Uses of Class
data.Matrix

Packages that use Matrix
core   
data   
data.exporters   
data.importers   
gui.matrixLibrary   
gui.myWindows   
gui.workSpace   
 

Uses of Matrix in core
 

Fields in core declared as Matrix
 Matrix Identifier.mat
          Reference matrix
 

Constructors in core with parameters of type Matrix
Bayes(Context con, Matrix mat, Configuration cnf)
          Default constructor for a none done test workspace
Bayes(Context con, Matrix mat, Configuration cnf, int[] test_resu)
          Constructs the Identifier and runs it with a single-step for all the non-missed test results supplied in the array
Identifier(Context con, Matrix mat, Configuration cnf)
          Creates a new Identifier with no done tests
Tree(Context con, Matrix mat, Configuration cnf)
          Creates a new Tree Identifier with no done tests
 

Uses of Matrix in data
 

Methods in data that return Matrix
static Matrix SerialManager.loadMatrix(java.lang.String filename)
          Return the Matrix previously saved with the given name
 

Methods in data with parameters of type Matrix
 int[][] Context.getIncoValues(Matrix m, Configuration c)
          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
static void SerialManager.saveMatrix(Matrix m, java.lang.String filename)
          Saves a matrix object with the given name
 Context[] Context.splitContex(int testId, Matrix m, Configuration cnf)
          Separates the current context in two others, discriminating one from each other using their estimation on the test result with especified identificator
 

Constructors in data with parameters of type Matrix
Context(Matrix m)
          Creates an empty context for the given matrix
Context(Matrix m, int[] testResRef)
          Creates an initial context from probability matrix.
 

Uses of Matrix in data.exporters
 

Methods in data.exporters with parameters of type Matrix
private static java.lang.String ExporterDOT.getNodeLine(TreeNode tn, Matrix m, boolean isTaxa)
          Returns the String of a node line of the tree
private static void ExporterDOT.writeDOT(TreeNode t, Matrix mat, java.io.OutputStreamWriter out)
          Writes recursively all the tree nodes
private static void ExporterTreeML.writeTreeML(TreeNode t, int level, Matrix mat, java.io.OutputStreamWriter out)
          Writes recursively all the tree nodes
private static void ExporterXML.writeXML(TreeNode t, int level, Matrix mat, java.io.OutputStreamWriter out)
          Writes recursively all the tree nodes
 

Uses of Matrix in data.importers
 

Methods in data.importers that return Matrix
static Matrix ImporterXLS.importFile(java.io.File f)
          Parses the data and put it in the new Matrix object
static Matrix ImporterMAT.importFile(java.io.File f)
          Parses the data and put it in the new Matrix object
static Matrix ImporterIMAT.importFile(java.io.File f)
          Parses the data and put it in the new Matrix object
static Matrix ImporterCSV.importFile(java.io.File f)
          Parses the data and put it in the new Matrix object
static Matrix Importer.importMatrix(java.io.File f)
          This function reads the given file and parse the data in it if applicable.
 

Uses of Matrix in gui.matrixLibrary
 

Fields in gui.matrixLibrary declared as Matrix
private  Matrix DialogMatrixImport.ref_mat
           
 

Constructors in gui.matrixLibrary with parameters of type Matrix
DialogMatrixImport(Matrix m)
           
 

Uses of Matrix in gui.myWindows
 

Fields in gui.myWindows declared as Matrix
private  Matrix PanelMatrixInfo.ref_mat
           
private  Matrix DialogMatrixInfo.refMat
           
 

Methods in gui.myWindows with parameters of type Matrix
 void PanelMatrixInfo.changeReferenceMatrix(Matrix m)
           
 

Constructors in gui.myWindows with parameters of type Matrix
PanelMatrixInfo(Matrix m, boolean editable)
           
 

Uses of Matrix in gui.workSpace
 

Fields in gui.workSpace declared as Matrix
 Matrix WorkspaceManager.refMat
           
 

Methods in gui.workSpace with parameters of type Matrix
private  java.lang.Object[][] PanelWSEnterResults.generateData(Matrix m, int[] test_res)
           
 

Constructors in gui.workSpace with parameters of type Matrix
PanelWSEnterResults(java.awt.Container pare, Matrix refMat, int[] test_res)