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

M

m_colNames - Variable in class edu.iastate.metnet.dataManager.TableDataModel

m_data - Variable in class edu.iastate.metnet.dataManager.TableDataModel

m_jEdgesBeingAdded - Variable in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

m_jEdgesBeingRemoved - Variable in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

m_jtEdgesBeingAdded - Variable in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

m_jtEdgesBeingRemoved - Variable in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

m_jtVerticesBeingAdded - Variable in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

m_jtVerticesBeingRemoved - Variable in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

m_jVerticesBeingAdded - Variable in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

m_jVerticesBeingRemoved - Variable in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

main(String[]) - Static method in class edu.iastate.biocyc.ui.BiocycForm

main(String[]) - Static method in class edu.iastate.jtm.assistant.GoogleScholar

main(String[]) - Static method in class edu.iastate.jtm.assistant.PubMedAssistant

main(String[]) - Static method in class edu.iastate.jtm.dic.HashDictionary

main(String[]) - Static method in class edu.iastate.jtm.gui.RowHeaderTable

main(String[]) - Static method in class edu.iastate.jtm.jmed.MedlineParser

For test.

main(String[]) - Static method in class edu.iastate.jtm.jmed.PubMedFetcher

main(String[]) - Static method in class edu.iastate.jtm.jmed.PubMedQuerier

For test.

main(String[]) - Static method in class edu.iastate.jtm.jmed.QueryParser

main(String[]) - Static method in class edu.iastate.jtm.jmed.UmlsQueryClient

For test.

main(String[]) - Static method in class edu.iastate.jtm.jmed.UmlsSocketClient

For test.

main(String[]) - Static method in class edu.iastate.jtm.PluralDetector

For test.

main(String[]) - Static method in class edu.iastate.jtm.PorterStemmer

Test program for demonstrating the Stemmer.

main(String[]) - Static method in class edu.iastate.jtm.SentenceParser

main(String[]) - Static method in class edu.iastate.jtm.TokenAnalyzer

main(String[]) - Static method in class edu.iastate.jtm.util.FileSplitter

Split a large file into small ones from command line execution.

main(String[]) - Static method in class edu.iastate.jtm.util.JarResources

Is a test driver.

main(String[]) - Static method in class edu.iastate.jtm.util.MySqlConnector

main(String[]) - Static method in class edu.iastate.jtm.util.ParenFinder

main(String[]) - Static method in class edu.iastate.jtm.util.ParenParser

main(String[]) - Static method in class edu.iastate.jtm.util.ProcessWrapper

main(String[]) - Static method in class edu.iastate.jtm.util.SlidingWindow

main(String[]) - Static method in class edu.iastate.jtm.util.TokenProcessor

main(String[]) - Static method in class edu.iastate.metnet.analysis.DefaultJExcelClient

main(String[]) - Static method in class edu.iastate.metnet.aracyc.AttributeFileReader

main(String[]) - Static method in class edu.iastate.metnet.aracyc.ChangeName

main(String[]) - Static method in class edu.iastate.metnet.aracyc.ClassesDatReader

main(String[]) - Static method in class edu.iastate.metnet.aracyc.CompoundsDatReader

main(String[]) - Static method in class edu.iastate.metnet.aracyc.GraphStatistics

run this example by "ant test -Dmainclass=aracyc.GraphStatistics --arg=opt"

main(String[]) - Static method in class edu.iastate.metnet.aracyc.TabularFileReader

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.Annotation

This method tests the Annotation class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.AnnotationTextPanel

This method tests the AnnotationTextPanel class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.BirdsEyeViewWindow

This method will launch a window that displays the bird's eye view of the given experimental data.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.ButtonPanel

This method tests the ButtonPanel class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.cellview.CellView

This method tests the CellView class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.cellview.CentricComparator

This method tests the CentricComparator class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.cellview.GenePanel

This method tests the GenePanel class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.cellview.PanelLocationsFactory

This method tests the PanelLocationsFactory class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.db.Database

This method tests the Database class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.ExperimentChooserPanel

This method tests the Experiment Chooser panel class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.GeneColor

This method tests the GeneColor class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.GenePanel

This method tests the GenePanel class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.GenePanelLayout

This method tests the GenePanelLayout class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.goview.GoBioProcessView

This method tests the GoBioProcessView class.

main(String[], String) - Static method in class edu.iastate.metnet.birdseyeview.goview.GoFunctionView

This method tests the GoFunctionView class.

main(String[], String) - Static method in class edu.iastate.metnet.birdseyeview.goview.GoNode

This method tests the GoNode class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.LegendPanel

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.Loader

This method tests the Loader class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.LoadPanel

This method tests the LoadPanel class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.LoadWindow

This method tests the LoadWindow class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.pathwayview.Compartment

This method tests the Compartment class.

main(String[], String) - Static method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway

This method tests the Pathway class.

main(String[], String) - Static method in class edu.iastate.metnet.birdseyeview.pathwayview.PathwayView

This method tests the PathwayView class.

main(String[], String) - Static method in class edu.iastate.metnet.birdseyeview.RootPanel

This method is used to test the RootPanel class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.TextArea

This method is used to test the TextArea class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.TextPanel

This method tests the TextPanel class.

main(String[]) - Static method in class edu.iastate.metnet.birdseyeview.TreePanel

main(String[], String) - Static method in class edu.iastate.metnet.birdseyeview.ViewPanel

This method is used to test the ViewPanel class.

main(String[]) - Static method in class edu.iastate.metnet.dataManager.DataManager

main(String[]) - Static method in class edu.iastate.metnet.export.GraphExporterImpl

global entry

main(String[]) - Static method in class edu.iastate.metnet.hivemindService.ExportJungPathway

main(String[]) - Static method in class edu.iastate.metnet.hivemindService.PathwayService

main(String[]) - Static method in class edu.iastate.metnet.launch.LaunchMetNet

main(String[]) - Static method in class edu.iastate.metnet.launch.MetNetAboutFrame

main(String[]) - Static method in class edu.iastate.metnet.launch.RunCytoscape

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.chart.OrderableTable

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.ComponentToImage

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.CorrelationValue

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.DualTablePanel

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.FilterableTableModel

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.ListPanel

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.MenuButton

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.PolygonPanel

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Test the RandomAccessFile class.

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.ServiceTest

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.test.AffyChipAnimationPanel

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.test.ColorBrickPanel

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.test.ColorPicker

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.throbber.FlippingSquaresThrobber

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.throbber.GlowyChipThrobber

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.throbber.ImageThrobber

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.throbber.MetaOmThrobber

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.throbber.PolygonThrobber

main(String[]) - Static method in class edu.iastate.metnet.metaomgraph.throbber.SpinningPolygonThrobber

main(String[]) - Static method in class edu.iastate.metnet.MetNetLAFTest

main(String[]) - Static method in class edu.iastate.metnet.soft.RandomAccessFile

Test the RandomAccessFile class.

main(String[]) - Static method in class edu.iastate.metnet.soft.SOFTParser

main(String[]) - Static method in class edu.iastate.metnet.soft.SOFTParserOptionPanel

main(String[]) - Static method in class edu.iastate.metnet.test.BlockunitFinderTest

main(String[]) - Static method in class edu.iastate.metnet.test.HibernateTest

main(String[]) - Static method in class edu.iastate.metnet.test.MD5DigestTest

main(String[]) - Static method in class edu.iastate.metnet.test.StringTest

main(String[]) - Static method in class edu.iastate.metnet.test.UtilsTest

main(String[]) - Static method in class edu.iastate.metnet.threads.AnnotationThread

main(String[]) - Static method in class edu.iastate.metnet.threads.DataThread

main(String[]) - Static method in class edu.iastate.metnet.ui.CytoMetnet

copy MainWindow2's main() but automatically log in as a guest

main(String[]) - Static method in class edu.iastate.metnet.ui.MainWindow2

main function of the whole program

main(String[]) - Static method in class edu.iastate.metnet.ui.PropertyTable

main(String[]) - Static method in class edu.iastate.metnet.ui.SBMLExporter

main(String[]) - Static method in class fcmodeler.MyClass

main(String[]) - Static method in class fcmodeler.pathbinder.DictionaryBuilder

main(String[]) - Static method in class fcmodeler.pathbinder.gui.PbFrame

main(String[]) - Static method in class fcmodeler.pathbinder.HintParse

main(String[]) - Static method in class fcmodeler.pathbinder.MedCrawler

main(String[]) - Static method in class fcmodeler.pathbinder.MetaCrawler

main(String[]) - Static method in class fcmodeler.pathbinder.PathBinder

main(String[]) - Static method in class fcmodeler.pathbinder.PmidFilter

main(String[]) - Static method in class fcmodeler.pathbinder.SentenceService

main(String[]) - Static method in class fcmodeler.pathbinder.updater.InteractionUpdatePanel

main(String[]) - Static method in class fcmodeler.pathbinder.updater.PathBinderUpdater

MainExperimentComboBoxListener - Class in edu.iastate.metnet.birdseyeview

The MainExperimentComboBoxListener Class handles selections of experiments in the 'Main' Experiment combo box on the button panel.

MainExperimentComboBoxListener(BirdsEyeView, JComboBox) - Constructor for class edu.iastate.metnet.birdseyeview.MainExperimentComboBoxListener

Constructor.

MainMenuListener - Class in edu.iastate.metnet.launch

Listener used to open web documentation for MetNet applications

MainMenuListener(LaunchMetNet) - Constructor for class edu.iastate.metnet.launch.MainMenuListener

MainWindow2 - Class in edu.iastate.metnet.ui

MainWindow2.java Standalone main window lauched by ShowTable, which is embedded in brower window.

MainWindow2() - Constructor for class edu.iastate.metnet.ui.MainWindow2

Creates new form MainWindow2

MainWindow2(String) - Constructor for class edu.iastate.metnet.ui.MainWindow2

automatically login

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

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

makeActive(Object[]) - Method in class edu.iastate.metnet.metaomgraph.DualListPanel

Removes the specified values from the inactive list and adds them to the active list.

makeActive(int[]) - Method in class edu.iastate.metnet.metaomgraph.DualTablePanel

Removes the specified rows from the inactive list and adds them to the active list.

makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class edu.iastate.jtm.gui.SpringUtilities

Aligns the first rows * cols components of parent in a grid.

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

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

makeGrid(Container, int, int, int, int, int, int) - Static method in class edu.iastate.jtm.gui.SpringUtilities

Aligns the first rows * cols components of parent in a grid.

makeInactive(Object[]) - Method in class edu.iastate.metnet.metaomgraph.DualListPanel

Removes the specified values from the active list and adds them to the inactive list.

makeInactive(int[]) - Method in class edu.iastate.metnet.metaomgraph.DualTablePanel

Removes the specified rows from the active list and adds them to the inactive list.

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

Compiles a String for querying a MySQL database from the results of a previous query.

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

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

makeReport() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel

Generates a report for the selected row.

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

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

Launches the annotation manager.

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

Displays a table of the chart's columns and allows the user to manually hide/show them.

MapbuilderHelpFrame - Class in edu.iastate.metnet.mapbuilder

A JFrame that displays information contained at a given anchor of a URL.

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

A JFrame that displays information contained at a given anchor of a URL.

MapBuilderPanel - Class in edu.iastate.metnet.mapbuilder

MapBuilderPanel() - Constructor for class edu.iastate.metnet.mapbuilder.MapBuilderPanel

MapBuilderPanel.BuildListener - Class in edu.iastate.metnet.mapbuilder

MapBuilderPanel.BuildListener() - Constructor for class edu.iastate.metnet.mapbuilder.MapBuilderPanel.BuildListener

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

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

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

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

Markable - Interface in edu.iastate.jtm.gui

MarkableHeaderRenderer - Class in edu.iastate.jtm.gui

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

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

markAll() - Method in interface edu.iastate.jtm.gui.Markable

markChanged(Markable) - Method in class edu.iastate.jtm.gui.MarkableHeaderRenderer

markChanged(Markable) - Method in interface edu.iastate.jtm.gui.MarkListener

markChanged(Markable) - Method in class edu.iastate.jtm.gui.TableMarker

MarkListener - Interface in edu.iastate.jtm.gui

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

markNone() - Method in interface edu.iastate.jtm.gui.Markable

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

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

markStatus() - Method in interface edu.iastate.jtm.gui.Markable

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

MATCH - Static variable in class edu.iastate.jtm.dic.AbstractDictionary

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

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

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

matchAll() - Method in class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel

matchAll - Variable in class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel.QuerySet

matchedValue - Variable in class edu.iastate.jtm.dic.AbstractDictionary

MAX_ENTRY_LENGTH - Static variable in class edu.iastate.jtm.dic.AbstractDictionary

MAX_IDS - Static variable in class edu.iastate.jtm.jmed.EUtility

Maximum number of IDs that can be sent in a URL.

MAX_TOKEN_LENGTH - Static variable in class edu.iastate.jtm.dic.AbstractDictionary

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

The button that maximizes the JInternalFrame.

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

The icon displayed in the maximize button.

maxIndex(double[]) - Static method in class edu.iastate.metnet.utils.Utils

MaxLevel - Static variable in class edu.iastate.metnet.birdseyeview.goview.GoView

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

MD5Digest - Class in edu.iastate.metnet.utils

MD5Digest() - Constructor for class edu.iastate.metnet.utils.MD5Digest

MD5DigestTest - Class in edu.iastate.metnet.test

MD5DigestTest(String) - Constructor for class edu.iastate.metnet.test.MD5DigestTest

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

MedCitation - Class in edu.iastate.jtm.jmed

MedCitation(String) - Constructor for class edu.iastate.jtm.jmed.MedCitation

MedCrawler - Class in fcmodeler.pathbinder

Search Medline XML files against a dictionary.

MedCrawler(MySqlConnector) - Constructor for class fcmodeler.pathbinder.MedCrawler

Creates a new instance of MedCrawler

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

MedCrawlerPanel - Class in fcmodeler.pathbinder.updater

MedCrawlerPanel(StatusBar, JFileChooser) - Constructor for class fcmodeler.pathbinder.updater.MedCrawlerPanel

MedLeaseClient - Class in fcmodeler.pathbinder

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

MedLeasePanel - Class in fcmodeler.pathbinder.updater

MedLeasePanel(StatusBar, JFileChooser) - Constructor for class fcmodeler.pathbinder.updater.MedLeasePanel

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

MedlineParser - Class in edu.iastate.jtm.jmed

Extract citation info from Medline/PubMed XML files.

MedlineParser(boolean) - Constructor for class edu.iastate.jtm.jmed.MedlineParser

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

Creates a new blank instance of MedlineParser in default MEDLINE mode.

MedlineParser(SAXReader, boolean) - Constructor for class edu.iastate.jtm.jmed.MedlineParser

MedlineParser(SAXReader) - Constructor for class edu.iastate.jtm.jmed.MedlineParser

Creates a new blank instance of MedlineParser in default MEDLINE mode.

MemberManagerForm - Class in edu.iastate.metnet.ui

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

MemberManagerForm(String) - Constructor for class edu.iastate.metnet.ui.MemberManagerForm

MemberManagerForm(String, Integer) - Constructor for class edu.iastate.metnet.ui.MemberManagerForm

MENU_AA_GRAPH_QUERY - Static variable in class edu.iastate.metnet.ui.PathwayEditor

after choose approximately amorphous graph query

MENU_ALIGN_ARACYC - Static variable in class edu.iastate.metnet.ui.PathwayEditor

after choose compare pathway 2, aracyc update

MENU_ALL_COMPARE - Static variable in class edu.iastate.metnet.ui.PathwayEditor

choose any type of pathway comparison

MENU_ALL_GRAPH_QUERY - Static variable in class edu.iastate.metnet.ui.PathwayEditor

choose any type of graph query

MENU_EA_GRAPH_QUERY - Static variable in class edu.iastate.metnet.ui.PathwayEditor

after choose exactly amorphous graph query

MENU_ES_GRAPH_QUERY - Static variable in class edu.iastate.metnet.ui.PathwayEditor

after choose exactly structural graph query

MENU_HIGHLIGHT_DELTA - Static variable in class edu.iastate.metnet.ui.PathwayEditor

after choose compare pathway 1, incremental change

MENU_ZERO_DEGREE - Static variable in class edu.iastate.metnet.ui.PathwayEditor

menu status

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

MenuActionListener - Class in edu.iastate.metnet.dataManager

Class is the action listener for all menu items in action Menu

MenuActionListener(DataManager) - Constructor for class edu.iastate.metnet.dataManager.MenuActionListener

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

MenuButton - Class in edu.iastate.metnet.metaomgraph

A JButton that displays a JPopupMenu beneath it when activated.

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

Constructs a MenuButton with no text, icon, or associated menu.

MenuButton(JPopupMenu) - Constructor for class edu.iastate.metnet.metaomgraph.MenuButton

Constructs a MenuButton with no text and no icon that displays the given menu when activated.

MenuButton(String, JPopupMenu) - Constructor for class edu.iastate.metnet.metaomgraph.MenuButton

Constructs a MenuButton with the given text and no icon.

MenuButton(ImageIcon, JPopupMenu) - Constructor for class edu.iastate.metnet.metaomgraph.MenuButton

Constructs a MenuButton with the given icon and no text.

MenuButton(String, ImageIcon, JPopupMenu) - Constructor for class edu.iastate.metnet.metaomgraph.MenuButton

Constructs a MenuButton with the given text and icon.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

merge(MyTreeAlgorithm.PolyLine, MyTreeAlgorithm.PolyLine, int) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

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

mergeBlockunit() - Method in class edu.iastate.metnet.controller.NodeSelectionController

merge two entitywithlocations.

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

merge the two blockunits in the database.

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

merge the two blockunits in the database.

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

merge comment for UI

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

copy entity reference to blockunit reference

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

merge synonym for UI

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

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

MeshDescriptor - Class in edu.iastate.jtm.jmed

MeshDescriptor(Element) - Constructor for class edu.iastate.jtm.jmed.MeshDescriptor

meshFields - Static variable in class fcmodeler.pathbinder.FilterUpdater

message - Variable in class edu.iastate.jtm.gui.DefaultMonitorable

MetaboliteObject - Interface in edu.iastate.metnet.hiveface

interface about additional metabolite information

MetaboliteObjectImpl - Class in edu.iastate.metnet.export

MetaboliteObjectImpl(ChebiObject) - Constructor for class edu.iastate.metnet.export.MetaboliteObjectImpl

metaboliteSearch(String) - Method in class edu.iastate.metnet.hivemindService.Browser

Search a metabolic using AtMetabolicSearch, opens broweser to the result page

MetaCrawler - Class in fcmodeler.pathbinder

Collect publication year, MeSHHeadingList, etc.

MetaCrawler(MySqlConnector) - Constructor for class fcmodeler.pathbinder.MetaCrawler

MetalUtils - Class in javax.swing.plaf.metal

Some utility and helper methods for the Metal Look & Feel.

MetalUtils() - Constructor for class javax.swing.plaf.metal.MetalUtils

MetalUtilsX - Class in edu.iastate.reload.skin

Some utility and helper methods for the Metal Look & Feel.

MetalUtilsX() - Constructor for class edu.iastate.reload.skin.MetalUtilsX

MetaOmAnalyzer - Class in edu.iastate.metnet.metaomgraph

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

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

A panel containing a chart of the given data.

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

Constructs a chart panel using the given values.

MetaOmChartPanel.ExperimentFormat - Class in edu.iastate.metnet.metaomgraph.chart

Replaces the domain axis tick mark labels with column names.

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

MetaOmChartPanel.MetaOmFrame - Class in edu.iastate.metnet.metaomgraph.chart

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

MetaOmGraph - Class in edu.iastate.metnet.metaomgraph

The main class of the MetaOmGraph.

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

MetaOmGraph.NewProjectWorker - Class in edu.iastate.metnet.metaomgraph

Worker that constructs a new project.

MetaOmGraph.NewProjectWorker(File, int, char, Object[][], Object[], File, boolean, Double) - Constructor for class edu.iastate.metnet.metaomgraph.MetaOmGraph.NewProjectWorker

Constructor.

MetaOmHelpListener - Class in edu.iastate.metnet.metaomgraph

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

MetaOmProject - Class in edu.iastate.metnet.metaomgraph

Class used for dealing with large data sets.

MetaOmProject(File, int, char, boolean, Double) - Constructor for class edu.iastate.metnet.metaomgraph.MetaOmProject

Constructs a MetaOmProject with the given parameters.

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

Constructs a MetaOmProject using the given MetaOmGraph project file.

MetaOmProject(InputStream, int, char) - Constructor for class edu.iastate.metnet.metaomgraph.MetaOmProject

Constructs a MetaOmProject from the given InputStream.

MetaOmProject(InputStream, int, char, boolean) - Constructor for class edu.iastate.metnet.metaomgraph.MetaOmProject

Constructs a MetaOmProject from the given InputStream.

MetaOmTablePanel - Class in edu.iastate.metnet.metaomgraph

A JPanel for displaying information related to a MetaOmProject, and accessing many of MetaOmGraph's functions.

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

Constructs a MetaOmTablePanel from the given MetaOmProject.

MetaOmTablePanel.ListNameComparator - Class in edu.iastate.metnet.metaomgraph

Comparator for comparing names of lists.

MetaOmTablePanel.ListNameComparator() - Constructor for class edu.iastate.metnet.metaomgraph.MetaOmTablePanel.ListNameComparator

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

MetaOmThrobber() - Constructor for class edu.iastate.metnet.metaomgraph.throbber.MetaOmThrobber

MetaOmTips - Class in edu.iastate.metnet.metaomgraph

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

MetaOmTips.MetaOmShowTipsChoice - Class in edu.iastate.metnet.metaomgraph

MetaOmTips.MetaOmShowTipsChoice() - Constructor for class edu.iastate.metnet.metaomgraph.MetaOmTips.MetaOmShowTipsChoice

MetaphorTypeInformation - Class in edu.iastate.metnet.graphmodel

obviously checking the edge type can be extended to any interaction inforation of specified edge, thus we need a wrapper of all information

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

metnet - Variable in class edu.iastate.metnet.actions.LaunchApplicationListener

MetNetAboutFrame - Class in edu.iastate.metnet.launch

About window that is shown when user clicks on "about" menuItem

MetNetAboutFrame() - Constructor for class edu.iastate.metnet.launch.MetNetAboutFrame

MetnetBlockUnit - Class in edu.iastate.metnet.dao

general node in the graph

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

default constuctor

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

default constructor when the blockunit is known

MetNetGUI - Class in edu.iastate.metnet.newgui

MetNetGUI() - Constructor for class edu.iastate.metnet.newgui.MetNetGUI

MetNetHelpBar - Class in edu.iastate.metnet.newgui

A JPanel which displays the ToolTipText of a JComponent when said component has focus.

MetNetHelpBar() - Constructor for class edu.iastate.metnet.newgui.MetNetHelpBar

Default constructor

MetnetInteraction - Class in edu.iastate.metnet.dao

interaction nodes in the graph, should handle catalysis secifically

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

default constructor

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

MetNetLAF - Class in edu.iastate.metnet

MetNetLAF() - Constructor for class edu.iastate.metnet.MetNetLAF

MetNetLAF - Class in edu.iastate.reload.skin

copy from MetNet Look and Feel

MetNetLAF() - Constructor for class edu.iastate.reload.skin.MetNetLAF

MetNetLAFTest - Class in edu.iastate.metnet

MetNetLAFTest() - Constructor for class edu.iastate.metnet.MetNetLAFTest

MetnetLiveEntity - Class in edu.iastate.metnet.dao

entitywithlocation node in the graph

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

default construtor

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

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

Interface represents MetnetLocation

MetNetMetalTheme - Class in edu.iastate.metnet

MetNetMetalTheme() - Constructor for class edu.iastate.metnet.MetNetMetalTheme

MetNetMetalTheme - Class in edu.iastate.reload.skin

copy from MetNet Look and Feel

MetNetMetalTheme() - Constructor for class edu.iastate.reload.skin.MetNetMetalTheme

MetNetOceanTheme - Class in edu.iastate.metnet

MetNetOceanTheme() - Constructor for class edu.iastate.metnet.MetNetOceanTheme

MetNetOceanTheme - Class in edu.iastate.reload.skin

copy from MetNet Look and Feel

MetNetOceanTheme() - Constructor for class edu.iastate.reload.skin.MetNetOceanTheme

MetnetPathway - Class in edu.iastate.metnet.dao

abstract pathway node in the graph, which should be invisible and not connect to other nodes, otherwise cause layout problem

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

default constructor

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

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

Interface represents MetnetPathway

MetNetStatusbar - Class in edu.iastate.metnet.newgui

A status bar with a status field and progress bar.

MetNetTitlePane - Class in edu.iastate.metnet

The component that renders the title bar for frames.

MetNetTitlePane(JRootPane) - Constructor for class edu.iastate.metnet.MetNetTitlePane

MetNetToolbar - Class in edu.iastate.metnet.newgui

Toolbar class for the new MetNet GUI.

MetNetToolbar() - Constructor for class edu.iastate.metnet.newgui.MetNetToolbar

mget(File, FTPFile[]) - Method in class fcmodeler.pathbinder.MedLeaseClient

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

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

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

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

minimalDistance(double, double) - Method in class edu.iastate.metnet.analysis.AbstractExcelSheet

minimumLayoutSize(Container) - Method in class edu.iastate.metnet.birdseyeview.GenePanelLayout

minIndex(double[]) - Static method in class edu.iastate.metnet.utils.Utils

MINUS - Static variable in class edu.iastate.jtm.util.NameCharType

minX - Variable in class edu.iastate.metnet.dao.ZVertex

left

minY - Variable in class edu.iastate.metnet.dao.ZVertex

top

MISMATCH - Static variable in class edu.iastate.jtm.dic.AbstractDictionary

MNBlue - Static variable in class edu.iastate.metnet.MetNetLAF

MNBlue - Static variable in class edu.iastate.reload.skin.MetNetLAF

MNDarkGreen - Static variable in class edu.iastate.metnet.MetNetLAF

MNDarkGreen - Static variable in class edu.iastate.reload.skin.MetNetLAF

MNGreen - Static variable in class edu.iastate.metnet.MetNetLAF

MNGreen - Static variable in class edu.iastate.reload.skin.MetNetLAF

MNYellow - Static variable in class edu.iastate.metnet.MetNetLAF

MNYellow - Static variable in class edu.iastate.reload.skin.MetNetLAF

mode() - Method in class edu.iastate.jtm.assistant.QueryPanel

mode - Variable in class edu.iastate.metnet.launch.RunCytoscape

mode - Variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile

The access mode of the file.

mode - Variable in class edu.iastate.metnet.soft.RandomAccessFile

The access mode of the file.

MODE_AND - Static variable in class edu.iastate.jtm.assistant.CitationPool

MODE_OR - Static variable in class edu.iastate.jtm.assistant.CitationPool

MODE_REPLACE - Static variable in class edu.iastate.jtm.assistant.CitationPool

model - Variable in class edu.iastate.jtm.gui.TableMap

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

original model

model - Variable in class edu.iastate.metnet.model.TableMap

modelChanged(CompositionGraphModelChangedEvent) - Method in interface edu.iastate.metnet.event.CompositionGraphModelChangedListener

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

modelIndex(int[]) - Method in class edu.iastate.metnet.metaomgraph.TableSorter

ModelListerner - Class in edu.iastate.reload.ui

the model change event listener of the graph

ModelListerner(NetworkEditForm) - Constructor for class edu.iastate.reload.ui.ModelListerner

default constrcutor

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

aligned model subgraph

modify(String, Query.Field) - Method in class edu.iastate.jtm.jmed.Query.SimpleTerm

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

monitorable - Variable in class edu.iastate.jtm.gui.DefaultMonitorable

Monitorable - Interface in edu.iastate.jtm.gui

MONTHLY - Static variable in class fcmodeler.pathbinder.MedLeaseClient

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

create more soybean annotation

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

create more soybean annotation

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

fill the category for soybean pathway

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

fill the category for soybean pathway

mouseClicked(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.GenePanelListener

mouseClicked(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GenePanelListener

mouseClicked(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNodeMouseListener

mouseClicked(MouseEvent) - Method in class edu.iastate.metnet.dataManager.FilesTableMouseListener

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

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

mouseClicked(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.MenuButton

mouseClicked(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorBrickPanel

mouseClicked(MouseEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

mouseClicked(MouseEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

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

mouseDragged(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorPicker

mouseDragged(MouseEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

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

mouseDragged(MouseEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

mouseEntered(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.GenePanelListener

mouseEntered(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GenePanelListener

mouseEntered(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNodeMouseListener

mouseEntered(MouseEvent) - Method in class edu.iastate.metnet.dataManager.FilesTableMouseListener

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

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

mouseEntered(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.MenuButton

mouseEntered(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorBrickPanel

mouseEntered(MouseEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

mouseEntered(MouseEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

mouseExited(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.GenePanelListener

mouseExited(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GenePanelListener

mouseExited(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNodeMouseListener

mouseExited(MouseEvent) - Method in class edu.iastate.metnet.dataManager.FilesTableMouseListener

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

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

mouseExited(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.MenuButton

mouseExited(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorBrickPanel

mouseExited(MouseEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

mouseExited(MouseEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

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

mouseMoved(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorPicker

mouseMoved(MouseEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

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

mouseMoved(MouseEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

mousePressed(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.GenePanelListener

mousePressed(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GenePanelListener

mousePressed(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNodeMouseListener

mousePressed(MouseEvent) - Method in class edu.iastate.metnet.dataManager.FilesTableMouseListener

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

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

mousePressed(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.MenuButton

mousePressed(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorBrickPanel

mousePressed(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorPicker

mousePressed(MouseEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

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

mousePressed(MouseEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

mouseReleased(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.GenePanelListener

mouseReleased(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GenePanelListener

mouseReleased(MouseEvent) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNodeMouseListener

mouseReleased(MouseEvent) - Method in class edu.iastate.metnet.dataManager.FilesTableMouseListener

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

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

mouseReleased(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.MenuButton

mouseReleased(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorBrickPanel

mouseReleased(MouseEvent) - Method in class edu.iastate.metnet.metaomgraph.test.ColorPicker

mouseReleased(MouseEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

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

mouseReleased(MouseEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

mouseWheelMoved(MouseWheelEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartScrollBar

move() - Method in class edu.iastate.metnet.metaomgraph.PolygonPanel.BouncingPolygon

moveAll() - Method in class edu.iastate.jtm.assistant.Highlighter

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

move the category to the new position

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

move the category to the new position

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

move the current interaction to the history

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

move the current interaction to the history

moveKeyword() - Method in class edu.iastate.jtm.assistant.Highlighter

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

move the current live entity to the history

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

move the current live entity to the history

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

move the current pathway to the history

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

move the current pathway to the history

MultiEntityDecorator - Class in edu.iastate.metnet.model

follow the EntitywithlocationDecorator, provides and formats aggregate tooltip infomration

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

default constructor

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

constructor

MultiEntityNode - Class in edu.iastate.metnet.dao

entity node in multiple pathway graph which holds multi entity node from multiple pathways.

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

default constructor

MultiEntityNode(PathwayElementNode, PathwayElementNode) - Constructor for class edu.iastate.metnet.dao.MultiEntityNode

constructor

MultiInteractionDecorator - Class in edu.iastate.metnet.model

tooltip decorator for interaction

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

default constructor

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

default constrictor

MultiInteractionNode - Class in edu.iastate.metnet.dao

interaction node for multiple pathway.

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

default constructor

MultiInteractionNode(PathwayElementNode, PathwayElementNode) - Constructor for class edu.iastate.metnet.dao.MultiInteractionNode

constructore

MultiNodeCell - Class in edu.iastate.metnet.graphmodel

define my cell for my view

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

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

multiNodeFlag - Variable in class edu.iastate.metnet.graphmodel.JMetaphorGraph

MultiPathwayElementNode - Interface in edu.iastate.metnet.dao

interface for multi-pathway graph element node

MultiPathwayGraph - Interface in edu.iastate.metnet.dao

a pathway graph containing several pathways based on the alignment information, we do not use Super- to prevent confusing

MultiPathwayGraphImpl - Class in edu.iastate.metnet.dao

implementation of multi-pathway graph

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

default constructor

MultiPathwayGraphImpl(PathwayAlignment) - Constructor for class edu.iastate.metnet.dao.MultiPathwayGraphImpl

get a merged multi-pathway graph based on the alignment information

MultiPathwayModel - Class in edu.iastate.metnet.graphmodel

this pathway model is used for displaying combination of multiple pathway.

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

default constructor

MultiPathwayModel(Map) - Constructor for class edu.iastate.metnet.graphmodel.MultiPathwayModel

construct the multiple pathway model based on the pathway map

MultiSelectionModel - Class in edu.iastate.metnet.model

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

MultiVertexView - Class in edu.iastate.metnet.graphmodel

implement a special vertex view and renderer which can use two background color.

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

special view for special renderer

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

default constructor

MultiVertexView.MultiVertexRenderer - Class in edu.iastate.metnet.graphmodel

customized the renderer to use two background colors for one node

MultiVertexView.MultiVertexRenderer() - Constructor for class edu.iastate.metnet.graphmodel.MultiVertexView.MultiVertexRenderer

default constructor

MyClass - Class in fcmodeler

MyClass() - Constructor for class fcmodeler.MyClass

MyFacade - Interface in edu.iastate.metnet.interfaces

Remote interface for MyFacade.

MyFacadeFactory - Class in edu.iastate.metnet.utils

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

MyFacadeHome - Interface in edu.iastate.metnet.interfaces

Home interface for MyFacade.

MyFacadeLocal - Interface in edu.iastate.metnet.interfaces

Local interface for MyFacade.

MyFacadeLocalHome - Interface in edu.iastate.metnet.interfaces

Local home interface for MyFacade.

MyFacadeTest - Class in edu.iastate.metnet.test

MyFacadeTest(String) - Constructor for class edu.iastate.metnet.test.MyFacadeTest

Constructor for MyFacadeTest.

MyFacadeTest.FacadeWorker - Class in edu.iastate.metnet.test

MyFacadeTest.FacadeWorker(MyFacade, String) - Constructor for class edu.iastate.metnet.test.MyFacadeTest.FacadeWorker

MyFacadeUtil - Class in edu.iastate.metnet.interfaces

Utility class for MyFacade.

MyFacadeUtil() - Constructor for class edu.iastate.metnet.interfaces.MyFacadeUtil

MyJGraphModelAdapter - Class in edu.iastate.metnet.graphmodel

MyJGraphModelAdapter(Graph) - Constructor for class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Constructs a new JGraph model adapter for the specified JGraphT graph.

MyJGraphModelAdapter(Graph, Map, Map) - Constructor for class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Constructs a new JGraph model adapter for the specified JGraphT graph.

MyJGraphModelAdapter(Graph, AttributeMap, AttributeMap, MyJGraphModelAdapter.ICellFactory) - Constructor for class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Constructs a new JGraph model adapter for the specified JGraphT graph.

MyJGraphModelAdapter(Graph, Map, Map, MyJGraphModelAdapter.ICellFactory) - Constructor for class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Constructs a new JGraph model adapter for the specified JGraphT graph.

MyJGraphModelAdapter.DefaultCellFactory - Class in edu.iastate.metnet.graphmodel

A simple default cell factory.

MyJGraphModelAdapter.DefaultCellFactory() - Constructor for class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter.DefaultCellFactory

MyJGraphModelAdapter.ICellFactory - Interface in edu.iastate.metnet.graphmodel

Creates the JGraph cells that reflect the respective JGraphT elements.

MyJTableEx - Class in edu.iastate.metnet.ui

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

MyJTableEx(TableModel) - Constructor for class edu.iastate.metnet.ui.MyJTableEx

MyJTableEx(TableModel, TableColumnModel) - Constructor for class edu.iastate.metnet.ui.MyJTableEx

MyJTableEx(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class edu.iastate.metnet.ui.MyJTableEx

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

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

MyJTableEx(Object[][], Object[]) - Constructor for class edu.iastate.metnet.ui.MyJTableEx

MyJTableEx(TableModel, RowEditorModel) - Constructor for class edu.iastate.metnet.ui.MyJTableEx

MyJTableEx(TableModel, ColumnEditorModel) - Constructor for class edu.iastate.metnet.ui.MyJTableEx

MyMarqueeHandler - Class in edu.iastate.reload.ui

support node and edge drawing, adapted from GPMarqueeHandler of JGraphpad

MyMarqueeHandler() - Constructor for class edu.iastate.reload.ui.MyMarqueeHandler

MyMarqueeHandler(NetworkEditForm) - Constructor for class edu.iastate.reload.ui.MyMarqueeHandler

myMenu - Variable in class edu.iastate.metnet.metaomgraph.MenuButton

The JPopupMenu to display

MyMetnetService - Interface in edu.iastate.metnet.interfaces

Remote interface for MyMetnetService.

MyMetnetServiceFactory - Class in edu.iastate.metnet.utils

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

MyMetnetServiceHome - Interface in edu.iastate.metnet.interfaces

Home interface for MyMetnetService.

MyMetnetServiceLocal - Interface in edu.iastate.metnet.interfaces

Local interface for MyMetnetService.

MyMetnetServiceLocalHome - Interface in edu.iastate.metnet.interfaces

Local home interface for MyMetnetService.

MyMetnetServiceUtil - Class in edu.iastate.metnet.interfaces

Utility class for MyMetnetService.

MyMetnetServiceUtil() - Constructor for class edu.iastate.metnet.interfaces.MyMetnetServiceUtil

MyPanel - Class in edu.iastate.metnet.ui

not used

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

MyPaper - Interface in edu.iastate.metnet.interfaces

Remote interface for MyPaper.

MyPaperFactory - Class in edu.iastate.metnet.utils

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

MyPaperHome - Interface in edu.iastate.metnet.interfaces

Home interface for MyPaper.

MyPaperTest - Class in edu.iastate.metnet.test

MyPaperTest(String) - Constructor for class edu.iastate.metnet.test.MyPaperTest

MyPaperTest.PaperWorker - Class in edu.iastate.metnet.test

MyPaperTest.PaperWorker(MyPaper, String) - Constructor for class edu.iastate.metnet.test.MyPaperTest.PaperWorker

MyPaperUtil - Class in edu.iastate.metnet.interfaces

Utility class for MyPaper.

MyPaperUtil() - Constructor for class edu.iastate.metnet.interfaces.MyPaperUtil

MyPathwayGraph - Class in edu.iastate.metnet.export

a simple pathway graph to detect the structure change.

MyPathwayGraph() - Constructor for class edu.iastate.metnet.export.MyPathwayGraph

default constructor

myPathwayPanel - Variable in class edu.iastate.metnet.mapbuilder.MapBuilderPanel

myPolygons - Variable in class edu.iastate.metnet.metaomgraph.PolygonPanel

MyRClient - Class in edu.iastate.metnet.analysis

MyRClient() - Constructor for class edu.iastate.metnet.analysis.MyRClient

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

this main window instance

MySolver - Class in edu.iastate.metnet.analysis

linear equation solver
this class solve the problem AX = B in which A, X, B are matrices A and B are type of java.util.List

MySolverTest - Class in edu.iastate.metnet.test

MySolverTest(String) - Constructor for class edu.iastate.metnet.test.MySolverTest

Constructor for MySolverTest.

MySqlConnector - Class in edu.iastate.jtm.util

MySqlConnector(String, String, String, String) - Constructor for class edu.iastate.jtm.util.MySqlConnector

Creates a new instance of DbManager

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

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

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

compute the old style encrypted mysql password from the plain text

MyTreeAlgorithm - Class in edu.iastate.metnet.graphmodel

copy from JGraph, modified for pathway category.

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

MyTreeAlgorithm.PolyLine - Class in edu.iastate.metnet.graphmodel

the polyline structure

MyTreeAlgorithm.PolyLine(int) - Constructor for class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.PolyLine

default constructor

MyTreeAlgorithm.TreeNode - Class in edu.iastate.metnet.graphmodel

tree node contains the relative position in the tree

MyTreeAlgorithm.TreeNode(CellView) - Constructor for class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.TreeNode

myTrivialPanel - Variable in class edu.iastate.metnet.mapbuilder.MapBuilderPanel

myValue - Variable in class edu.iastate.metnet.metaomgraph.CorrelationValue

MyVersionGraph - Class in edu.iastate.metnet.dao

a simple graph structure supporting transfering over network.

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

default constructor

myVersionGraph - Variable in class edu.iastate.metnet.graphmodel.VersionGraphModel

version graph structure

MyVersionNode - Class in edu.iastate.metnet.dao

a simple node graph support transfering over network.

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

default constructor

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

constructor by the record id

MyXmlRpcClientFactory - Class in edu.iastate.metnet.utils

XML-RPC data type

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