A B C D E F G H I J K L M N O P R S T U V W Z

G

generateData(Matrix, int[]) - Method in class gui.workSpace.PanelWSEnterResults
 
getAllFilenameFilter() - Static method in class data.importers.Importer
 
getBestScoredCount() - Method in class data.Configuration
 
getBestTaxaIndex() - Method in class core.Identifier
Returns the index of the taxon with the higher relative probability
getBestTaxaIndex() - Method in class data.Context
Returns the taxon with the best probability (any of them, in case of tie)
getBestTestIndex() - Method in class core.Identifier
Returns the key of the test with best value (all taxa vs. all others).
getBestTestIndex(Context) - Method in class core.Identifier
Returns the key of the test with best value (all taxa vs. all others).
getBestTestIndex(int) - Method in class core.Identifier
Returns the key of the test with best value (one taxon vs. all others).
getBestTestIndex(int, Context) - Method in class core.Identifier
Returns the key of the test with best value (one taxon vs. all others).
getCellEditorValue() - Method in class gui.myClasses.CellEditorRadioButton
 
getCellRenderer() - Method in class gui.myClasses.JListMatrix
Return the wrapped cell renderer.
getCellRenderer() - Method in class gui.myClasses.JListWorkspace
Return the wrapped cell renderer.
getCharset(File) - Static method in class utils.FileUtils
Naive charset autodetector.
getChoosenMatrix() - Method in class gui.workSpace.DialogWSCreate
 
getColor(VisualItem) - Method in class gui.matrixLibrary.TreeView.NodeColorAction
 
getConfig() - Method in class gui.myWindows.PanelConfig
 
getConfig() - Method in class gui.workSpace.DialogWSCreate
 
getDefaultName() - Static method in class data.Workspace
Generates a default name for a new Workspace using a timestamp
getDescription() - Method in class data.importers.ImporterCSV.MatrixFileFilterCSV
 
getDescription() - Method in class data.importers.ImporterIMAT.MatrixFileFilterIMAT
 
getDescription() - Method in class data.importers.ImporterMAT.MatrixFileFilterMAT
 
getDescription() - Method in class data.importers.ImporterXLS.MatrixFileFilterXLS
 
getExtension(File) - Static method in class utils.FileUtils
Returns the extension (last string after the ".") of a file
getFileFilter(String, String) - Static method in class utils.FileUtils
Returns a custom FileFilter that accepts the files with the given extension
getFileNames(String, String) - Static method in class data.SerialManager
Return the names of the files with the given extension in the given path
getFoundValue() - Method in class data.Configuration
 
getFreeName(String) - Static method in class data.importers.Importer
Finds a free name (identificator) for the matrix
getImage(String) - Static method in class utils.FileUtils
Returns an image inside "img" folder
getIncoValues(Matrix, Configuration) - Method in class data.Context
Return the set of done tests that give an unexpected result for the best taxon founded till this moment A test is unexpected only if it has non-variable probabilities and signal opposite results have been supplied
getInstance() - Static method in class data.PropsManager
Return the singleton instance of this class
getInstance() - Static method in class gui.GuiManager
 
getInstance() - Static method in class gui.MainFrame
 
getInstance() - Static method in class gui.myClasses.MessageCenter
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class gui.myClasses.JListMatrix.RendererWrapper
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class gui.myClasses.JListWorkspace.RendererWrapper
 
getMainBar() - Static method in class gui.MainFrame
 
getMainPanel() - Static method in class gui.MainFrame
 
getMatrixInfo() - Method in class gui.matrixLibrary.DialogMatrixImport
 
getMatrixName() - Method in class gui.matrixLibrary.DialogMatrixImport
 
getMatrixNames() - Static method in class data.SerialManager
Retun the names of all Matrix in the Library
getMinAliveScore() - Method in class data.Configuration
 
getNameNoExtension(File) - Static method in class utils.FileUtils
Returns the name (the string before the ".") of a file
getNodeId(TreeNode) - Static method in class data.exporters.ExporterDOT
Returns the Strign used to identify a node in tree.
getNodeLine(TreeNode, Matrix, boolean) - Static method in class data.exporters.ExporterDOT
Returns the String of a node line of the tree
getProp(String) - Static method in class data.PropsManager
Gets the property in the current file
getScrollableTracksViewportHeight() - Method in class gui.myClasses.JTableRadioButtons
 
getSignalScoreLimitLow() - Method in class data.Configuration
 
getSignalScoreLimitUpp() - Method in class data.Configuration
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class gui.myClasses.CellEditorRadioButton
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class gui.myClasses.RendererRadioButton
 
getTaxaIndex() - Method in class core.Identifier
Returns an ordered array (sorted from best to worse) with the index of all alive taxa (the ones which till this moment haven't been discarded)
getTestIndex() - Method in class core.Identifier
Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one.
getTestIndex(Context) - Method in class core.Identifier
Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one.
getTestIndex(int) - Method in class core.Identifier
Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one.
getTestIndex(int, Context) - Method in class core.Identifier
Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one.
getTestIndex() - Method in class gui.myClasses.JRadioButtonTest
 
getTestResult() - Method in class gui.myClasses.JRadioButtonTest
 
getTXT(WorkspaceManager) - Static method in class data.exporters.ExporterTXT
Generates the report.
getVersion() - Static method in class gui.MainFrame
 
getWorkspaceNames() - Static method in class data.SerialManager
Retun the names of all Workspace saved
getWSInfo() - Method in class gui.workSpace.DialogWSCreate
 
getWSName() - Method in class gui.workSpace.DialogWSCreate
 
getZeroSkipValue() - Method in class data.Configuration
 
groupButton - Variable in class gui.workSpace.PanelWSShowInfo
 
gui - package gui
 
gui.matrixLibrary - package gui.matrixLibrary
 
gui.myClasses - package gui.myClasses
 
gui.myWindows - package gui.myWindows
 
gui.workSpace - package gui.workSpace
 
GuiException - Exception in gui
Exception throwed by user interface layer
GuiException() - Constructor for exception gui.GuiException
 
GuiException(String) - Constructor for exception gui.GuiException
 
GuiException(Throwable) - Constructor for exception gui.GuiException
 
GuiException(String, Throwable) - Constructor for exception gui.GuiException
 
GuiManager - Class in gui
Singleton class
GuiManager() - Constructor for class gui.GuiManager
 

A B C D E F G H I J K L M N O P R S T U V W Z