePassword
statement - Static variable in class edu.iastate.metnet.ui.MainWindow2: SQL statement instance
statement - Variable in class edu.iastate.metnet.ui.RegisterForm2: SQL statement
status() - Method in class edu.iastate.jtm.assistant.CitationPool
status() - Method in interface edu.iastate.jtm.util.Queue
status - Variable in class edu.iastate.metnet.hibernate.BackgroundTask: queued, running, completed
statusBar - Static variable in class edu.iastate.jtm.assistant.Controller
StatusBar - Class in edu.iastate.jtm.gui
StatusBar(String) - Constructor for class edu.iastate.jtm.gui.StatusBar
Stemmer - Interface in edu.iastate.jtm: Remove word suffix.
stemSentence(String) - Method in class edu.iastate.jtm.PorterStemmer: Stem a sentence.
stemSentence(String) - Method in interface edu.iastate.jtm.Stemmer: Stem a sentence.
stemWord(String, int) - Method in class edu.iastate.jtm.PorterStemmer: Stem a word.
stemWord(String) - Method in class edu.iastate.jtm.PorterStemmer: Stem a lower-cased word.
stemWord(String, int) - Method in interface edu.iastate.jtm.Stemmer: Stem a word.
stemWord(String) - Method in interface edu.iastate.jtm.Stemmer: Stem a lower-cased word.
stop() - Method in class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel
stop() - Method in class edu.iastate.metnet.metaomgraph.throbber.Throbber
stop() - Method in class edu.iastate.metnet.ui.Blip: Stops the animation timer.
stop() - Static method in class edu.iastate.metnet.ui.WaitingDialog: stop the running of waiting dialog
stopService(boolean) - Static method in class edu.iastate.jtm.jmed.EUtility
StreamXMLParser - Class in edu.iastate.jtm.jmed: Parse large XML files in a stream-like mode.
StreamXMLParser(int) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser: Creates a new instance of StreamXMLParser without unit tags.
StreamXMLParser(SAXReader, int) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
StreamXMLParser() - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser: Creates a new instance of StreamXMLParser of default buffer size without unit tags.
StreamXMLParser(SAXReader) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
StreamXMLParser(String, String, int) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser: Creates a new instance of StreamXMLParser
StreamXMLParser(SAXReader, String, String, int) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
StreamXMLParser(String, String) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
StreamXMLParser(SAXReader, String, String) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
StreamXMLParser(SAXReader, Matcher, int) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
StreamXMLParser(Matcher, int) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
StreamXMLParser(Matcher) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
StreamXMLParser(SAXReader, Matcher) - Constructor for class edu.iastate.jtm.jmed.StreamXMLParser
STRICT_TYPE - Static variable in class edu.iastate.jtm.util.ParenParser
string2Double(String) - Static method in class edu.iastate.metnet.utils.Utils: convert the string to double without throwing exception
string2Integer(String) - Static method in class edu.iastate.metnet.utils.Utils: conver tth estring to integer without throwing exception
StringTest - Class in edu.iastate.metnet.test
StringTest() - Constructor for class edu.iastate.metnet.test.StringTest
stringToHex(String) - Static method in class edu.iastate.metnet.utils.HexUtil: Returns a string containing the hexadecimal representation of the input string.
strip(String) - Method in class edu.iastate.jtm.util.TokenProcessor
strip(String, boolean) - Method in class edu.iastate.jtm.util.TokenProcessor
strip(CharBuffer) - Method in class edu.iastate.jtm.util.TokenProcessor
strip(CharBuffer, boolean) - Method in class edu.iastate.jtm.util.TokenProcessor
StripedTable - Class in edu.iastate.metnet
StripedTable(TableModel) - Constructor for class edu.iastate.metnet.StripedTable
StripedTable.ColorEditor - Class in edu.iastate.metnet
StripedTable.ColorEditor() - Constructor for class edu.iastate.metnet.StripedTable.ColorEditor
StripedTable.ColorRenderer - Class in edu.iastate.metnet
StripedTable.ColorRenderer(boolean) - Constructor for class edu.iastate.metnet.StripedTable.ColorRenderer
StripedTable.myColorRenderer - Class in edu.iastate.metnet
StripedTable.myColorRenderer() - Constructor for class edu.iastate.metnet.StripedTable.myColorRenderer
stroke - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
stroke - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
StructuralQueryForm - Class in edu.iastate.metnet.ui: Structural Query.
StructuralQueryForm(Object) - Constructor for class edu.iastate.metnet.ui.StructuralQueryForm: Creates new form NetworkQuery
STRUCTURE - Static variable in class edu.iastate.jtm.jmed.Entrez
StructureQueryHelper - Class in edu.iastate.metnet.ui: helper functions
StructureQueryHelper() - Constructor for class edu.iastate.metnet.ui.StructureQueryHelper
subFamily - Variable in class edu.iastate.metnet.dao.SoybeanHomology: sub family
SUBHEADING - Static variable in class edu.iastate.jtm.jmed.Limits
submitTime - Variable in class edu.iastate.metnet.hibernate.BackgroundTask
subsetBEVtoMOG(ArrayList<Annotation>, ArrayList<String>, ArrayList<String>, Hashtable) - Method in interface edu.iastate.metnet.hivemindService.ExportToMetaOmGraph: Creates a MOG project containing only the data selected from BEV
subsetBEVtoMOG(ArrayList<Annotation>, ArrayList<String>, ArrayList<String>, Hashtable) - Method in class edu.iastate.metnet.hivemindService.ExportToMetaOmGraphImpl
subsetToBirdsEyeView(MetaOmProject, ArrayList<SimpleGeneObj>) - Method in class edu.iastate.metnet.hivemindService.ExportToBirdsEyeView: Method sends selected data to BirdsEyeView.
SUBSTANCE - Static variable in class edu.iastate.jtm.jmed.Limits
substrates - Variable in class edu.iastate.metnet.dao.InteractionInformation: left part of the interactions
subSystem - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor: current sub-system label, if 0, none is selected
succGuidSet - Variable in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode: succ multi-node
superSetOf(FilterEntry) - Method in class fcmodeler.pathbinder.FilterEntry
supportedCharacters() - Method in class edu.iastate.jtm.dic.AbstractTrieNode: Return supported characters by this TrieNode.
supportedCharacters() - Method in class edu.iastate.jtm.dic.Trie: Return supported characters by this Trie.
supportedCharacters() - Method in interface edu.iastate.jtm.dic.TrieNode: Return supported characters by this TrieNode.
SW_CORNER - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
SW_CORNER - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
swap(int, int) - Method in class edu.iastate.jtm.gui.TableSorter
swap(int, int) - Method in class edu.iastate.metnet.model.TableSorter
SwingWorker - Class in edu.iastate.jtm.gui: This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class edu.iastate.jtm.gui.SwingWorker: Start a thread that will call the construct method and then exit.
SwingWorker - Class in edu.iastate.metnet.metaomgraph: This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class edu.iastate.metnet.metaomgraph.SwingWorker: Start a thread that will call the construct method and then exit.
SwingWorker - Class in edu.iastate.metnet.utils: This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class edu.iastate.metnet.utils.SwingWorker: Start a thread that will call the construct method and then exit.
SwingWorker(Object) - Constructor for class edu.iastate.metnet.utils.SwingWorker: Start a thread that will call the construct method and then exit.
SwingWorker2 - Class in edu.iastate.metnet.utils: An abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker2() - Constructor for class edu.iastate.metnet.utils.SwingWorker2: Creates new SwingWorker with no timeout.
SwingWorker2(long) - Constructor for class edu.iastate.metnet.utils.SwingWorker2: Creates new SwingWorker with specified timeout.
SwingWorker2(ThreadFactory, long) - Constructor for class edu.iastate.metnet.utils.SwingWorker2: Creates new SwingWorker with specified thread factory and timeout.
synchronizeGraphTable() - Method in class edu.iastate.reload.ui.NetworkEditForm: update the content of the table
synchViewportWithPanner() - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
synchViewportWithPanner() - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
synonym - Variable in class edu.iastate.metnet.dao.SynonymObject
SynonymCandidate - Class in edu.iastate.metnet.ui
SynonymCandidate() - Constructor for class edu.iastate.metnet.ui.SynonymCandidate
SynonymCandidate_btnApprove_actionAdapter - Class in edu.iastate.metnet.ui
SynonymCandidate_btnApprove_actionAdapter(SynonymCandidate) - Constructor for class edu.iastate.metnet.ui.SynonymCandidate_btnApprove_actionAdapter
SynonymCandidate_btnCheckAll_actionAdapter - Class in edu.iastate.metnet.ui
SynonymCandidate_btnCheckAll_actionAdapter(SynonymCandidate) - Constructor for class edu.iastate.metnet.ui.SynonymCandidate_btnCheckAll_actionAdapter
SynonymCandidate_btnExtractLimit_actionAdapter - Class in edu.iastate.metnet.ui
SynonymCandidate_btnExtractLimit_actionAdapter(SynonymCandidate) - Constructor for class edu.iastate.metnet.ui.SynonymCandidate_btnExtractLimit_actionAdapter
SynonymCandidate_btnUncheckAll_actionAdapter - Class in edu.iastate.metnet.ui
SynonymCandidate_btnUncheckAll_actionAdapter(SynonymCandidate) - Constructor for class edu.iastate.metnet.ui.SynonymCandidate_btnUncheckAll_actionAdapter
SynonymEditForm - Class in edu.iastate.reload.ui
SynonymEditForm(ArrayListModel, Blockunitsynonym) - Constructor for class edu.iastate.reload.ui.SynonymEditForm: Creates new form SynonymEditForm
synonymList - Variable in class edu.iastate.metnet.dao.PathwayObject: synonym list
SynonymObject - Class in edu.iastate.metnet.dao
SynonymObject(Integer, String, boolean) - Constructor for class edu.iastate.metnet.dao.SynonymObject
SynonymObject(String) - Constructor for class edu.iastate.metnet.dao.SynonymObject
synonymOrigin - Variable in class edu.iastate.reload.ui.SynonymEditForm: original synonym
synonyms - Variable in class edu.iastate.metnet.aracyc.AracycEntity: UNIQUE-ID # N+1-NAME # N-1-NAME # N-NAME # SMILES # SYNONYMS # SYSTEMATIC-NAME
synonyms - Variable in class edu.iastate.metnet.aracyc.AracycInteraction: UNIQUE-ID # SYNONYMS
synonymSources - Variable in class edu.iastate.metnet.dao.ChebiOntologyName
SynonymTableModel - Class in edu.iastate.metnet.model
SynonymTableModel(ListModel) - Constructor for class edu.iastate.metnet.model.SynonymTableModel
SynonymTableModel - Class in edu.iastate.reload.model
SynonymTableModel(ListModel) - Constructor for class edu.iastate.reload.model.SynonymTableModel

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