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

D

darkColor - Static variable in class edu.iastate.reload.skin.MetalUtilsX
The dark color to draw to draw the pattern.
darkColor - Static variable in class javax.swing.plaf.metal.MetalUtils
The dark color to draw to draw the pattern.
DASH - Static variable in class edu.iastate.jtm.util.SlidingWindow
 
dash1 - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
 
dash1 - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
 
dashStroke - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
 
dashStroke - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
 
data - Variable in class edu.iastate.metnet.analysis.AbstractExcelSheet
 
data - Variable in class edu.iastate.metnet.aracyc.AbstractAracycEntity
 
data - Variable in class edu.iastate.metnet.aracyc.AracycClass
 
data - Variable in class edu.iastate.metnet.aracyc.AracycCompound
 
data - Variable in class edu.iastate.metnet.launch.ListNode
 
data - Variable in class edu.iastate.metnet.model.AbstractPlotData
 
data - Variable in class edu.iastate.metnet.newgui.NoneditableTableModel
 
data - Variable in class edu.iastate.metnet.NoneditableTableModel
The data for the table
data - Variable in class edu.iastate.metnet.threads.DataThread
 
database - Variable in class edu.iastate.jtm.jmed.EUtility
 
Database - Class in edu.iastate.metnet.birdseyeview.db
The Database Class encapsulates the functionality that interacts with the Metnet MySQL database.
Database() - Constructor for class edu.iastate.metnet.birdseyeview.db.Database
Constructor.
DATABASE_NODE - Variable in class edu.iastate.metnet.aracyc.ConsoleApplication
data node in the configure file
databases - Static variable in class edu.iastate.jtm.jmed.Entrez
 
dataEnd - Variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile
The offset in bytes of the end of the data in the buffer, from the start of the file.
dataEnd - Variable in class edu.iastate.metnet.soft.RandomAccessFile
The offset in bytes of the end of the data in the buffer, from the start of the file.
dataFolder - Variable in class edu.iastate.biocyc.ui.BiocycForm
specify the data folder
DataManager - Class in edu.iastate.metnet.dataManager
Main class for DataManager
dataMap - Variable in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement
the attribute value
dataObject - Variable in class edu.iastate.metnet.dao.MyVersionNode
untyped data object
DataOpener - Class in edu.iastate.metnet.newgui
 
DataOpener() - Constructor for class edu.iastate.metnet.newgui.DataOpener
 
dataPanel - Variable in class edu.iastate.metnet.dataManager.DataManager
 
dataSize - Variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile
The size of the data stored in the buffer, in bytes.
dataSize - Variable in class edu.iastate.metnet.soft.RandomAccessFile
The size of the data stored in the buffer, in bytes.
DataSorter - Class in edu.iastate.metnet.metaomgraph.chart
Constructs sort-order arrays for MetaOmChartPanels.
DataSorter(MetaOmChartPanel) - Constructor for class edu.iastate.metnet.metaomgraph.chart.DataSorter
 
dataTable - Variable in class edu.iastate.metnet.dataManager.DataManager
 
dataThread - Static variable in class edu.iastate.metnet.launch.LaunchMetNet
 
DataThread - Class in edu.iastate.metnet.threads
 
DataThread() - Constructor for class edu.iastate.metnet.threads.DataThread
 
date - Variable in class edu.iastate.metnet.dao.InteractionInformation
submit date
db - Variable in class edu.iastate.jtm.DuplicationChecker
 
DBNAME_KEY - Variable in class edu.iastate.metnet.aracyc.ConsoleApplication
database name node in the configure file
DBSearchForm - Class in edu.iastate.reload.ui
 
DBSearchForm() - Constructor for class edu.iastate.reload.ui.DBSearchForm
Creates new form DBSearchForm
dcipher - Variable in class edu.iastate.metnet.utils.DesEncrypter
 
debugOn - Variable in class edu.iastate.jtm.util.JarResources
 
decap(String) - Static method in class edu.iastate.jtm.TokenAnalyzer
 
decomposePathway(DirectedGraph, Map, Collection) - Method in class edu.iastate.biocyc.io.BiocycImporter
get the graph model containing specified pathways
DECORATION_SIZE - Static variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
 
DECORATION_SIZE - Static variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
 
decrypt(String) - Method in class edu.iastate.metnet.utils.DesEncrypter
 
deepCopy(Object) - Static method in class edu.iastate.metnet.utils.Utils
Returns a copy of the object, or null if the object cannot be serialized.
DEF_MAXDATE - Static variable in class edu.iastate.jtm.jmed.Limits
 
DEF_MINDATE - Static variable in class edu.iastate.jtm.jmed.Limits
 
DEF_PAREN_TYPE - Static variable in class edu.iastate.jtm.util.ParenFinder
 
DEFAULT - Static variable in class edu.iastate.jtm.jmed.Limits
 
DEFAULT_BACKGROUND - Static variable in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor
default background color
DEFAULT_FOREGROUND - Static variable in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor
default foreground color
DEFAULT_LINE_WIDTH - Static variable in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor
default line width for recovery
defaultBufferSize - Static variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile
The default buffer size, in bytes.
defaultBufferSize - Static variable in class edu.iastate.metnet.soft.RandomAccessFile
The default buffer size, in bytes.
DefaultExcelSheet - Class in edu.iastate.metnet.analysis
 
DefaultExcelSheet(Sheet) - Constructor for class edu.iastate.metnet.analysis.DefaultExcelSheet
 
DefaultGraphMetaphor - Class in edu.iastate.metnet.graphmodel
interface for graph metaphor, which describe the mapping of the presentation layer of the graph and the content of the pathways.
DefaultGraphMetaphor() - Constructor for class edu.iastate.metnet.graphmodel.DefaultGraphMetaphor
 
DefaultJExcelClient - Class in edu.iastate.metnet.analysis
 
DefaultJExcelClient() - Constructor for class edu.iastate.metnet.analysis.DefaultJExcelClient
 
DefaultJExcelClient(String) - Constructor for class edu.iastate.metnet.analysis.DefaultJExcelClient
 
DefaultMetalTheme - Class in javax.swing.plaf.metal
The default theme for the MetalLookAndFeel.
DefaultMetalTheme() - Constructor for class javax.swing.plaf.metal.DefaultMetalTheme
Creates a new instance of this theme.
DefaultMetalThemeX - Class in edu.iastate.reload.skin
The default theme for the MetalLookAndFeel.
DefaultMetalThemeX() - Constructor for class edu.iastate.reload.skin.DefaultMetalThemeX
Creates a new instance of this theme.
DefaultMonitorable - Class in edu.iastate.jtm.gui
 
DefaultMonitorable() - Constructor for class edu.iastate.jtm.gui.DefaultMonitorable
 
defaultOrder() - Method in class edu.iastate.metnet.metaomgraph.chart.DataSorter
Sorts the data as it appeared in the original data file.
DefaultPlotData - Class in edu.iastate.metnet.model
 
DefaultPlotData() - Constructor for class edu.iastate.metnet.model.DefaultPlotData
 
DefaultPlotData(DefaultExcelSheet) - Constructor for class edu.iastate.metnet.model.DefaultPlotData
 
defaultProcessor - Variable in class edu.iastate.jtm.jmed.EUtility
A processor that parses the response into a DOM document.
DefaultRClient - Class in edu.iastate.metnet.analysis
 
DefaultRClient() - Constructor for class edu.iastate.metnet.analysis.DefaultRClient
 
defaultTheme - Static variable in class edu.iastate.metnet.ui.MainWindow2
default look and feel theme
DefaultViewID - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
 
defineVisualStyle(VisualStyle, VisualMappingManager, CalculatorCatalog) - Static method in class edu.iastate.metnet.launch.RunCytoscape
 
degree - Variable in class edu.iastate.metnet.dao.TrivialMetabolite
the degree of the entity
DEL - Static variable in class edu.iastate.jtm.util.TokenProcessor
 
DEL_LEFT - Static variable in class edu.iastate.jtm.util.TokenProcessor
 
DEL_RIGHT - Static variable in class edu.iastate.jtm.util.TokenProcessor
 
DELAY - Static variable in class edu.iastate.metnet.ui.Blip
Delay per frame, in milliseconds.
DelegatingTableModel - Class in com.jgoodies.binding.extras
This implementation of the TableModel interface delegates all requests to an underlying TableModel delegate.
DelegatingTableModel(ValueModel) - Constructor for class com.jgoodies.binding.extras.DelegatingTableModel
Constructs a TableAdaptor that holds the delegated TableModel in the given delegate channel.
DelegatingTableModel(TableModel) - Constructor for class com.jgoodies.binding.extras.DelegatingTableModel
Constructs a TableAdaptor on the given delegate TableModel.
DelegatingTableModel() - Constructor for class com.jgoodies.binding.extras.DelegatingTableModel
Constructs a TableAdaptor on a dummy TableModel.
delete(String, String) - Static method in class edu.iastate.metnet.db.TableAbbreviationRules
 
DELETE_INFO_COLUMN_CAUSE - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmProject
 
DELETE_LIST_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
 
DELETE_SORT_ACTION_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog
 
deleteAbbreviation(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
delete the abbreviation for the blockunit and potential entity, if the abbreviation exists in the entity's table, move the abbreviation to all other blockunit' synonym table
deleteAbbreviation(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper
delete the abbreviation for the blockunit and potential entity, if the abbreviation exists in the entity's table, move the abbreviation to all other blockunit' synonym table
deleteAbbreviationRule(String, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
delete the abbreviation rule
deleteAbbreviationRule(String, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper
delete the abbreviation rule
deleteBlockunit(Integer, String, int) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
delete a blockunit
deleteBlockunit(Integer, String, int) - Method in interface edu.iastate.metnet.interfaces.MyPaper
delete a blockunit
deleteCategory(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
delete one category from the database
deleteCategory(Integer) - Method in interface edu.iastate.metnet.interfaces.MyPaper
delete one category from the database
deleteColumn(int) - Method in class edu.iastate.metnet.NoneditableTableModel
 
deleteComment(Integer, CommentObject) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
delete the comment from the blockunit
deleteComment(Integer, CommentObject) - Method in interface edu.iastate.metnet.interfaces.MyPaper
delete the comment from the blockunit
deleteDuplicate(String) - Method in class fcmodeler.pathbinder.FilterUpdater
 
deleteFiles(ArrayList<String>) - Method in class edu.iastate.metnet.dataManager.DataManager
 
deleteGeneList(String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
Deletes a gene list from this project.
deleteInfoColumn(int) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject
 
deleteListItem - Variable in class edu.iastate.metnet.dataManager.DataManager
 
deletePathway() - Method in class edu.iastate.metnet.controller.AddPathwayController
 
deleteReference(Integer, ReferenceObject) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
delete the reference from the blockunit
deleteReference(Integer, ReferenceObject) - Method in interface edu.iastate.metnet.interfaces.MyPaper
delete the reference from the blockunit
deleteRow(int) - Method in class edu.iastate.metnet.NoneditableTableModel
 
deleteRows(int[]) - Method in class edu.iastate.metnet.NoneditableTableModel
 
deleteSelected() - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
deleteSelectedList() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
 
deleteSynonym(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
delete the synonym for the blockunit and potential entity, if the synonym exists in the entity's table, move the synonym to all other blockunit'
deleteSynonym(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper
delete the synonym for the blockunit and potential entity, if the synonym exists in the entity's table, move the synonym to all other blockunit'
deleteTerm(Query.Term) - Method in class edu.iastate.jtm.jmed.Query
 
delimiters - Static variable in interface edu.iastate.jtm.Stemmer
 
depth - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.TreeNode
 
dequeue() - Method in class edu.iastate.metnet.launch.Queue
 
derivedNodeSet - Variable in class edu.iastate.metnet.graphmodel.FCMetaphor
derived system nodes also need to be highlighted
DESCEND - Static variable in class edu.iastate.jtm.gui.TableSorter
 
DESCENDING - Static variable in class edu.iastate.metnet.metaomgraph.TableSorter
 
descFile - Variable in class edu.iastate.metnet.dataManager.DataManager
 
descFont - Variable in class edu.iastate.metnet.dataManager.DataManager
 
descPanel - Variable in class edu.iastate.metnet.dataManager.DataManager
 
description - Variable in class edu.iastate.jtm.assistant.QueryBuilder.QueryTemplate
 
description - Variable in class edu.iastate.metnet.dao.HistoryInformation
additional information
description - Variable in class edu.iastate.metnet.dataManager.DataManager
 
description - Variable in class edu.iastate.metnet.hibernate.BackgroundTask
 
DescriptionFrame - Class in edu.iastate.metnet.dataManager
 
DescriptionFrame() - Constructor for class edu.iastate.metnet.dataManager.DescriptionFrame
 
DesEncrypter - Class in edu.iastate.metnet.utils
usage:
DesEncrypter(SecretKey) - Constructor for class edu.iastate.metnet.utils.DesEncrypter
 
Desert - Class in edu.iastate.metnet.ui
 
Desert() - Constructor for class edu.iastate.metnet.ui.Desert
 
desktopPanel - Static variable in class edu.iastate.metnet.MetNetLAFTest
 
DESTINATION_BROWSE_COMMAND - Static variable in class edu.iastate.metnet.soft.SOFTParserOptionPanel
 
detachPathway(Integer, Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
detach the interaction from the pathway
detachPathway(Integer, Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper
detach the interaction from the pathway
detachPathwayFromClass(Integer, Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
detach the pathway from the class
detachPathwayFromClass(Integer, Collection) - Method in interface edu.iastate.metnet.interfaces.MyPaper
detach the pathway from the class
detachProcess() - Method in class edu.iastate.jtm.gui.StatusBar
Detach the monitored process.
detectAbnormalEntitywithcontext() - Method in interface edu.iastate.metnet.interfaces.MyFacade
detect abnormal record in the table entitywithcontext.
detectAbnormalEntitywithcontext() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
detect abnormal record in the table entitywithcontext.
detectDuplicationInteractions() - Method in interface edu.iastate.metnet.interfaces.MyFacade
get the group of same structure interactions by encoding the structure and compute the digest
detectDuplicationInteractions() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
get the group of same structure interactions by encoding the structure and compute the digest
detectOrphanInteraction() - Method in interface edu.iastate.metnet.interfaces.MyFacade
detect all orphan interaction in the database
detectOrphanInteraction() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
detect all orphan interaction in the database
detectOrphanInteraction2() - Method in interface edu.iastate.metnet.interfaces.MyFacade
detect all orphan interaction in the database
detectOrphanInteraction2() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
detect all orphan interaction in the database
detectWrongInteraction() - Method in class edu.iastate.metnet.aracyc.InteractionFix
 
detectWrongInteraction() - Method in interface edu.iastate.metnet.interfaces.MyFacade
detect the wrong interaction which contains entitywithcontext
detectWrongInteraction() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
detect the wrong interaction which contains entitywithcontext
determineColor(double) - Static method in class edu.iastate.metnet.birdseyeview.GeneColor
This method determines the color of a gene panel based on the given variance.
DF - Static variable in class edu.iastate.jtm.util.VocabularyCounter
 
df - Variable in class edu.iastate.jtm.util.VocabularyCounter.TfDf
 
dialog - Variable in class edu.iastate.metnet.hivemindService.ExportToBirdsEyeView
 
dialog - Variable in class edu.iastate.metnet.StripedTable.ColorEditor
 
dialogPanel - Static variable in class edu.iastate.metnet.MetNetLAFTest
 
DictionaryBuilder - Class in fcmodeler.pathbinder
Create dictionaries from the Entity and EntitySynonym tables.
DictionaryBuilder(MySqlConnector) - Constructor for class fcmodeler.pathbinder.DictionaryBuilder
 
DictionaryPanel - Class in fcmodeler.pathbinder.updater
 
DictionaryPanel(StatusBar, JFileChooser) - Constructor for class fcmodeler.pathbinder.updater.DictionaryPanel
 
difference(String) - Method in class edu.iastate.metnet.model.DisplayObject
determine if two display object are equal
DIGIT - Static variable in class edu.iastate.jtm.util.NameCharType
 
DIGIT - Static variable in class edu.iastate.jtm.util.SlidingWindow
 
DigitTrieNode - Class in edu.iastate.jtm.dic
A trie supporting digits.
DigitTrieNode() - Constructor for class edu.iastate.jtm.dic.DigitTrieNode
 
directdetermineColor(double) - Static method in class edu.iastate.metnet.birdseyeview.GeneColor
This method determines the color of a gene panel based on the given variance.
directedGraph - Variable in class edu.iastate.metnet.ui.CompileWorker
query graph
DirectForm - Class in edu.iastate.metnet.admin
 
DirectForm() - Constructor for class edu.iastate.metnet.admin.DirectForm
Creates new form DirectForm
disable(boolean) - Method in class edu.iastate.metnet.birdseyeview.LoadPanel
This method disable the flie choose button to switch between separates files style and integrated style
display() - Method in class edu.iastate.metnet.launch.MetNetAboutFrame
 
display - Variable in class edu.iastate.metnet.model.DisplayObject
 
displayaddAnnotations(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
This method instructs the root panel to display the given annotation in addition to the annotations that are already being displayed.
displayaddAnnotations(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.RootPanel
This method displays the new additional given annotation List in the text panel.
displayaddAnnotations(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.TextPanel
This method displays
displayAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
This method instructs the root panel to display the given annotation in addition to the annotations that are already being displayed.
displayAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.RootPanel
This method displays the given annotation in the text panel.
displayAnnotations(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.RootPanel
This method sets the annotations to be displayed in the text panel.
displayChildren(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode
This method sets the panel to show the child panels.
displayChildren(GoNode, boolean) - Method in class edu.iastate.metnet.birdseyeview.goview.GoView
This method displays the child nodes for the given node.
displayGenes() - Method in class edu.iastate.metnet.birdseyeview.goview.GoLevel
This method calls all the nodes at this level to display their children.
displayGenes() - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode
This method sets the panel to show the gene panels.
DisplayObject - Class in edu.iastate.metnet.model
store the pair of display string and value object in the combobox data model
DisplayObject(Object, Object) - Constructor for class edu.iastate.metnet.model.DisplayObject
 
DisplayObject() - Constructor for class edu.iastate.metnet.model.DisplayObject
 
displayOrHideAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
This method instructs the root panel to display or hide the given annotation based on the current status of the annotation.
displayOrHideAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.RootPanel
This method displays or hides the given annotation in the text panel based on the annotations current status.
displayOrHideAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.TextPanel
This method changes the display status of the given annotation.
displaySpePathGenes(String) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
This method lets program only show the genes belonging to special pathway
distance(double, double, double, double, double, double) - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet
P0 is the point, and P1 and P2 specify the line segment
distance(int, double, double) - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet
 
distance(double, double, double, double) - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet
 
distance(MyTreeAlgorithm.PolyLine, MyTreeAlgorithm.PolyLine) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm
accumulate the delta x of both contour
distance(double, double, double, double, double, double) - Method in class edu.iastate.metnet.model.AbstractPlotData
 
distance(int, double, double) - Method in class edu.iastate.metnet.model.AbstractPlotData
 
distance(double, double, double, double) - Method in class edu.iastate.metnet.model.AbstractPlotData
 
DnDTree - Class in edu.iastate.jtm.gui
A simple easy-to-use Drag&Drop JTree with mouse-over and drop-under feedback.
DnDTree(DefaultTreeModel) - Constructor for class edu.iastate.jtm.gui.DnDTree
Returns a new instance of the DNDTree for the specified TreeModel.
DnDTree.DnDTreeCellRenderer - Class in edu.iastate.jtm.gui
 
DnDTree.DnDTreeCellRenderer() - Constructor for class edu.iastate.jtm.gui.DnDTree.DnDTreeCellRenderer
 
doAnalysis(MetaOmProject, String, int, String, int) - Static method in class edu.iastate.metnet.metaomgraph.MetaOmAnalyzer
Runs an analysis of the given row, in a given list, in a given project.
DOCSET - Static variable in class edu.iastate.jtm.jmed.Limits
 
doImport(MetaOmProject) - Static method in class edu.iastate.metnet.metaomgraph.ImportListDialog
Shows a modal import dialog, and returns the user-entered values that match row names in the active project.
doInBackground() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView.Task
 
DomainObjectListModel - Class in edu.iastate.metnet.model
 
DomainObjectListModel() - Constructor for class edu.iastate.metnet.model.DomainObjectListModel
 
DOMAINS - Static variable in class edu.iastate.jtm.jmed.Entrez
 
done() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView.Task
 
doneFlag - Static variable in class edu.iastate.metnet.threads.PathwayGeneThread
 
doOK() - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog
 
doQuery(String) - Static method in class edu.iastate.metnet.metaomgraph.AtGeneSearch
 
doSearch(TreeSearcher.Query) - Method in class edu.iastate.metnet.metaomgraph.TreeSearcher
Searches the tree specified by this TreeSearcher's constructor using the given query.
doSearch(TreeSearcher.Query[]) - Method in class edu.iastate.metnet.metaomgraph.TreeSearcher
Searches the tree specified by this TreeSearcher's constructor using the given queries.
doubleValue() - Method in class edu.iastate.metnet.metaomgraph.CorrelationValue
 
doubleValue() - Method in class edu.iastate.metnet.metaomgraph.SortableData
 
DP - Static variable in class edu.iastate.jtm.jmed.Query.Field
 
dragDropEnd(DragSourceDropEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dragEnter(DropTargetDragEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.OrderableTable
 
dragEnter(DropTargetDragEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dragEnter(DragSourceDragEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dragExit(DropTargetEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.OrderableTable
 
dragExit(DropTargetEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dragExit(DragSourceEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dragGestureRecognized(DragGestureEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dragOver(DropTargetDragEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.OrderableTable
 
dragOver(DropTargetDragEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dragOver(DragSourceDragEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
drawThrobber(Graphics2D) - Method in class edu.iastate.metnet.metaomgraph.throbber.FlippingSquaresThrobber
 
drawThrobber(Graphics2D) - Method in class edu.iastate.metnet.metaomgraph.throbber.GlowyChipThrobber
 
drawThrobber(Graphics2D) - Method in class edu.iastate.metnet.metaomgraph.throbber.ImageThrobber
 
drawThrobber(Graphics2D) - Method in class edu.iastate.metnet.metaomgraph.throbber.MetaOmThrobber
 
drawThrobber(Graphics2D) - Method in class edu.iastate.metnet.metaomgraph.throbber.PolygonThrobber
 
drawThrobber(Graphics2D) - Method in class edu.iastate.metnet.metaomgraph.throbber.SpinningPolygonThrobber
 
drawThrobber(Graphics2D) - Method in class edu.iastate.metnet.metaomgraph.throbber.Throbber
 
drop(DropTargetDropEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.OrderableTable
 
drop(DropTargetDropEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dropActionChanged(DropTargetDragEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.OrderableTable
 
dropActionChanged(DropTargetDragEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dropActionChanged(DragSourceDragEvent) - Method in class edu.iastate.metnet.metaomgraph.ListTree
 
dscIcon - Variable in class edu.iastate.jtm.gui.SortableHeaderRenderer
 
DualListPanel - Class in edu.iastate.metnet.metaomgraph
A panel with two lists that allows you to move values between them.
DualListPanel(Object[]) - Constructor for class edu.iastate.metnet.metaomgraph.DualListPanel
Creates a dual-list panel with the given data in the inactive list, and a blank active list.
DualListPanel(Object[], Object[]) - Constructor for class edu.iastate.metnet.metaomgraph.DualListPanel
Creates a dual-list panel with the given data in the inactive and active lists.
DualTablePanel - Class in edu.iastate.metnet.metaomgraph
 
DualTablePanel(Object[][], String[]) - Constructor for class edu.iastate.metnet.metaomgraph.DualTablePanel
Creates a dual-list panel with the given data in the inactive list, and a blank active list.
DualTablePanel(Object[][], Object[][], String[]) - Constructor for class edu.iastate.metnet.metaomgraph.DualTablePanel
Creates a dual-list panel with the given data in the inactive and active lists.
dummyLabel(Container, int, int) - Method in class edu.iastate.metnet.utils.Utils
 
DummyPath - Class in edu.iastate.metnet.utils
 
DummyPath() - Constructor for class edu.iastate.metnet.utils.DummyPath
Creates a new instance of DummyPath
duplicatedName(Map) - Static method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement
collect duplicate common name.
DuplicationChecker - Class in edu.iastate.jtm
 
DuplicationChecker(MySqlConnector, String) - Constructor for class edu.iastate.jtm.DuplicationChecker
 
dx - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.PolyLine
relative offset position

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