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
 

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