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)