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

I

IAracycEntity - Interface in edu.iastate.metnet.aracyc

IAracycEntityWithLocation - Interface in edu.iastate.metnet.aracyc

IAracycFileReader - Interface in edu.iastate.metnet.aracyc

the interface to read the aracyc dump file

ibid - Variable in class edu.iastate.metnet.dao.InteractionStructure

blockid of the interaction

ibid - Variable in class edu.iastate.metnet.ui.AddInteractionForm

blockid of the interaction

ibidList - Variable in class edu.iastate.metnet.ui.InteractionWorker

interaction blockid list

ICodePresentation - Interface in edu.iastate.metnet.model

iconButton - Variable in class edu.iastate.metnet.MetNetTitlePane

The button that iconifies the JInternalFrame.

iconButtonSize - Static variable in class edu.iastate.jtm.assistant.Controller

IconLib - Class in edu.iastate.jtm.gui

IconLib() - Constructor for class edu.iastate.jtm.gui.IconLib

id - Variable in class edu.iastate.metnet.dao.AbbreviationObject

id - Variable in class edu.iastate.metnet.dao.CommentObject

ID - Variable in class edu.iastate.metnet.dao.MetnetBlockUnit

any identify to make the node unique in the pathway graph, normally this will be blockid

id - Variable in class edu.iastate.metnet.dao.ReferenceObject

id - Variable in class edu.iastate.metnet.dao.SynonymObject

id - Variable in class fcmodeler.pathbinder.Entity

id(String) - Method in class fcmodeler.pathbinder.Entity

id() - Method in class fcmodeler.pathbinder.Entity

idMatches(int) - Method in class edu.iastate.metnet.birdseyeview.ViewInfo

This method checks the given integer to see if it matches the ID of this object.

IExcelClient - Interface in edu.iastate.metnet.analysis

IExcelSheet - Interface in edu.iastate.metnet.analysis

ignoreConsecutiveDelimiters() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

IGraphMetaphor - Interface 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.

IGraphProcessor - Interface in edu.iastate.metnet.graphmodel

change the graph struture, while IGraphMetaphor only change the graph attribute

ImagePanel - Class in edu.iastate.metnet.birdseyeview

The ImagePanel Class is a panel that consists of an image.

ImagePanel(Dimension, Image) - Constructor for class edu.iastate.metnet.birdseyeview.ImagePanel

Constructor.

ImageThrobber - Class in edu.iastate.metnet.metaomgraph.throbber

ImageThrobber(File[]) - Constructor for class edu.iastate.metnet.metaomgraph.throbber.ImageThrobber

IMetnetBlockUnit - Interface in edu.iastate.metnet.dao

general node in the graph

IMetNETTable - Interface in edu.iastate.metnet.db

IMetnetWindow - Interface in edu.iastate.metnet.ui

implode(String[], String) - Static method in class edu.iastate.metnet.utils.Utils

join the string by delim

implode(Object[], String) - Static method in class edu.iastate.metnet.utils.Utils

implode(String[]) - Static method in class edu.iastate.metnet.utils.Utils

join string from array

importAracyc2MetNET(String[]) - Method in class edu.iastate.metnet.aracyc.ClassesDatReader

importAracyc2MetNET(String[]) - Method in class edu.iastate.metnet.aracyc.CompoundsDatReader

importData(JComponent, Transferable) - Method in class edu.iastate.metnet.metaomgraph.ListTransferHandler

importDate - Variable in class edu.iastate.metnet.dao.MyVersionNode

when the data is input

ImportListDialog - Class in edu.iastate.metnet.metaomgraph

A modal JDialog that's used for importing rows into a list.

INACTIVE_CONTROL_TEXT - Static variable in class edu.iastate.reload.skin.OceanThemeX

The OceanTheme value for inactive control text.

INACTIVE_CONTROL_TEXT - Static variable in class javax.swing.plaf.metal.OceanTheme

The OceanTheme value for inactive control text.

includeEmpty - Variable in class edu.iastate.metnet.ui.PathwayObjectWorker

inlcude empty structure?

incrementalGet(CharSequence, TrieNode) - Method in class edu.iastate.jtm.dic.Trie

Find and return the node of a specific key.

indexes - Variable in class edu.iastate.metnet.model.TableSorter

InfoPopupManager - Class in edu.iastate.metnet.metaomgraph.chart

InfoPopupManager(MetaOmChartPanel) - Constructor for class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

information - Variable in class edu.iastate.metnet.dao.MyVersionNode

information to display in the interface

InfoTheory - Class in edu.iastate.jtm.util

Calculate entropy, mutual information, ...

InfoTheory() - Constructor for class edu.iastate.jtm.util.InfoTheory

init(Map, ArrayList<GobiNode>, ArrayList<String>) - Method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame

init() - Method in class edu.iastate.metnet.dataManager.AboutWindow

init(DataManager, String) - Method in class edu.iastate.metnet.dataManager.DescriptionFrame

init(Map, ArrayList<GobiNode>, ArrayList<String>) - Method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame

init() - Method in class edu.iastate.metnet.dataManager.PropsWindow

init() - Method in class edu.iastate.metnet.launch.RunCytoscape

init() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph

init(Map, ArrayList<GobiNode>, ArrayList<String>) - Method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame

initColumnWidths(JTable, Object[], int[]) - Static method in class edu.iastate.jtm.gui.TableUtil

initComponents() - Method in class edu.iastate.metnet.ui.ChangePassword

initComponents() - Method in class edu.iastate.metnet.ui.RegisterForm2

user interface

initData() - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree

Prompts the user to select an XML file, the initializes this tree from the selected file.

initData(InputStream) - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree

Initializes this tree from the given InputStream.

initData(File) - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree

Initializes this tree from a given XML file.

initData(Element) - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree

initialize(Dimension, String) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

This method initializes the Bird's Eye View.

initialize(ArrayList, ArrayList) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView.Task

initialize(String) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeViewWindow

This method initializes the JFrame and the Bird's Eye View object.

initialize() - Method in class edu.iastate.metnet.birdseyeview.db.Database

This method makes the connection to the Metnet DB.

initializeDataset() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel

Constructs the chart.

initializePattern(Color, Color) - Static method in class edu.iastate.reload.skin.MetalUtilsX

Initializes the pattern image.

initializePattern(Color, Color) - Static method in class javax.swing.plaf.metal.MetalUtils

Initializes the pattern image.

initMarkModel(Vector<RangeMarker>) - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

initMetNetLAF() - Static method in class edu.iastate.metnet.MetNetLAF

Initializes and installs the MetNet Look and Feel.

initMetNetLAF() - Static method in class edu.iastate.reload.skin.MetNetLAF

Initializes and installs the MetNet Look and Feel.

initSortModel(int[]) - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

inParen(int) - Method in class edu.iastate.jtm.util.ParenFinder

Check whether a position is inside enclosing marks.

inParen(int, int) - Method in class edu.iastate.jtm.util.ParenFinder

Check whether a position is inside the parenthesis pair "pid".

inParen(Element, int, boolean) - Method in class edu.iastate.jtm.util.ParenParser

inParen(int, boolean) - Method in class edu.iastate.jtm.util.ParenParser

inPlatform - Static variable in class edu.iastate.metnet.ui.MainWindow2

if current running in MetNet platform

input - Variable in class edu.iastate.metnet.dao.AlignmentObject

original input

InputEncoder - Class in edu.iastate.metnet.graphmodel

input graph encoder

InputEncoder() - Constructor for class edu.iastate.metnet.graphmodel.InputEncoder

InputLayoutAlgorithm - Class in edu.iastate.metnet.graphmodel

input graph layout

InputLayoutAlgorithm() - Constructor for class edu.iastate.metnet.graphmodel.InputLayoutAlgorithm

InputNode - Class in edu.iastate.metnet.dao

use to store the input graph node data while adapt to the display requirement of JGraph

InputNode() - Constructor for class edu.iastate.metnet.dao.InputNode

default construct

InputNode(Blockunit) - Constructor for class edu.iastate.metnet.dao.InputNode

default construct

inputUsed - Variable in class edu.iastate.metnet.dao.AlignmentObject

aligned input subgraph

insert(Object) - Static method in class edu.iastate.metnet.db.ReturnCode

insert(MutableTreeNode, int) - Method in class fcmodeler.pathbinder.gui.VerbNode

insertAtBack(Object) - Method in class edu.iastate.metnet.launch.List

insertAtFront(Object) - Method in class edu.iastate.metnet.launch.List

insertBlockunitConfidence(int, int, int) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

insert new confidence

insertBlockunitConfidence(int, int, int) - Method in interface edu.iastate.metnet.interfaces.MyPaper

insert new confidence

insertNodeInto(MutableTreeNode, MutableTreeNode, int) - Method in class edu.iastate.jtm.gui.XmlTreeModel

insertPathway() - Method in class edu.iastate.metnet.controller.AddPathwayController

insertRowAt(Object[], int) - Method in class edu.iastate.metnet.NoneditableTableModel

insertRowsBefore(Object[][], int) - Method in class edu.iastate.metnet.NoneditableTableModel

insertTime - Variable in class edu.iastate.biocyc.dao.rdb.ClassName

insert time

insertTime - Variable in class edu.iastate.metnet.dao.HistoryBlockunitImpl

insert time

insets - Variable in class edu.iastate.metnet.ui.AddPathwayForm

dummy swing

insets - Variable in class edu.iastate.metnet.ui.HelpWindow

insets - Variable in class edu.iastate.metnet.ui.Splash

installTitlePane() - Method in class edu.iastate.metnet.MetNetTitlePane

This method installs the TitlePane onto the JInternalFrameTitlePane.

instance - Static variable in class edu.iastate.metnet.export.GraphExporterImpl

singleton

IntegrationData - Static variable in class edu.iastate.metnet.birdseyeview.LoadController

Interaction - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'interaction' table.

Interaction() - Constructor for class edu.iastate.metnet.hibernate.Interaction

Simple constructor of Interaction instances.

Interaction(Integer) - Constructor for class edu.iastate.metnet.hibernate.Interaction

Constructor of Interaction instances given a simple primary key.

InteractionDecorator - Class in edu.iastate.metnet.model

provide decorator function for interaction

InteractionDecorator() - Constructor for class edu.iastate.metnet.model.InteractionDecorator

InteractionDecorator(Blockunit) - Constructor for class edu.iastate.metnet.model.InteractionDecorator

InteractionFix - Class in edu.iastate.metnet.aracyc

interactionFix - Static variable in class edu.iastate.metnet.aracyc.InteractionFix

InteractionInfo - Class in edu.iastate.metnet.mapbuilder

Stores information about reactions.

InteractionInfo(String, String, String, String, String, String, String, String) - Constructor for class edu.iastate.metnet.mapbuilder.InteractionInfo

InteractionInformation - Class in edu.iastate.metnet.dao

dummy display for interaction selector

InteractionInformation() - Constructor for class edu.iastate.metnet.dao.InteractionInformation

interactionList - Variable in class edu.iastate.metnet.ui.InteractionSelector

interaction list model

InteractionNode - Class in edu.iastate.metnet.dao

InteractionNode() - Constructor for class edu.iastate.metnet.dao.InteractionNode

default constructor

InteractionNode(Integer) - Constructor for class edu.iastate.metnet.dao.InteractionNode

constructor

InteractionObject - Class in edu.iastate.metnet.dao

similarf to AtGeneSearchObject and ChebiObject, store the information for tooltips in the pathway preview

InteractionObject() - Constructor for class edu.iastate.metnet.dao.InteractionObject

InteractionObjectTableModel - Class in edu.iastate.reload.model

InteractionObjectTableModel(ListModel) - Constructor for class edu.iastate.reload.model.InteractionObjectTableModel

InteractionObjectTableModel(ListModel, JGraph, NetworkEditHelper) - Constructor for class edu.iastate.reload.model.InteractionObjectTableModel

Interactionparts - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'interactionparts' table.

Interactionparts() - Constructor for class edu.iastate.metnet.hibernate.Interactionparts

Simple constructor of Interactionparts instances.

Interactionparts(InteractionpartsKey) - Constructor for class edu.iastate.metnet.hibernate.Interactionparts

Constructor of Interactionparts instances given a composite primary key.

InteractionpartsKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the interactionparts table.

InteractionpartsKey() - Constructor for class edu.iastate.metnet.hibernate.InteractionpartsKey

Simple constructor of InteractionpartsKey instances.

InteractionPartsModel - Class in edu.iastate.metnet.model

represents the interaction parts table in the form addinteraction

InteractionPartsModel(ListModel) - Constructor for class edu.iastate.metnet.model.InteractionPartsModel

Interactionproperties - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'interactionproperties' table.

Interactionproperties() - Constructor for class edu.iastate.metnet.hibernate.Interactionproperties

Simple constructor of Interactionproperties instances.

Interactionproperties(Integer) - Constructor for class edu.iastate.metnet.hibernate.Interactionproperties

Constructor of Interactionproperties instances given a simple primary key.

InteractionSearchForm - Class in edu.iastate.reload.ui

InteractionSearchForm(Object) - Constructor for class edu.iastate.reload.ui.InteractionSearchForm

Creates new form InteractionSearchForm

InteractionSearchTableModel - Class in edu.iastate.reload.model

used in interaction search

InteractionSearchTableModel(ListModel) - Constructor for class edu.iastate.reload.model.InteractionSearchTableModel

table structure

InteractionSelector - Class in edu.iastate.metnet.ui

The table model of interaction used by Edit interaction window

InteractionSelector(AddInteractionForm) - Constructor for class edu.iastate.metnet.ui.InteractionSelector

The constructor of the interaction selector, list the random 10 interactions in the MetNet database

InteractionSelector(AddInteractionForm, String) - Constructor for class edu.iastate.metnet.ui.InteractionSelector

InteractionSelectorModel - Class in edu.iastate.metnet.model

InteractionSelectorModel(ListModel) - Constructor for class edu.iastate.metnet.model.InteractionSelectorModel

interactionSet - Variable in class edu.iastate.metnet.dao.MetnetPathway

interactionSink - Variable in class edu.iastate.metnet.ui.InteractionWorker

interaction sink

interactionSourceList - Variable in class edu.iastate.metnet.dao.PathwayObject

data source list of all interactions in this pathway

InteractionStructure - Class in edu.iastate.metnet.dao

define the comparable property of interactions

InteractionStructure() - Constructor for class edu.iastate.metnet.dao.InteractionStructure

InteractionUpdatePanel - Class in fcmodeler.pathbinder.updater

InteractionUpdatePanel(StatusBar) - Constructor for class fcmodeler.pathbinder.updater.InteractionUpdatePanel

interactionUserList - Variable in class edu.iastate.metnet.dao.PathwayObject

user list of all interactions in this pathway

InteractionWorker - Class in edu.iastate.metnet.ui

InteractionWorker(Collection, Vector) - Constructor for class edu.iastate.metnet.ui.InteractionWorker

default constructor

InteractUpdate - Class in fcmodeler.pathbinder

InteractUpdate() - Constructor for class fcmodeler.pathbinder.InteractUpdate

IntermediumEntityInformation - Class in edu.iastate.metnet.model

IntermediumEntityInformation() - Constructor for class edu.iastate.metnet.model.IntermediumEntityInformation

constructor

internalFrameActivated(InternalFrameEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

internalFrameClosed(InternalFrameEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

internalFrameClosing(InternalFrameEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

internalFrameDeactivated(InternalFrameEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

internalFrameDeiconified(InternalFrameEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

internalFrameIconified(InternalFrameEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

internalFrameOpened(InternalFrameEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

interrupt() - Method in class edu.iastate.jtm.gui.SwingWorker

A new method that interrupts the worker thread.

interrupt() - Method in class edu.iastate.metnet.metaomgraph.AnimatedSwingWorker

A new method that interrupts the worker thread.

interrupt() - Method in class edu.iastate.metnet.metaomgraph.SwingWorker

A new method that interrupts the worker thread.

interrupt() - Method in class edu.iastate.metnet.utils.SwingWorker

A new method that interrupts the worker thread.

interrupt() - Method in class edu.iastate.metnet.utils.SwingWorker2

Stops the worker and sets the exception to InterruptedException.

intValue() - Method in class edu.iastate.metnet.metaomgraph.CorrelationValue

intValue() - Method in class edu.iastate.metnet.metaomgraph.SortableData

IP - Static variable in class edu.iastate.jtm.jmed.Query.Field

IPlotData - Interface in edu.iastate.metnet.model

IR - Static variable in class edu.iastate.jtm.jmed.Query.Field

IRClient - Interface in edu.iastate.metnet.analysis

client for R (google: CRAN) server

isActive() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway

This method returns the active flag.

isActive - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

isActive - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

isAndRelation(Integer, Integer) - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

isAndRelation() - Method in class edu.iastate.metnet.graphmodel.RelationObject

isAnimating() - Method in class edu.iastate.metnet.metaomgraph.throbber.Throbber

isApproved() - Method in class edu.iastate.metnet.model.CheckCandidate

isAracycUpdate() - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph

isAracycUpdate() - Method in class edu.iastate.reload.ui.NetworkEditForm

isAscending() - Method in class edu.iastate.metnet.metaomgraph.SortableData

isAutosort() - Method in class edu.iastate.metnet.metaomgraph.ListTree

isBalanced() - Method in class edu.iastate.jtm.util.ParenFinder

Check whether all pairs are balanced.

isBordered - Variable in class edu.iastate.metnet.StripedTable.ColorRenderer

isCancelled() - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

isCancelled() - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog

isCaseSensitive() - Method in class edu.iastate.jtm.dic.AbstractDictionary

isCaseSensitive() - Method in class edu.iastate.jtm.dic.AbstractTrieNode

isCaseSensitive() - Method in class edu.iastate.jtm.dic.AsciiTrieNode

isCaseSensitive() - Method in class edu.iastate.jtm.dic.HashDictionary

isCaseSensitive() - Method in class edu.iastate.jtm.dic.LowerTrieNode

isCaseSensitive() - Method in class edu.iastate.jtm.dic.Trie

isCaseSensitive() - Method in class edu.iastate.jtm.dic.TrieDictionary

isCaseSensitive() - Method in interface edu.iastate.jtm.dic.TrieNode

isCellEditable(int, int) - Method in class edu.iastate.biocyc.ui.PathwayChoiceModel

isCellEditable(int, int) - Method in class edu.iastate.jtm.assistant.CitationPool

isCellEditable(int, int) - Method in class edu.iastate.jtm.gui.TableMap

isCellEditable(int, int) - Method in class edu.iastate.jtm.gui.TableSorter

isCellEditable(Object) - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph

override the parent method with our definition

isCellEditable(int, int) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel

isCellEditable(int, int) - Method in class edu.iastate.metnet.metaomgraph.TableSorter

isCellEditable(int, int) - Method in class edu.iastate.metnet.model.AbbreviationRulesModel

isCellEditable(int, int) - Method in class edu.iastate.metnet.model.CandidateModel

isCellEditable(int, int) - Method in class edu.iastate.metnet.model.CompositionSelectionModel

isCellEditable(int, int) - Method in class edu.iastate.metnet.model.GroupShareTableModel

isCellEditable(int, int) - Method in class edu.iastate.metnet.model.InteractionPartsModel

if the cell is editable

isCellEditable(int, int) - Method in class edu.iastate.metnet.model.MultiSelectionModel

isCellEditable(int, int) - Method in class edu.iastate.metnet.model.SpeciesTableModel

if editable

isCellEditable(int, int) - Method in class edu.iastate.metnet.model.TableMap

isCellEditable(int, int) - Method in class edu.iastate.metnet.NoneditableTableModel

isCellEditable(int, int) - Method in class edu.iastate.metnet.ui.PathwayChoiceTableModel

if editable

isCenterRoot() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

isChanged() - Method in class com.jgoodies.binding.extras.ChangeTracker

Answers whether one of the registered ValueModels has changed since this tracker has been reset last time.

isChanged() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Determines if there are unsaved changes to this project.

isChemicalName(CharSequence) - Method in class edu.iastate.jtm.util.TokenProcessor

isChild() - Method in class edu.iastate.metnet.model.CompositionBlockunit

isCombineLevelNodes() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

isCompatible(List, List) - Method in class edu.iastate.metnet.analysis.MySolver

check if the a and b has compatible dimension since a is a squar matrix, a.length == b.length and each line of a should has same length

isCompatible(float[][], float[]) - Method in class edu.iastate.metnet.analysis.MySolver

check if the a and b has compatible dimension since a is a squar matrix, a.length == b.length and each line of a should has same length

isControlInteraction - Variable in class edu.iastate.metnet.dao.InteractionStructure

if it is a control interaction.

isControlInteraction() - Method in class edu.iastate.metnet.dao.InteractionStructure

isControlInteraction(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph

if this is a control interaction

isControlInteraction(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

isControlInteraction(Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph

if this is a control interaction

isCorrelationList() - Method in class edu.iastate.metnet.metaomgraph.GeneList

isCreatedFromStream() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Determines whether this project was created from a stream or a file.

isCytoscape() - Static method in class edu.iastate.metnet.launch.LaunchMetNet

isDataFlavorSupported(DataFlavor) - Method in class edu.iastate.metnet.metaomgraph.GeneList

isDataFlavorSupported(DataFlavor) - Method in class edu.iastate.metnet.metaomgraph.ListTransferHandler.DraggableRows

isDataFlavorSupported(DataFlavor) - Method in class edu.iastate.metnet.metaomgraph.ListTree.DraggableNode

isDetachableInteraction(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

check if the node specified by the blockid can be detached from the pathway structure

isDeterministic() - Method in class edu.iastate.jtm.assistant.CitationPool

isDeterministic() - Method in class edu.iastate.jtm.gui.DefaultMonitorable

isDeterministic() - Method in interface edu.iastate.jtm.gui.Monitorable

isDeterministic() - Method in class fcmodeler.pathbinder.MedLeaseClient

isDuplicated() - Method in class edu.iastate.metnet.db.ReturnCode

isEdge(GraphModel, Object) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper

detect if it is a vertex

isEdge(JGraph, Object) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper

detect if it is a vertex

isEdge(GraphModel, Object) - Method in class edu.iastate.metnet.ui.StructureQueryHelper

detect if it is a vertex

isEmpty() - Method in class edu.iastate.metnet.dao.MyVersionGraph

if there is any history records

isEmpty() - Method in class edu.iastate.metnet.launch.List

isEnabled() - Method in class edu.iastate.metnet.metaomgraph.chart.InfoPopupManager

isEnableModelListener() - Method in class edu.iastate.reload.ui.NetworkEditForm

isEntity - Variable in class edu.iastate.metnet.dao.AbbreviationObject

isEntity() - Method in class edu.iastate.metnet.dao.AbbreviationObject

isEntity - Variable in class edu.iastate.metnet.dao.CommentObject

isEntity() - Method in class edu.iastate.metnet.dao.CommentObject

isEntity - Variable in class edu.iastate.metnet.dao.ReferenceObject

isEntity() - Method in class edu.iastate.metnet.dao.ReferenceObject

isEntity - Variable in class edu.iastate.metnet.dao.SynonymObject

isEntity() - Method in class edu.iastate.metnet.dao.SynonymObject

isEntity() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isEntity() - Method in class edu.iastate.metnet.hibernate.Blockunit

type

isEntity() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

if this is an entity

isEntity() - Method in class edu.iastate.metnet.model.CompositionBlockunit

isEntity() - Method in class edu.iastate.metnet.model.SelectedBlockunit

isEntitywithlocation(String) - Method in interface edu.iastate.metnet.dao.MultiPathwayGraph

determine if this is an entity node

isEntitywithlocation(String) - Method in class edu.iastate.metnet.dao.MultiPathwayGraphImpl

determine if this is an entity node

isEntitywithlocation(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph

if it is an entitywithlocation

isEntitywithlocation(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

isEntitywithlocation(Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph

if it is an entitywithlocation

isExactSearch() - Method in class edu.iastate.metnet.ui.NodeSelectionForm

isFilterUsed() - Method in class fcmodeler.pathbinder.HiddenLink

isFilterUsed() - Method in class fcmodeler.pathbinder.PathBinder

isFinished() - Method in class edu.iastate.jtm.assistant.CitationPool

isFinished() - Method in class edu.iastate.jtm.gui.DefaultMonitorable

isFinished() - Method in interface edu.iastate.jtm.gui.Monitorable

isFinished() - Method in class fcmodeler.pathbinder.MedLeaseClient

isFirstRunning() - Static method in class edu.iastate.metnet.utils.Utils

test if there is an instance of the application already

isForceMarqueeEvent(MouseEvent) - Method in class edu.iastate.reload.ui.MyMarqueeHandler

isFullList() - Method in class edu.iastate.metnet.metaomgraph.GeneList

isGene() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isGene() - Method in class edu.iastate.metnet.hibernate.Blockunit

isGene() - Method in class edu.iastate.metnet.hibernate.Entity

isGene() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

if this is a gene

isGeneID(String) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils

Determines if the given String represents a gene ID.

isIdenticalSpecies() - Method in class edu.iastate.metnet.ui.AddPathwayForm

detect if the pathway map and current ready-to-insert pathway are same species.

isImported() - Method in class edu.iastate.metnet.birdseyeview.LoadController

isIn(int, int[]) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils

isInChloroplast() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isInChloroplast() - Method in class edu.iastate.metnet.hibernate.Blockunit

isInChloroplast() - Method in class edu.iastate.metnet.hibernate.Entity

isInChloroplast() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isIndexed() - Method in class edu.iastate.jtm.jmed.ESearch

isIndexed() - Method in class edu.iastate.jtm.jmed.PubMedQuerier

isInitialized() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Determines whether or not this project has been initialized successfully.

isInMitochondrion() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isInMitochondrion() - Method in class edu.iastate.metnet.hibernate.Blockunit

isInMitochondrion() - Method in class edu.iastate.metnet.hibernate.Entity

isInMitochondrion() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isInPlatform() - Static method in class edu.iastate.metnet.ui.MainWindow2

isInserted() - Method in class edu.iastate.metnet.db.ReturnCode

isInteraction(String) - Method in interface edu.iastate.metnet.dao.MultiPathwayGraph

determine if this is an interaction node

isInteraction(String) - Method in class edu.iastate.metnet.dao.MultiPathwayGraphImpl

determine if this is an interaction node

isInteraction(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph

if it is an interaction

isInteraction(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

isInteraction() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isInteraction(Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph

if it is an interaction

isInteraction() - Method in class edu.iastate.metnet.hibernate.Blockunit

type

isInteraction() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isInteraction() - Method in class edu.iastate.metnet.model.CompositionBlockunit

isInteraction() - Method in class edu.iastate.metnet.model.SelectedBlockunit

isJustified() - Method in class edu.iastate.metnet.dataManager.JMultilineLabel

isLast() - Method in class edu.iastate.metnet.newgui.oldWizardPanel

isLeaf() - Method in class edu.iastate.jtm.jmed.Query.CompositeTerm

isLeaf() - Method in class edu.iastate.jtm.jmed.Query.SimpleTerm

isLeaf(Object) - Method in class edu.iastate.metnet.model.CategoryTreeModel

if it is a leaf

isLeaf() - Method in class fcmodeler.pathbinder.gui.VerbNode

isLeftBalanced(int) - Method in class edu.iastate.jtm.util.ParenFinder

Check whether a left is balanced.

isLegendVisible() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel

isLocus() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isLocus() - Method in class edu.iastate.metnet.hibernate.Blockunit

isLocus() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isMajorTopic() - Method in class edu.iastate.jtm.jmed.MeshDescriptor

isMarked() - Method in class edu.iastate.jtm.jmed.MedCitation

isMetabolite() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isMetabolite() - Method in class edu.iastate.metnet.hibernate.Blockunit

isMetabolite() - Method in class edu.iastate.metnet.hibernate.Entity

isMetabolite() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isMonitorable() - Method in class edu.iastate.jtm.assistant.CitationPool

isMonitorable() - Method in class edu.iastate.jtm.gui.DefaultMonitorable

isMonitorable() - Method in interface edu.iastate.jtm.gui.Monitorable

isMonitorable() - Method in class fcmodeler.pathbinder.MedLeaseClient

isNewBlockunit() - Method in class edu.iastate.metnet.model.SelectedBlockunit

isNormalInteraction(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph

if it is a normal interaction

isNormalInteraction(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

isNormalInteraction(Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph

if it is a normal interaction

isNumeric(String) - Static method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement

detect if a string is a integer

isOK() - Method in class edu.iastate.metnet.db.ReturnCode

isOK() - Method in class edu.iastate.metnet.soft.SOFTParserOptionPanel

isOldBlockunit() - Method in class edu.iastate.metnet.model.SelectedBlockunit

isomorphism(PathwayGraph, AlignmentAlgorithm) - Method in interface edu.iastate.metnet.dao.PathwayGraph

run isomorphism

isomorphism(PathwayGraph, AlignmentAlgorithm) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

run isomorphism

IsomorphismMetaphor - Class in edu.iastate.metnet.graphmodel

special metaphor for subgraph isomorphism

IsomorphismMetaphor() - Constructor for class edu.iastate.metnet.graphmodel.IsomorphismMetaphor

default constrcutor

IsomorphismMetaphor(AlignmentObject) - Constructor for class edu.iastate.metnet.graphmodel.IsomorphismMetaphor

default constructor

isOrphanInteraction(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

detect if the blockunit is orphan

isOrphanInteraction(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

detect if the blockunit is orphan

isPairBalanced(int) - Method in class edu.iastate.jtm.util.ParenFinder

Check whether the specified pair is balanced.

isParent() - Method in class edu.iastate.metnet.model.CompositionBlockunit

isPathway() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isPathway() - Method in class edu.iastate.metnet.hibernate.Blockunit

type

isPathway() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isPerfect() - Method in class edu.iastate.metnet.graphmodel.GraphValidity

if there is no error and no warning, used for highlight

isPolypeptide() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isPolypeptide() - Method in class edu.iastate.metnet.hibernate.Blockunit

isPolypeptide() - Method in class edu.iastate.metnet.hibernate.Entity

isPolypeptide() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isPopupEnabled() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel

isPopupTrigger(MouseEvent) - Method in class edu.iastate.reload.ui.MyMarqueeHandler

detect if this is a right click mouse request

isPropertyChanged() - Method in interface edu.iastate.metnet.dao.IMetnetBlockUnit

detect if the content is changed, for the interaction, it means the properties, not the structure

isPropertyChanged() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit

isPropertyChanged() - Method in class edu.iastate.metnet.dao.MetnetInteraction

detect if the content is changed or not.

isPropertyChanged() - Method in class edu.iastate.metnet.dao.MetnetLiveEntity

determine if the content if changed.

isPropertyChanged() - Method in class edu.iastate.metnet.dao.MetnetPathway

detect if something is changed, only consider name, the function confidence is not enough for a credit

isProtein() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isProtein() - Method in class edu.iastate.metnet.hibernate.Blockunit

isProtein() - Method in class edu.iastate.metnet.hibernate.Entity

isProtein() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isProteinComplex() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isProteinComplex() - Method in class edu.iastate.metnet.hibernate.Blockunit

isProteinComplex() - Method in class edu.iastate.metnet.hibernate.Entity

isProteinComplex() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isPubMode() - Method in class edu.iastate.jtm.jmed.MedlineParser

isReady() - Method in class edu.iastate.metnet.utils.SwingWorker2

Return whether the get method is ready to return a value.

isResizing - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

isResizing - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

isReversible() - Method in class edu.iastate.metnet.graphmodel.MetaphorTypeInformation

isRightBalanced(int) - Method in class edu.iastate.jtm.util.ParenFinder

Check whether a right is balanced.

isRNA() - Method in class edu.iastate.metnet.export.BlockunitObjectImpl

isRNA() - Method in class edu.iastate.metnet.hibernate.Blockunit

isRNA() - Method in class edu.iastate.metnet.hibernate.Entity

isRNA() - Method in interface edu.iastate.metnet.hiveface.BlockunitObject

isRNode() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo

isRoot(String) - Static method in class edu.iastate.biocyc.dao.txt.BiocycClass

determine if this is a root class

isRoot(String) - Static method in class edu.iastate.metnet.aracyc.AracycClass

isRoot(String) - Static method in class edu.iastate.metnet.aracyc.AracycCompound

isRunning() - Method in class edu.iastate.jtm.assistant.CitationPool

isRunning() - Method in class edu.iastate.jtm.gui.DefaultMonitorable

isRunning() - Method in interface edu.iastate.jtm.gui.Monitorable

isRunning() - Method in class fcmodeler.pathbinder.MedLeaseClient

isSelected() - Method in class edu.iastate.biocyc.dao.rdb.BlockunitChoice

isSelected() - Method in class edu.iastate.metnet.model.PathwayObjectChoice

isSelected() - Method in class edu.iastate.metnet.model.SpeciesChoice

isShapePainted() - Method in class edu.iastate.metnet.metaomgraph.chart.ChartToolBar

isShowingOnStartup() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTips.MetaOmShowTipsChoice

isSortByData() - Method in class edu.iastate.metnet.metaomgraph.SortableData

isSorting() - Method in class edu.iastate.metnet.metaomgraph.TableSorter

isSortSeriesSelected() - Method in class edu.iastate.metnet.soft.SOFTParserOptionPanel

isStoreInteraction() - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

isStoreInteraction() - Method in class edu.iastate.metnet.graphmodel.RemoveBridgeNodes

isStructureChanged() - Method in class edu.iastate.metnet.dao.MetnetInteraction

interaction is only determined by the structure, so if some other properties are changed, the credit still goes to original user and source

ISSUE - Static variable in class edu.iastate.jtm.jmed.Limits

issueCommand(String) - Method in class edu.iastate.metnet.threads.ExploRaseThread

isTerminated() - Method in class edu.iastate.jtm.util.ProcessWrapper

isTransport() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo

isUnit(String) - Static method in class edu.iastate.jtm.TokenAnalyzer

isValid() - Method in class edu.iastate.jtm.jmed.Query.CompositeTerm

isValid() - Method in class edu.iastate.jtm.jmed.Query.SimpleTerm

isValid() - Method in class edu.iastate.jtm.jmed.Query.Term

isValid() - Method in class edu.iastate.metnet.graphmodel.GraphValidity

if the current informaiton is valid, used for saving

isValid(Integer) - Method in class edu.iastate.metnet.graphmodel.GraphValidity

detect if the model id represents a correct data entry

isValid(String) - Static method in class edu.iastate.metnet.utils.Utils

isValidAttribute(String) - Method in class edu.iastate.metnet.soft.Entity

isValidAttribute(String) - Method in class edu.iastate.metnet.soft.Platform

isValidAttribute(String) - Method in class edu.iastate.metnet.soft.Sample

isValidAttribute(String) - Method in class edu.iastate.metnet.soft.Series

isValidViewID(int) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

This method checks the given ID to see if it is a valid view ID.

isVertex(GraphModel, Object) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper

detect if it is a vertex

isVertex(JGraph, Object) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper

detect if it is a vertex

isVertex(GraphModel, Object) - Method in class edu.iastate.metnet.ui.StructureQueryHelper

detect if it is a vertex

isVisibleBlockunit(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacade

determine the visibility of the blockunit based on the share capability

isVisibleBlockunit(Blockunit, String) - Method in interface edu.iastate.metnet.interfaces.MyFacade

determine the visibility of the blockunit based on the share capability

isVisibleBlockunit(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

determine the visibility of the blockunit based on the share capability

isVisibleBlockunit(Blockunit, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

determine the visibility of the blockunit based on the share capability

isWillDeleted() - Method in class edu.iastate.metnet.model.SelectedBlockunit

ite - Variable in class edu.iastate.metnet.birdseyeview.LegendPanel

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.birdseyeview.CheckBoxHandler

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.birdseyeview.ExperimentComboBoxListener

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.birdseyeview.ExploRaseBoxHandler

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.birdseyeview.MainExperimentComboBoxListener

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.birdseyeview.ViewComboBoxListener

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.dataManager.CheckBoxHandler

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.metaomgraph.CheckBoxHandler

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.metaomgraph.ExploRaseBoxHandler

itemStateChanged(ItemEvent) - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog

iterateCompositionInteraction(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

iterate the searching of the many-to-one interactions, be careful about loops.

iterateCompositionInteraction(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

iterate the searching of the many-to-one interactions, be careful about loops.