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Packages that use Matrix | |
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core | |
data | |
data.exporters | |
data.importers | |
gui.matrixLibrary | |
gui.myWindows | |
gui.workSpace |
Uses of Matrix in core |
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Fields in core declared as Matrix | |
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Matrix |
Identifier.mat
Reference matrix |
Constructors in core with parameters of type Matrix | |
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Bayes(Context con,
Matrix mat,
Configuration cnf)
Default constructor for a none done test workspace |
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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 |
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Identifier(Context con,
Matrix mat,
Configuration cnf)
Creates a new Identifier with no done tests |
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Tree(Context con,
Matrix mat,
Configuration cnf)
Creates a new Tree Identifier with no done tests |
Uses of Matrix in data |
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Methods in data that return Matrix | |
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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 | |
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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 | |
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Context(Matrix m)
Creates an empty context for the given matrix |
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Context(Matrix m,
int[] testResRef)
Creates an initial context from probability matrix. |
Uses of Matrix in data.exporters |
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Methods in data.exporters with parameters of type Matrix | |
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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 |
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Methods in data.importers that return Matrix | |
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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 |
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Fields in gui.matrixLibrary declared as Matrix | |
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private Matrix |
DialogMatrixImport.ref_mat
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Constructors in gui.matrixLibrary with parameters of type Matrix | |
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DialogMatrixImport(Matrix m)
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Uses of Matrix in gui.myWindows |
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Fields in gui.myWindows declared as Matrix | |
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private Matrix |
PanelMatrixInfo.ref_mat
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private Matrix |
DialogMatrixInfo.refMat
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Methods in gui.myWindows with parameters of type Matrix | |
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void |
PanelMatrixInfo.changeReferenceMatrix(Matrix m)
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Constructors in gui.myWindows with parameters of type Matrix | |
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PanelMatrixInfo(Matrix m,
boolean editable)
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Uses of Matrix in gui.workSpace |
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Fields in gui.workSpace declared as Matrix | |
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Matrix |
WorkspaceManager.refMat
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Methods in gui.workSpace with parameters of type Matrix | |
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private java.lang.Object[][] |
PanelWSEnterResults.generateData(Matrix m,
int[] test_res)
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Constructors in gui.workSpace with parameters of type Matrix | |
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PanelWSEnterResults(java.awt.Container pare,
Matrix refMat,
int[] test_res)
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