A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

S

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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