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

C

cache(int, int) - Method in class edu.iastate.jtm.DuplicationChecker

CANCEL_ACTION_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

CANCEL_COMMAND - Static variable in class edu.iastate.metnet.soft.SOFTParserOptionPanel

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

This method resets all the temporary variables and closes the load window.

CANCERCHROMOSOMES - Static variable in class edu.iastate.jtm.jmed.Entrez

Candidate - Class in edu.iastate.metnet.dao

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

CandidateModel - Class in edu.iastate.metnet.model

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

CandidateModel(int) - Constructor for class edu.iastate.metnet.model.CandidateModel

candy - Variable in class edu.iastate.metnet.model.CheckCandidate

canImport(JComponent, DataFlavor[]) - Method in class edu.iastate.metnet.metaomgraph.ListTransferHandler

capacity() - Method in class edu.iastate.jtm.util.RunningBuffer

capacity - Variable in class edu.iastate.metnet.birdseyeview.goview.GoBioProcessView

capacity - Variable in class edu.iastate.metnet.birdseyeview.goview.GoFunctionView

capacity - Variable in class edu.iastate.metnet.birdseyeview.goview.GoLevel

captureGraphModel(JGraph) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper

capture the graph model represented in the current graph, do not consider the bridge interaction right now

CategoryChooseForm - Class in edu.iastate.metnet.ui

Choose a pathway category here.

CategoryChooseForm(CategoryEditForm, int) - Constructor for class edu.iastate.metnet.ui.CategoryChooseForm

Creates new form CategoryChooseForm

CategoryCreateForm - Class in edu.iastate.metnet.ui

create new category

CategoryCreateForm(CategoryEditForm, int) - Constructor for class edu.iastate.metnet.ui.CategoryCreateForm

Creates new form CategoryCreateForm

CategoryEditForm - Class in edu.iastate.metnet.ui

pathway categor editor

CategoryEditForm() - Constructor for class edu.iastate.metnet.ui.CategoryEditForm

Creates new form CategoryEditForm

CategoryEncoder - Class in edu.iastate.metnet.graphmodel

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

CategoryException - Exception in edu.iastate.metnet.ui

special exception for category node operation

CategoryException() - Constructor for exception edu.iastate.metnet.ui.CategoryException

CategoryException(String) - Constructor for exception edu.iastate.metnet.ui.CategoryException

CategoryLayoutAlgorithm - Class in edu.iastate.metnet.graphmodel

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

CategoryMetaphor - Class in edu.iastate.metnet.graphmodel

metaphor of pathway categroy graph

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

default constructor

CategoryMetaphor(Object) - Constructor for class edu.iastate.metnet.graphmodel.CategoryMetaphor

CategoryNode - Class in edu.iastate.metnet.dao

store the node in category graph

CategoryNode(Integer, String) - Constructor for class edu.iastate.metnet.dao.CategoryNode

default constructor

CategoryRenameForm - Class in edu.iastate.metnet.ui

rename the category

CategoryRenameForm(CategoryEditForm, int, String) - Constructor for class edu.iastate.metnet.ui.CategoryRenameForm

Creates new form CategoryRenameForm

CategoryTreeModel - Class in edu.iastate.metnet.model

tree model for pathway category

CategoryTreeModel(DirectedGraph) - Constructor for class edu.iastate.metnet.model.CategoryTreeModel

default constrcutor

CDD - Static variable in class edu.iastate.jtm.jmed.Entrez

cell2node - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

CellView -> TreeNode

cellCreateType - Variable in class edu.iastate.reload.ui.NetworkEditForm

current graph element creation type

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

change the cell editor of the coefficient which will use a text field (default?)

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

chage the cell editor of the entitytype column which will use combobox

cellEditorListener - Variable in class edu.iastate.metnet.graphmodel.JMetaphorGraph.EditorGraphUI

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

change the cell editor of the substrate table ad product table, this is for the location column which will use combobix

CellularLocation - Class in edu.iastate.metnet.birdseyeview.cellview

The CellularLocation Class holds information on a cellular location (i.e.

CellularLocation(ArrayList, ArrayList, Integer) - Constructor for class edu.iastate.metnet.birdseyeview.cellview.CellularLocation

Constructor.

CellView - Class in edu.iastate.metnet.birdseyeview.cellview

The CellView Class displays the Bird's Eye View of the gene products' location in cellular compartments.

CellView(ViewInfo, BirdsEyeView, ArrayList, Dimension, String) - Constructor for class edu.iastate.metnet.birdseyeview.cellview.CellView

Constructor.

CellViewID - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView

CellViewName - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView

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

dummy swing

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

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

centerComponent(Component) - Static method in class edu.iastate.jtm.gui.ScreenUtil

centerRoot - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

center root, if we put the root in the center of the screen border, depending on the orientation of the root

CentricComparator - Class in edu.iastate.metnet.birdseyeview.cellview

The CentricComparator Class compares 2 different points based on their distance from the center point of a given rectangle.

CentricComparator(Rectangle, Dimension) - Constructor for class edu.iastate.metnet.birdseyeview.cellview.CentricComparator

Constructor.

changeAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.AnnotationTextPanel

This method modifies the annotation data to display the given annotation.

changeBackground(Color) - Method in class edu.iastate.metnet.birdseyeview.AnnotationTextPanel

This method changes the background color of this panel and all its children.

changeEdgeColor(JGraph, Object, CellView, Color) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

change the line color

changeEdgeDualColor(JGraph, Object, CellView, Color, Color) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

change the line color to two parallel foreground color to indicate the different interaction type

changeEdgePattern(JGraph, Object, CellView, float[]) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

change the edge or border's line pattern

changeEdgeWidth(JGraph, Object, CellView, float) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

change the edge width

changeImage(Image) - Method in class edu.iastate.metnet.birdseyeview.ImagePanel

Change the image.

ChangeName - Class in edu.iastate.metnet.aracyc

turn the name in our database to the common name

ChangeName() - Constructor for class edu.iastate.metnet.aracyc.ChangeName

ChangePassword - Class in edu.iastate.metnet.ui

change passwords for normal users and more powerful users

ChangePassword() - Constructor for class edu.iastate.metnet.ui.ChangePassword

Main window for change the password

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

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

change the duplicate soybean probes in the network to the OR relation except for those exising OR relation, use flattern OR relation.

changeSoybeanOR() - Method in interface edu.iastate.metnet.interfaces.MyPaper

change the duplicate soybean probes in the network to the OR relation except for those exising OR relation, use flattern OR relation.

ChangeTracker - Class in com.jgoodies.binding.extras

Tracks changes in a set of bound bean properties.

ChangeTracker() - Constructor for class com.jgoodies.binding.extras.ChangeTracker

Constructs a change tracker with change state set to false.

changeVertexBackgroundColor(JGraph, Object, CellView, Color) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

set the normal background

changeVertexBorderColor(JGraph, Object, CellView, Color) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

change the vertext border color

changeVertexBorderWidth(JGraph, Object, CellView, float) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

change the edge width

changeVertexDualColor(JGraph, Object, CellView, Color, Color) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

things are complicated if we want two or more background color

changeVertexForegroundColor(JGraph, Object, CellView, Color) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

change the font color in the vertex

characters(char[], int, int) - Method in class fcmodeler.pathbinder.echo

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

Class that handles clicking and mouse moving for a MetaOmChartPanel.

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

Constructor

chartChanged(ChartChangeEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartScrollBar

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

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

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

chartMouseClicked(ChartMouseEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartAnnotator

Adds an annotation when the user clicks the chart

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

chartMouseMoved(ChartMouseEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartAnnotator

Set the cursor based on what the mouse is hovering over

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

chartProgress(ChartProgressEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartAnnotator

chartProgress(ChartProgressEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartScrollBar

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

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

ChartScrollBar(MetaOmChartPanel, int) - Constructor for class edu.iastate.metnet.metaomgraph.chart.ChartScrollBar

ChartSelectionListener - Interface in edu.iastate.metnet.metaomgraph.chart

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

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

chartToScreen(Point2D) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel

CharType - Class in edu.iastate.jtm.util

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

ChebiChemicalData - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiChemicalData instances.

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

Constructor of ChebiChemicalData instances given a simple primary key.

ChebiComments - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiComments instances.

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

Constructor of ChebiComments instances given a simple primary key.

ChebiCompounds - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiCompounds instances.

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

Constructor of ChebiCompounds instances given a simple primary key.

ChebiDatabaseAccession - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiDatabaseAccession instances.

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

Constructor of ChebiDatabaseAccession instances given a simple primary key.

chebiid - Variable in class edu.iastate.metnet.dao.ChebiOntologyName

ChebiImporter - Class in edu.iastate.metnet.aracyc

import data from chebi ontology into chebi_* tables notice the data does not have same order with its create table sql.

ChebiImporter() - Constructor for class edu.iastate.metnet.aracyc.ChebiImporter

ChebiNameConverter - Class in edu.iastate.metnet.aracyc

mapping the blockunit and entity name to chebi name.

ChebiNames - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiNames instances.

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

Constructor of ChebiNames instances given a simple primary key.

ChebiObject - Class in edu.iastate.metnet.dao

chebi info data object.

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

ChebiOntology - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiOntology instances.

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

Constructor of ChebiOntology instances given a simple primary key.

ChebiOntologyName - Class in edu.iastate.metnet.dao

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

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

ChebiOntologyTableModel - Class in edu.iastate.metnet.model

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

ChebiReference - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiReference instances.

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

Constructor of ChebiReference instances given a simple primary key.

ChebiRelation - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiRelation instances.

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

Constructor of ChebiRelation instances given a simple primary key.

ChebiVertices - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ChebiVertices instances.

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

Constructor of ChebiVertices instances given a simple primary key.

check(int, boolean) - Method in class edu.iastate.jtm.DuplicationChecker

checkAll() - Method in class edu.iastate.metnet.model.CandidateModel

CheckBoxHandler - Class in edu.iastate.metnet.birdseyeview

CheckBoxHandler() - Constructor for class edu.iastate.metnet.birdseyeview.CheckBoxHandler

CheckBoxHandler - Class in edu.iastate.metnet.dataManager

CheckBoxHandler() - Constructor for class edu.iastate.metnet.dataManager.CheckBoxHandler

CheckBoxHandler - Class in edu.iastate.metnet.metaomgraph

CheckBoxHandler() - Constructor for class edu.iastate.metnet.metaomgraph.CheckBoxHandler

checkBoxList - Static variable in class edu.iastate.metnet.birdseyeview.ExploRaseExpFrame

checkBoxList - Static variable in class edu.iastate.metnet.metaomgraph.ExploRaseFrame

checkBoxList - Static variable in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame

CheckCandidate - Class in edu.iastate.metnet.model

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

CheckCandidate(Candidate) - Constructor for class edu.iastate.metnet.model.CheckCandidate

checkInteraction(Vector, Vector) - Method in interface edu.iastate.metnet.interfaces.MyFacade

check if there is an interaction contains the same topolgy structure or super structure covers the provided adjacent nodes.

checkInteraction(Vector, Vector) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

check if there is an interaction contains the same topolgy structure or super structure covers the provided adjacent nodes.

checkModel() - Method in class edu.iastate.jtm.gui.TableSorter

checkModel() - Method in class edu.iastate.metnet.model.TableSorter

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

since things are complicated to create all initial history in advance, we move this step to the action on the normal blockunit operation

checkOrCreateLatestHistory(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

since things are complicated to create all initial history in advance, we move this step to the action on the normal blockunit operation

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

insert the abbreviation for the blockunit

checkOrInsertAbbreviation(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

insert the abbreviation for the blockunit

checkOrInsertComment(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

check or insert comment

checkOrInsertComment(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyPaper

check or insert comment

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

check if the entity exists, if not, create a new one

checkOrInsertEntity(String, String, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

check if the entity exists, if not, create a new one

checkOrInsertEntitySynonym(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

insert the synonym list for the entity

checkOrInsertEntitySynonym(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyPaper

insert the synonym list for the entity

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

fix the entitywithcontext at background

checkOrInsertEntitywithcontext(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyPaper

fix the entitywithcontext at background

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

checkOrInsertPathway(Collection, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

check or create a pathway based on the interaction list

checkOrInsertPathway(Collection, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

check or create a pathway based on the interaction list

checkOrInsertReference(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

check or insert reference

checkOrInsertReference(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyPaper

check or insert reference

checkOrInsertSynonym(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

check or insert the synonym

checkOrInsertSynonym(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyPaper

check or insert the synonym

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

create an transport, translation or transcription interaction and return the blockid of the interaction.

checkOrInsertTransInteraction(Integer, Integer, String, String, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

create an transport, translation or transcription interaction and return the blockid of the interaction.

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

create an transport, translation or transcription interaction and return the blockid of the interaction.

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

create an transport, translation or transcription interaction and return the blockid of the interaction.

ChemicalReactionMetaphor - Class in edu.iastate.metnet.graphmodel

flux analysis on this collect all valid edges collect all valid interaction nodes (including hidden transport node) get the component graph or subsystem pop up dialog with table which displays the sub-system (in combobox) and corresponding interaction, and rates field, and freedom hint (require user continue input) set up the linear equation system and solve it metaphor the sub-system with the solution

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

childCount(Object) - Method in class edu.iastate.metnet.aracyc.GenericTree

the child count

children - Variable in class edu.iastate.jtm.dic.AbstractTrieNode

Child node array.

children - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.TreeNode

child nodes of this node

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

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

specify if search exactly

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

if only update substrates only

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

chooseFileToOpen(FileFilter, Component) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils

chooseFileToSave(FileFilter, String, Component, boolean) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils

Displays a JFileChooser that lets the user select a destination file.

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

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

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

CitationListener - Interface in edu.iastate.jtm.assistant

CitationManager - Class in edu.iastate.jtm.jmed

CitationManager() - Constructor for class edu.iastate.jtm.jmed.CitationManager

CitationPanel - Class in edu.iastate.jtm.assistant

CitationPanel(EntityFinder) - Constructor for class edu.iastate.jtm.assistant.CitationPanel

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

CitationPool - Class in edu.iastate.jtm.assistant

CitationPool(int) - Constructor for class edu.iastate.jtm.assistant.CitationPool

citations - Variable in class edu.iastate.metnet.aracyc.AracycEntity

CITATIONS

citations - Variable in class edu.iastate.metnet.aracyc.AracycInteraction

CITATIONS

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

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

ClassEditForm - Class in edu.iastate.metnet.ui

ClassEditForm() - Constructor for class edu.iastate.metnet.ui.ClassEditForm

Creates new form ClassEditorForm

ClassesDatReader - Class in edu.iastate.metnet.aracyc

ClassesDatReader() - Constructor for class edu.iastate.metnet.aracyc.ClassesDatReader

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

class id

classId - Variable in class edu.iastate.metnet.dao.CategoryNode

class id if this is a class

ClassName - Class in edu.iastate.biocyc.dao.rdb

define the class_name table object

ClassName() - Constructor for class edu.iastate.biocyc.dao.rdb.ClassName

default constructor

ClassName(Integer) - Constructor for class edu.iastate.biocyc.dao.rdb.ClassName

default constructor

ClassName - Class in edu.iastate.metnet.hibernate

hibenrate class

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

default constructor

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

default constructor

ClassTree - Class in edu.iastate.metnet.aracyc

ClassTree() - Constructor for class edu.iastate.metnet.aracyc.ClassTree

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

Strips off spaces and quotes from the ends of a String.

cleanHTML(String) - Method in class edu.iastate.metnet.metaomgraph.chart.PointInfoPanel

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

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

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

Remove all child nodes.

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

clear() - Method in class edu.iastate.jtm.jmed.Limits

clear() - Method in class edu.iastate.jtm.util.RunningBuffer

clear() - Method in class edu.iastate.jtm.util.SlidingWindow.Stride

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

clear error message

clear(JList) - Method in class fcmodeler.pathbinder.gui.EntityPanel

clearActionListeners() - Method in class edu.iastate.metnet.metaomgraph.chart.RangeSelector

clearFilter() - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel

clearFilter() - Method in class fcmodeler.pathbinder.PmidFilter

clearOut() - Method in class edu.iastate.metnet.birdseyeview.AnnotationTextPanel

This method clears out the panel by replacing the text with blank strings.

client - Static variable in class edu.iastate.metnet.utils.MyXmlRpcClientFactory

XmlRpc client

clone() - Method in class edu.iastate.jtm.jmed.Query.Field

clone() - Method in class edu.iastate.jtm.jmed.Query.Operator

close() - Method in class edu.iastate.jtm.jmed.StreamXMLParser

Close the inputsource

close() - Method in class edu.iastate.jtm.jmed.UmlsSocketClient

Close the socket connection to the server.

close() - Method in class edu.iastate.jtm.util.MySqlConnector

close() - Method in class edu.iastate.metnet.db.ResultSetAdapter

close() - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Close the file, and release any associated system resources.

close() - Method in class edu.iastate.metnet.soft.RandomAccessFile

Close the file, and release any associated system resources.

CLOSE_PROJECT_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmGraph

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

The button that closes the JInternalFrame.

closeDatabaseConnection() - Method in class fcmodeler.pathbinder.MedCrawler

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

Closes the RandomAccessFile used to read data.

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

The icon displayed in the close button.

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

Closes the active project.

cmbInteractionType - Variable in class edu.iastate.metnet.ui.SearchDialog

CMD_CATEGORY_COPY - Static variable in class edu.iastate.metnet.ui.CategoryEditForm

copy category command

CMD_CATEGORY_CREATE - Static variable in class edu.iastate.metnet.ui.CategoryEditForm

create category command

CMD_CATEGORY_MOVE - Static variable in class edu.iastate.metnet.ui.CategoryEditForm

move category command

CMD_CATEGORY_RENAME - Static variable in class edu.iastate.metnet.ui.CategoryEditForm

rename category command

CMD_PATHWAY_ADD - Static variable in class edu.iastate.metnet.ui.CategoryEditForm

add pathway to selected category

CMD_PATHWAY_MOVE - Static variable in class edu.iastate.metnet.ui.CategoryEditForm

move the pathway to selected category

cmdline - Variable in class edu.iastate.jtm.util.ProcessWrapper

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

Codeconfidence - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Codeconfidence instances.

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

Constructor of Codeconfidence instances given a simple primary key.

Codedatasource - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Codedatasource instances.

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

Constructor of Codedatasource instances given a simple primary key.

Codeentitytype - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Codeentitytype instances.

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

Constructor of Codeentitytype instances given a simple primary key.

Codeinteractiontype - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Codeinteractiontype instances.

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

Constructor of Codeinteractiontype instances given a simple primary key.

Codelocation - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Codelocation instances.

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

Constructor of Codelocation instances given a simple primary key.

CodelocationListModel - Class in edu.iastate.metnet.model

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

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

location list model

Codeorganism - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Codeorganism instances.

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

Constructor of Codeorganism instances given a simple primary key.

Codereferencetype - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Codereferencetype instances.

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

Constructor of Codereferencetype instances given a simple primary key.

Coderule - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Coderule instances.

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

Constructor of Coderule instances given a simple primary key.

CoderuleCellEditor - Class in edu.iastate.metnet.model

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

CoderuleCellRenderer - Class in edu.iastate.metnet.model

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

coderulelist - Variable in class edu.iastate.metnet.model.CoderuleCellEditor

coderulelist - Variable in class edu.iastate.metnet.model.CoderuleCellRenderer

CodeRulePresentation - Class in edu.iastate.metnet.model

CodeRulePresentation(Coderule) - Constructor for class edu.iastate.metnet.model.CodeRulePresentation

colEditorModel - Variable in class edu.iastate.metnet.ui.MyJTableEx

colHeaderRenderer - Variable in class edu.iastate.jtm.gui.RowHeaderTable.TableRowHeaderRenderer

collectInteractionIDListInSubSystem(Integer) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

collect the interaction in the sub-system

colorBrew - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView

ColorBrickPanel - Class in edu.iastate.metnet.metaomgraph.test

ColorBrickPanel(InputStream) - Constructor for class edu.iastate.metnet.metaomgraph.test.ColorBrickPanel

ColorChooseButton - Class in edu.iastate.metnet

A colored button that launches a color chooser dialog when clicked.

ColorChooseButton(Color, String) - Constructor for class edu.iastate.metnet.ColorChooseButton

Constructor.

colorChooser - Variable in class edu.iastate.metnet.StripedTable.ColorEditor

ColoredTableCellRenderer - Class in edu.iastate.metnet.dataManager

Rendered used to color background of rows

ColoredTableCellRenderer() - Constructor for class edu.iastate.metnet.dataManager.ColoredTableCellRenderer

colorForRow(int) - Method in class edu.iastate.metnet.StripedTable

Returns the appropriate background color for the given row.

ColorPanel - Class in edu.iastate.metnet.birdseyeview

ColorPanel(int) - Constructor for class edu.iastate.metnet.birdseyeview.ColorPanel

ColorPicker - Class in edu.iastate.metnet.metaomgraph.test

ColorPicker() - Constructor for class edu.iastate.metnet.metaomgraph.test.ColorPicker

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

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

coefficient column

COLUMN_COUNT - Static variable in class edu.iastate.metnet.metaomgraph.AtGeneSearch

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

entity type column

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

location column

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

column order number of the interaction parts

ColumnEditorModel - Class in edu.iastate.metnet.model

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

columnHeader - Variable in class edu.iastate.metnet.model.AbbreviationRulesModel

store the list of the map, which contain the tuples (ruleid, shortterm, longterm)

columnName - Variable in class edu.iastate.metnet.analysis.AbstractExcelSheet

columnName - Variable in class edu.iastate.metnet.model.AbstractPlotData

columnNames - Variable in class edu.iastate.metnet.newgui.NoneditableTableModel

columnNames - Variable in class edu.iastate.metnet.NoneditableTableModel

The column headers

com.jgoodies.binding.extras - package com.jgoodies.binding.extras

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

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

combineLevelNodes - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

combine level, if align same level nodes, if false, may save spaces

combineTerms(String[], int, String, String[], boolean) - Method in class edu.iastate.jtm.jmed.ESearch

Concatenate a list of terms into a single query.

combineTerms(List, String, String[], boolean) - Method in class edu.iastate.jtm.jmed.ESearch

combineTerms(String[], int, String, String[], boolean, boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

Concatenate a list of terms into a single query.

combineTerms(List, String, String[], boolean, boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

command - Variable in class edu.iastate.metnet.ui.CategoryChooseForm

command type

command - Variable in class edu.iastate.metnet.ui.CategoryCreateForm

command

command - Variable in class edu.iastate.metnet.ui.CategoryRenameForm

rename command

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

Comment - Interface in edu.iastate.metnet.datamodel.attributes

Interface representing Comment

CommentEditForm - Class in edu.iastate.reload.ui

CommentEditForm(ArrayListModel, Blockunitcomment) - Constructor for class edu.iastate.reload.ui.CommentEditForm

Creates new form CommentEditForm

CommentObject - Class in edu.iastate.metnet.dao

CommentObject(Integer, String, String, boolean) - Constructor for class edu.iastate.metnet.dao.CommentObject

CommentObject(String, String) - Constructor for class edu.iastate.metnet.dao.CommentObject

commentOrigin - Variable in class edu.iastate.reload.ui.CommentEditForm

original comment

comments - Variable in class edu.iastate.metnet.aracyc.AracycEntity

COMMENT # DBLINKS (CAS, TAIR, PIR, WIT-PWY, SWISSPROT, METACYC, LIGAND-CPD, NCI, LIGAND, ENTREZ, SOYBASE, SWISSMODEL, we can not predict all source of dblinks and their format, it's better to put in the comment field.)

comments - Variable in class edu.iastate.metnet.aracyc.AracycInteraction

COMMENT # DBLINKS (CAS, TAIR, PIR, WIT-PWY, SWISSPROT, METACYC, LIGAND-CPD, NCI, LIGAND, ENTREZ, SOYBASE, SWISSMODEL, we can not predict all source of dblinks and their format, it's better to put in the comment field.)

CommentTableModel - Class in edu.iastate.metnet.model

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

CommentTableModel - Class in edu.iastate.reload.model

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

commit() - Method in class edu.iastate.jtm.util.MySqlConnector

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

This method finalizes the loading of the new data for the Bird's Eye View.

COMP_NAME - Static variable in interface edu.iastate.metnet.interfaces.MyFacadeHome

COMP_NAME - Static variable in interface edu.iastate.metnet.interfaces.MyFacadeLocalHome

COMP_NAME - Static variable in interface edu.iastate.metnet.interfaces.MyMetnetServiceHome

COMP_NAME - Static variable in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocalHome

COMP_NAME - Static variable in interface edu.iastate.metnet.interfaces.MyPaperHome

COMPARABLE_COMAPRATOR - Static variable in class edu.iastate.metnet.metaomgraph.TableSorter

ComparativeMetaphor - Class in edu.iastate.metnet.graphmodel

in the case of multiple pathways in a preview window.

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

default constructor

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

compare(Object, Object) - Method in class edu.iastate.metnet.birdseyeview.cellview.CentricComparator

compare(String, String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel.ListNameComparator

compare(int, int) - Method in class edu.iastate.metnet.model.TableSorter

compareGenes(Gene, Gene) - Method in class edu.iastate.metnet.hivemindService.CompareInPathBinder

Search for common sentences using Gene objects

CompareInPathBinder - Class in edu.iastate.metnet.hivemindService

HiveMind Service search for common sentences between two genes

CompareInPathBinder() - Constructor for class edu.iastate.metnet.hivemindService.CompareInPathBinder

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

Compare a string to this node's key.

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

Compare a string to this node's key.

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

compareRowsByColumn(int, int, int) - Method in class edu.iastate.metnet.model.TableSorter

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

compareTo(Object) - Method in class edu.iastate.jtm.util.VocabularyCounter.TfDf

compareTo(Annotation) - Method in class edu.iastate.metnet.birdseyeview.Annotation

This method implements the interface's method compareTo in order to sort the list

compareTo(Object) - Method in class edu.iastate.metnet.hibernate.Abbreviationrules

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

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

compareTo(Object) - Method in class fcmodeler.pathbinder.Entity

compareTo(Object) - Method in class fcmodeler.pathbinder.FilterEntry

compareTo(Object) - Method in class fcmodeler.pathbinder.gui.EntityPanel.EntityScore

compareTo(Object) - Method in class fcmodeler.pathbinder.PbSentence

compareType - Static variable in class edu.iastate.metnet.hibernate.Abbreviationrules

specify the compare rule

Compartment - Class in edu.iastate.metnet.birdseyeview.pathwayview

The Compartment Class encapsulates the functionality of one cellular compartment component in the pathway view.

Compartment(Color, String) - Constructor for class edu.iastate.metnet.birdseyeview.pathwayview.Compartment

Constructor.

CompileWorker - Class in edu.iastate.metnet.ui

network compilation thread

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

XXX !!! to prevent any conflict, using deepCopy to send the parameter except the sink

COMPLETE_LIST - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmProject

The name of the "complete list" list.

completeEditing(boolean, boolean, boolean) - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph.EditorGraphUI

Stops the editing session.

complexID - Variable in class edu.iastate.metnet.graphmodel.RelationObject

componentAdded(ContainerEvent) - Method in class edu.iastate.metnet.ui.AddEntityForm

perform the component add event

componentAdded(ContainerEvent) - Method in class edu.iastate.metnet.ui.AddInteractionForm

perform the component add event

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

perform the component add event

componentAdded(ContainerEvent) - Method in class edu.iastate.metnet.ui.MainWindow2

perform the component add event

componentAdded(ContainerEvent) - Method in class edu.iastate.metnet.ui.StructuralQueryForm

perform the component add event

componentAdded(ContainerEvent) - Method in class edu.iastate.metnet.ui.TrivialSelector

perform the component add event

componentCenter(Component) - Static method in class edu.iastate.jtm.gui.ScreenUtil

componentCoefficient - Variable in class edu.iastate.metnet.graphmodel.RelationObject

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

componentHidden(ComponentEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel

componentHidden(ComponentEvent) - Method in class edu.iastate.reload.ui.OverviewPanel

componentHidden(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.EntityPanel

componentHidden(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.PbFrame

componentHidden(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.TaxonomyPanel

componentID - Variable in class edu.iastate.metnet.graphmodel.RelationObject

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

componentMoved(ComponentEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel

componentMoved(ComponentEvent) - Method in class edu.iastate.reload.ui.OverviewPanel

componentMoved(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.EntityPanel

componentMoved(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.PbFrame

componentMoved(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.TaxonomyPanel

componentRemoved(ContainerEvent) - Method in class edu.iastate.metnet.ui.AddEntityForm

perform the component remove event

componentRemoved(ContainerEvent) - Method in class edu.iastate.metnet.ui.AddInteractionForm

perform the component remove event

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

perform the component remove event

componentRemoved(ContainerEvent) - Method in class edu.iastate.metnet.ui.MainWindow2

perform the component remove event

componentRemoved(ContainerEvent) - Method in class edu.iastate.metnet.ui.StructuralQueryForm

perform the component remove event

componentRemoved(ContainerEvent) - Method in class edu.iastate.metnet.ui.TrivialSelector

perform the component remove event

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

componentResized(ComponentEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel

componentResized(ComponentEvent) - Method in class edu.iastate.reload.ui.OverviewPanel

componentResized(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.EntityPanel

componentResized(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.PbFrame

componentResized(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.TaxonomyPanel

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

componentShown(ComponentEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel

componentShown(ComponentEvent) - Method in class edu.iastate.reload.ui.OverviewPanel

componentShown(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.EntityPanel

componentShown(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.PbFrame

componentShown(ComponentEvent) - Method in class fcmodeler.pathbinder.gui.TaxonomyPanel

ComponentToImage - Class in edu.iastate.metnet.metaomgraph

ComponentToImage() - Constructor for class edu.iastate.metnet.metaomgraph.ComponentToImage

componentToSwitch - Variable in class edu.iastate.metnet.event.UISwitchListener

CompositeTermPanel - Class in edu.iastate.jtm.assistant

CompositeTermPanel() - Constructor for class edu.iastate.jtm.assistant.CompositeTermPanel

CompositionBlockunit - Class in edu.iastate.metnet.model

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

CompositionGraphModel - Class in edu.iastate.metnet.graphmodel

contain the nodes of the current graph.

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

CompositionGraphModelChangedEvent - Class in edu.iastate.metnet.event

CompositionGraphModelChangedEvent(Object) - Constructor for class edu.iastate.metnet.event.CompositionGraphModelChangedEvent

CompositionGraphModelChangedListener - Interface in edu.iastate.metnet.event

CompositionRelationMetaphor - Class in edu.iastate.metnet.graphmodel

use normal location metaphor and color the and relation as red, or relation as blue

CompositionRelationMetaphor(CompositionGraphModel) - Constructor for class edu.iastate.metnet.graphmodel.CompositionRelationMetaphor

mandatory construct the class with argument

CompositionSelectionModel - Class in edu.iastate.metnet.model

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

CompoundsDatReader - Class in edu.iastate.metnet.aracyc

contain keyword:

CompoundsDatReader() - Constructor for class edu.iastate.metnet.aracyc.CompoundsDatReader

compPanel - Static variable in class edu.iastate.metnet.MetNetLAFTest

computeDegreeOfFreedom(int, int) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

compute the degree of the freedom of the linear equation system.

confidence - Variable in class edu.iastate.metnet.dao.InteractionObject

interaction confidence

ConfidenceModel - Class in edu.iastate.metnet.model

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

configureFile - Variable in class edu.iastate.metnet.aracyc.ConsoleApplication

configure file name

confirmQuit() - Method in class edu.iastate.metnet.launch.LaunchMetNet

Methods ask for a confirmation from user whether to close the platform or not.

connect(ValueModel, SpinnerModel) - Static method in class com.jgoodies.binding.extras.SpinnerAdapterFactory

Connects the given ValueModel and SpinnerModel by synchronizing their values.

CONNECT_FAIL - Static variable in class edu.iastate.jtm.jmed.ESearch

CONNECT_FAIL - Static variable in class edu.iastate.jtm.jmed.PubMedQuerier

connection - Variable in class edu.iastate.metnet.birdseyeview.db.Database

connection - Variable in class edu.iastate.metnet.export.GraphExporterImpl

database connection

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

compose the password for the database accession

ConsoleApplication - Class in edu.iastate.metnet.aracyc

common task for console application the subclass should implement like MapPubchemName.java

ConsoleApplication() - Constructor for class edu.iastate.metnet.aracyc.ConsoleApplication

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

Compute the value to be returned by the get method.

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

Compute the value to be returned by the get method.

construct() - Method in class edu.iastate.metnet.metaomgraph.MetaOmGraph.NewProjectWorker

Creates the project.

construct() - Method in class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel.ColorFader

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

Compute the value to be returned by the get method.

construct() - Method in class edu.iastate.metnet.test.MyFacadeTest.FacadeWorker

construct() - Method in class edu.iastate.metnet.test.MyPaperTest.PaperWorker

construct() - Method in class edu.iastate.metnet.ui.BlockunitWorker

call remote finder

construct() - Method in class edu.iastate.metnet.ui.CompileWorker

call remote compilation

construct() - Method in class edu.iastate.metnet.ui.InteractionWorker

call remote finder

construct() - Method in class edu.iastate.metnet.ui.PathwayObjectWorker

call remote finder

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

Compute the value to be returned by the get method.

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

Computes the value to be returned by the get method.

constructAlignmentMode(AlignmentObject) - Method in interface edu.iastate.metnet.interfaces.MyFacade

(include all input graph element) we need construct the graph model for the alignment.

constructAlignmentMode(AlignmentObject) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

(include all input graph element) we need construct the graph model for the alignment.

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

for a matrix, construct the string like "[1 3 5; 2 5 1; 2 3 8]"; notice that the parser of the scipy is very picky and we must follow the format without additional blank or semicolon

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

for a matrix, construct the string like "[1 3 5; 2 5 1; 2 3 8]"; notice that the parser of the scipy is very picky and we must follow the format without additional blank or semicolon

constructMultiPathwayGraph(ArrayList) - Method in interface edu.iastate.metnet.interfaces.MyFacade

construct the multi-pathway graph model for TWO pathways

constructMultiPathwayGraph(ArrayList) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

construct the multi-pathway graph model for TWO pathways

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

cnstruct the representation of one row of the matrix

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

for a vector, construct the string like "[10;8;3]";

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

for a vector, construct the string like "[10;8;3]";

cont - Variable in class fcmodeler.pathbinder.Entity

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

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

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

ContextFactory - Class in edu.iastate.metnet.utils

ContextFactory() - Constructor for class edu.iastate.metnet.utils.ContextFactory

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

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

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

Controller - Class in edu.iastate.jtm.assistant

Controller() - Constructor for class edu.iastate.jtm.assistant.Controller

controlPanel - Variable in class edu.iastate.metnet.ui.SynonymCandidate

convert(Element) - Method in class edu.iastate.jtm.assistant.BibTex

convert(Element) - Method in class edu.iastate.jtm.assistant.EndNote

convert(Element) - Method in class edu.iastate.jtm.assistant.ProCite

convert(Element) - Method in class edu.iastate.jtm.jmed.CitationManager

convert(String) - Method in class edu.iastate.metnet.metaomgraph.utils.FlatFileConverter

Converts a given Affymetrix ID to a Locus ID

convert() - Method in class edu.iastate.metnet.ui.SBMLExporter

convert(String, String) - Method in class edu.iastate.metnet.ui.SBMLExporter

convertGraph(DirectedGraph, Map) - Method in class edu.iastate.biocyc.io.BiocycImporter

convert to the JUNG graph

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

convertToValidXMLName(String) - Method in class edu.iastate.metnet.soft.SOFTParser

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

copy the category to the new position

copyCategory(Integer, Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyPaper

copy the category to the new position

copyFromMark(CharBuffer) - Method in class edu.iastate.jtm.util.SlidingWindow

copyFromTo(CharBuffer, int, int) - Method in class edu.iastate.jtm.util.SlidingWindow

copyPathway(Collection, String, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

This funciton copy the pathway specified by the blockid to a new pathway belongs to the specified organism.

copyPathway(Collection, String, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

This funciton copy the pathway specified by the blockid to a new pathway belongs to the specified organism.

copySampleGroup(String[], int) - Method in class edu.iastate.jtm.jmed.PubMedSampler

copySentence(int, CharBuffer) - Method in class edu.iastate.jtm.SentenceParser

copyText(CharBuffer) - Method in class edu.iastate.jtm.util.SlidingWindow.Stride

copyToMark(CharBuffer) - Method in class edu.iastate.jtm.util.SlidingWindow

copyUnit(Writer) - Method in class edu.iastate.jtm.jmed.StreamXMLParser

copyWindow(CharBuffer) - Method in class edu.iastate.jtm.util.SlidingWindow

CorrelationCalc - Class in edu.iastate.metnet.metaomgraph

Calculates Pearson Correlations for sets of data.

CorrelationCalc(double[]) - Constructor for class edu.iastate.metnet.metaomgraph.CorrelationCalc

Constructs a correlation calculator for a given set of data

CorrelationCalc(Number[]) - Constructor for class edu.iastate.metnet.metaomgraph.CorrelationCalc

Constructs a correlation calculator for a given set of data

CorrelationCalc(Object[]) - Constructor for class edu.iastate.metnet.metaomgraph.CorrelationCalc

Constructs a correlation calculator for a given set of data.

CorrelationValue - Class in edu.iastate.metnet.metaomgraph

Enables the analyzation panel to display results as percentages, but still sort the table using doubles.

CorrelationValue(double) - Constructor for class edu.iastate.metnet.metaomgraph.CorrelationValue

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

align cost

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

count(File) - Method in class edu.iastate.jtm.util.VocabularyCounter

Count word frequency in input.

counter - Static variable in class edu.iastate.metnet.utils.GUID

create() - Static method in class edu.iastate.metnet.birdseyeview.PrototypeAnnotations

This method creates a list of annotations.

create(ViewInfo, BirdsEyeView, ArrayList, Dimension, String) - Static method in class edu.iastate.metnet.birdseyeview.ViewFactory

create() - Method in interface edu.iastate.metnet.interfaces.MyFacadeHome

create() - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocalHome

create() - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceHome

create() - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocalHome

create() - Method in interface edu.iastate.metnet.interfaces.MyPaperHome

CREATE - Static variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Create the file rather than overwriting it.

CREATE - Static variable in class edu.iastate.metnet.soft.RandomAccessFile

Create the file rather than overwriting it.

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

create the AGRIS regulatory network pathways.

createAgrisNetwork() - Method in interface edu.iastate.metnet.interfaces.MyPaper

create the AGRIS regulatory network pathways.

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

create the pathway for AGRIS data, must after the network is created and expanded

createAgrisPathway() - Method in interface edu.iastate.metnet.interfaces.MyPaper

create the pathway for AGRIS data, must after the network is created and expanded

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

create pathway without the structure

createBasicPathway(Blockunit, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

create pathway without the structure

createBigMap() - Method in class edu.iastate.biocyc.io.BiocycImporter

create a big map containing all instances.

createBirdsEyeViewProject(MetaOmProject) - Method in class edu.iastate.metnet.hivemindService.ExportToBirdsEyeView

Method sends the entire set of data from MetaOmGraph to BirdsEyeView.

createBirdsEyeViewProject(Hashtable, ArrayList<String>, ArrayList<String>) - Method in class edu.iastate.metnet.hivemindService.ExportToBirdsEyeView

Method recieves experiment names, gene ids, and expression data and loads it to BEV

createBlockunit(String, String, String) - Method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement

createBlockunit(String, String, String) - Method in class edu.iastate.biocyc.dao.txt.BiocycClass

createBlockunit(String, String, String) - Method in class edu.iastate.biocyc.dao.txt.BiocycCompound

createBlockunit(String, String, String) - Method in interface edu.iastate.biocyc.dao.txt.BiocycElement

create the blockunit

createBlockunit(String, String, String) - Method in class edu.iastate.biocyc.dao.txt.BiocycEnzrxn

createBlockunit(String, String, String) - Method in class edu.iastate.biocyc.dao.txt.BiocycGene

createBlockunit(String, String, String) - Method in class edu.iastate.biocyc.dao.txt.BiocycPathway

create a blckunit object from this aracyc object

createBlockunit(String, String, String) - Method in class edu.iastate.biocyc.dao.txt.BiocycProtein

createBlockunit(String, String, String) - Method in class edu.iastate.biocyc.dao.txt.BiocycReaction

createBounds(CellView, Color, int, int) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper

create the box for the label

createBounds(CellView, Color) - Method in class edu.iastate.metnet.ui.StructureQueryHelper

create the box for the label

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

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

create new category

createCategory(Integer, String, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

create new category

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

Create a new child node at the specified array index.

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

Create a new child node at the specified array index.

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

Allocate memory for a node's child node array.

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

Allocate memory for a node's child node array.

createChildren() - Method in class edu.iastate.jtm.dic.DigitTrieNode

Allocate memory for a node's child node array.

createChildren() - Method in class edu.iastate.jtm.dic.FuzzyTrieNode

Allocate memory for a node's child node array.

createChildren() - Method in class edu.iastate.jtm.dic.LetterDigitTrieNode

Allocate memory for a node's child node array.

createChildren() - Method in class edu.iastate.jtm.dic.LetterTrieNode

Allocate memory for a node's child node array.

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

Allocate memory for a node's child node array.

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

Allocate memory for a node's child node array.

createChildren() - Method in class edu.iastate.jtm.dic.WordTrieNode

Allocate memory for a node's child node array.

createClassName() - Method in class edu.iastate.biocyc.dao.txt.BiocycClass

get the data object class name

createClassNetwork(Map) - Method in class edu.iastate.biocyc.io.BiocycImporter

create the class network

createClassPathway(Map) - Method in class edu.iastate.biocyc.io.BiocycImporter

get the pathway and class relation

createCyNetwork(Integer, String, ArrayList<String>, String) - Method in class edu.iastate.metnet.hivemindService.CytoscapeHMService

Returns a CyNetwork representing selected pathway.

createCyNetwork(ArrayList<GobiNode>, ArrayList<String>, String) - Method in class edu.iastate.metnet.hivemindService.CytoscapeHMService

Returns CyNetwork containing all pathways of selected genes.

createDateAdapter(ValueModel) - Static method in class com.jgoodies.binding.extras.SpinnerAdapterFactory

Creates and returns a SpinnerDateModel bound to the given valueModel.

createDateAdapter(ValueModel, Comparable, Comparable, int) - Static method in class com.jgoodies.binding.extras.SpinnerAdapterFactory

Creates and returns a SpinnerDateModel that represents a sequence of dates and is bound to the given valueModel.

createDefaultEdgeAttributes(Graph) - Static method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Creates and returns a map of attributes to be used as defaults for edge attributes, depending on the specified graph.

createDefaultVertexAttributes() - Static method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Creates and returns a map of attributes to be used as defaults for vertex attributes.

createEdgeCell(Edge) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter.DefaultCellFactory

createEdgeCell(Edge) - Method in interface edu.iastate.metnet.graphmodel.MyJGraphModelAdapter.ICellFactory

Creates an edge cell that contains its respective JGraphT edge.

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

Create the dialog using the cell's editing component.

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

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

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

create initial history for all blockunits in the database

createInitialHistory() - Method in interface edu.iastate.metnet.interfaces.MyPaper

create initial history for all blockunits in the database

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

Constructs and displays an internal frame on the MetaOmGraph desktop containg this chart panel.

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

createLevelColors(double, double, double, double, double, double) - Method in class edu.iastate.metnet.birdseyeview.goview.GoView

This method creates an array with slightly different colors.

createLines(CellView, Color) - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper

create an line

createLines(CellView, Color) - Method in class edu.iastate.metnet.ui.StructureQueryHelper

create an line

CreateListFrame - Class in edu.iastate.metnet.metaomgraph

JInternalFrame that handles list creation for MetaOmGraph.

CreateListFrame(MetaOmProject) - Constructor for class edu.iastate.metnet.metaomgraph.CreateListFrame

Creates an empty CreateListFrame for creating a new list.

CreateListFrame(MetaOmProject, String) - Constructor for class edu.iastate.metnet.metaomgraph.CreateListFrame

Creates a CreateListFrame for editing the passed list (or creating a new list, if listName is null)

createListString(String, ArrayList) - Static method in class edu.iastate.metnet.birdseyeview.Annotation

This method turns a list of strings into a comma-delimited string.

createLocDic(File) - Method in class fcmodeler.pathbinder.DictionaryBuilder

createMenuItem(JMenu, int, String, ImageIcon, int, String) - Method in class edu.iastate.metnet.dataManager.DataManager

createMetaOmProject(ArrayList<String>, ArrayList<String>, Hashtable) - Method in interface edu.iastate.metnet.hivemindService.ExportToMetaOmGraph

Creates a MOG project containing all data from BEV

createMetaOmProject(ArrayList<String>, ArrayList<String>, Hashtable) - Method in class edu.iastate.metnet.hivemindService.ExportToMetaOmGraphImpl

createNestedNetwork(Map) - Method in class edu.iastate.biocyc.io.BiocycImporter

create the super pathway network

createNewList(boolean) - Method in class edu.iastate.metnet.dataManager.DataManager

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

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

Create a new child node at the specified array index.

createNodeInstance() - Method in class edu.iastate.jtm.dic.DigitTrieNode

Create a new child node at the specified array index.

createNodeInstance() - Method in class edu.iastate.jtm.dic.FuzzyTrieNode

Create a new child node at the specified array index.

createNodeInstance() - Method in class edu.iastate.jtm.dic.LetterDigitTrieNode

Create a new child node at the specified array index.

createNodeInstance() - Method in class edu.iastate.jtm.dic.LetterTrieNode

Create a new child node at the specified array index.

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

Create a new child node at the specified array index.

createNodeInstance() - Method in class edu.iastate.jtm.dic.WordTrieNode

Create a new node at the specified array index.

createNumberAdapter(ValueModel, int, int, int) - Static method in class com.jgoodies.binding.extras.SpinnerAdapterFactory

Creates and returns a SpinnerNumberModel that is connected to the given ValueModel and that honors the specified minimum, maximum and step values.

createOverviewPanel(JGraph, JViewport) - Static method in class edu.iastate.metnet.ui.OverviewPanel

GPOverviewPanel factory that returns instance with small inset as a buffer.

createOverviewPanel(JGraph, JViewport) - Static method in class edu.iastate.reload.ui.OverviewPanel

GPOverviewPanel factory that returns instance with small inset as a buffer.

createPathwayA(Integer, Collection) - Method in class edu.iastate.biocyc.dao.txt.BiocycPathway

construct the pathwayA object

createPredefinedTable() - Method in class fcmodeler.pathbinder.PmidFilter

createProjectFromFile(SOFTFile, File, String[]) - Method in class edu.iastate.metnet.soft.SOFTParser

createProjectFromFiles(SOFTFile[], File, String[]) - Method in class edu.iastate.metnet.soft.SOFTParser

createReactionNetwork(Map) - Method in class edu.iastate.biocyc.io.BiocycImporter

create a big network of all Biocyc information

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

create the soybean locus

createSoybeanLocus() - Method in interface edu.iastate.metnet.interfaces.MyPaper

create the soybean locus

createStatement() - Method in class edu.iastate.jtm.util.MySqlConnector

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

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

createTermDic(File) - Method in class fcmodeler.pathbinder.DictionaryBuilder

createTransferable(JComponent) - Method in class edu.iastate.metnet.metaomgraph.ListTransferHandler

createUser(User) - Method in interface edu.iastate.metnet.interfaces.MyFacade

create a new user and presume that the user does not exist

createUser(User) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

create a new user and presume that the user does not exist

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

assign the species to the username, so this guy can only edit the data of the species.

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

assign the species to the username, so this guy can only edit the data of the species.

createVertexCell(Object) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter.DefaultCellFactory

createVertexCell(Object) - Method in interface edu.iastate.metnet.graphmodel.MyJGraphModelAdapter.ICellFactory

Creates a vertex cell that contains its respective JGraphT vertex.

currentBlockID - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

current focus blockunit, if null, none is selected

currentBlockIDSubSystemMap - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

since node is not always same hash I have to create another map say currentBlockIDSubSystemMap, the key is (blockid, blockunittype)

currentCells - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

current graph cells in the jgraph instance

currentColor - Variable in class edu.iastate.metnet.StripedTable.ColorEditor

currentFile - Variable in class edu.iastate.metnet.dataManager.DataManager

currentFileProps - Variable in class edu.iastate.metnet.dataManager.DataManager

currentGraph - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

current jgraph instance

currentIntermediumMap - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

hold the information of the intermedium compound the key is node->{blockid, incomingreactionids, outgoingreactionids, subsystem, }

currentLevel - Variable in class edu.iastate.metnet.birdseyeview.goview.GoView

currentNodeSubSystemMap - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

node and their corresponding sub-system-id

currentValidEdgeMap - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

edges covered by current chemical reaction set

currentValidNodeMap - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

current chemical reaction nodes and their substrate nodes

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

CustomSortDialog(int[], MetaOmChartPanel) - Constructor for class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

A dialog for sorting columns.

CustomSortDialog.ColumnValueRenderer - Class in edu.iastate.metnet.metaomgraph.chart

CustomSortDialog.ColumnValueRenderer() - Constructor for class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog.ColumnValueRenderer

CustomSortDialog.CustomSortObject - Class in edu.iastate.metnet.metaomgraph.chart

CustomSortDialog.CustomSortObject() - Constructor for class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog.CustomSortObject

CustomSortDialog.CustomSortObject(int[], Vector<RangeMarker>) - Constructor for class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog.CustomSortObject

CytoMetnet - Class in edu.iastate.metnet.ui

CytoMetnet() - Constructor for class edu.iastate.metnet.ui.CytoMetnet

CytoscapeHMService - Class in edu.iastate.metnet.hivemindService

Class used to translate the JUNG graphs recieved from MetNetDB to CyNetwork Objects that can be displayed in Cytoscape

CytoscapeHMService() - Constructor for class edu.iastate.metnet.hivemindService.CytoscapeHMService

cytoSession - Variable in class edu.iastate.biocyc.ui.BiocycForm

if cytoscape is started.