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

C

calculateGOFrontEnd(Bicluster, String, String) - Method in class biggests.gui.PanelAnalyzingFunctionTable
Calculates the GO frontend for the given bicluster.
calculateGOFrontEnd(Bicluster) - Method in class biggests.gui.PanelAnalyzingFunctionTable
Calculates the GO frontend for the given bicluster.
calculateGOFrontEnd(IMatrix, String, String) - Method in class biggests.gui.PanelAnalyzingFunctionTable
Calculates the GO frontend for the given biclusters' group.
calculateGOFrontEnd(IMatrix) - Method in class biggests.gui.PanelAnalyzingFunctionTable
Calculates the GO frontend for the given expression matrix.
calculateGOFrontEnd(Biclustering, String, String) - Method in class biggests.gui.PanelAnalyzingFunctionTable
Calculates the GO frontend for the given biclusters' group.
calculateGOFrontEnd(Biclustering) - Method in class biggests.gui.PanelAnalyzingFunctionTable
Calculates the GO frontend for the given biclusters' group.
calculateWeights(double[][], int[][], double[], boolean, char, double, double) - Static method in class biggests.clustering.HierarchicalClustering
This function calculates the weights using the weighting scheme proposed by Michael Eisen: w[i] = 1.0 / sum_{j where d[i][j]cancelButton_actionPerformed(ActionEvent) - Method in class biggests.gui.SaveChartImageDialog
Handles the event fired when the user clicks cancel button.
cancelButton_actionPerformed(ActionEvent) - Method in class biggests.utils.ProgressBarFrame
When using the cancel button, handles a user's click on this button.
CC_TSB_BICLUSTERING - Static variable in class biggests.gui.PanelBiclustering
CC-TSB-Biclustering algorithm name.
CCC_BICLUSTERING - Static variable in class biggests.gui.PanelBiclustering
CCC-Biclustering algorithm name.
CDNA - Static variable in class biggests.gui.PanelLoading
Type of gene expression data: cDNA.
CENTROID_LINKAGE - Static variable in class biggests.clustering.HierarchicalClustering
Pairwise centroid-linkage (clustering method).
centroidLinkageClustering(double[][], int[][], double[], double[][], char, boolean) - Method in class biggests.clustering.HierarchicalClustering
Performs clustering using pairwise centroid-linking on a given set of gene expression data (specified by expressionData and missingsMask), using the distance matrix given by distanceMatrix.
checkAndAddFileExtension(String) - Method in class biggests.utils.FileFilterDirectory
Checks if filePath has the required file extension on it.
checkAndAddFileExtension(String) - Method in class biggests.utils.FileFilterExtension
Checks if filePath has the required file extension on it.
checkDOTFile(String) - Static method in class biggests.utils.BiggestsInstall
 
checkGOFiles(boolean) - Method in class biggests.gui.PanelFunctionAnalysis
Checks the existence of the required gene ontology files (the gene ontology file and the specific gene association file for the specified organism) in the GO Files directory.
checkPValue() - Method in class biggests.gui.PanelFunctionAnalysis
Checks the input of the p-value on pvalueTextField
chooseDirectoryForSaving(String) - Method in class biggests.gui.BiggestsFrame
 
chooseDOTFile() - Static method in class biggests.utils.BiggestsInstall
 
chooseFileForSaving(String, String) - Method in class biggests.gui.BiggestsFrame
 
CITYBLOCK_DISTANCE - Static variable in class biggests.clustering.AbstractMetricClustering
Cityblock distance (distance metric).
cityblockDistance(double[][], double[][], int[][], int[][], double[], int, int, boolean) - Static method in class biggests.clustering.AbstractMetricClustering
Calculates the weighted "City Block" distance between two genes/rows or conditions/columns in a matrix.
clear() - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
Clears this panel.
clear() - Method in class biggests.gui.PanelAnalyzingFunctionTable
Clears this panel's components.
clear() - Method in class biggests.gui.PanelAnalyzingMatrixDendrogram
Clears this panel.
clear() - Method in class biggests.gui.PanelAnalyzingMatrixTables
Clears the panel.
clear() - Method in class biggests.gui.PanelBiclustering
Clears this panel's components and other attributes that are no longer needed.
clear() - Method in class biggests.gui.PanelExpression
Clears this panel.
clear() - Method in class biggests.gui.PanelFunctionAnalysis
Clears this panel.
clear() - Method in class biggests.gui.PanelLoading
Clears this loading functionality panel (sets the loading panel ready to load a new dataset file).
clear() - Method in class biggests.gui.PanelPostProcessing
Clears post-processing panel.
clearAllPanels() - Method in class biggests.gui.BiggestsFrame
Clears all application's panels, so that they contain no information.
clone() - Method in class biggests.clustering.ClusterTreeNode
Overrides Object's clone method.
closeOperation(boolean) - Method in class biggests.gui.BiggestsFrame
Close operation.
clusterConditionsCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelAnalyzingMatrixDendrogram
Handles the event fired when the item state of cluster conditions check box changes.
clusterGenesCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelAnalyzingMatrixDendrogram
Handles the event fired when the item state of cluster genes check box changes.
clusteringMethods - Static variable in class biggests.gui.PanelAnalyzingMatrixDendrogram
Clustering methods (names to display).
clusteringMethodsAlias - Static variable in class biggests.gui.PanelAnalyzingMatrixDendrogram
Clustering methods alias (the arguments to pass to hierarchical methods).
ClusterTreeNode - Class in biggests.clustering
Title: Hierarchical Cluster Tree Node Description: ClusterTreeNode's class describes a single node in a tree created by hierarchical clustering.
ClusterTreeNode() - Constructor for class biggests.clustering.ClusterTreeNode
Creates a new ClusterTreeNode with left, right and distance attributes initialized to 0.
ClusterTreeNode(int, int, double) - Constructor for class biggests.clustering.ClusterTreeNode
Creates a new ClusterTreeNode with left, right and distance attributes initialized to left, right and distance argument values, respectively.
ClusterTreeNode(ClusterTreeNode) - Constructor for class biggests.clustering.ClusterTreeNode
Copy constructor.
ClusterTreeNodeComparator - Class in biggests.clustering
Title: Hierarchical Cluster Tree Node Comparator Description: Implements Comparator interface.
ClusterTreeNodeComparator() - Constructor for class biggests.clustering.ClusterTreeNodeComparator
Creates a new cluster tree node comparator.
COLORS - Static variable in class biggests.gui.PanelAnalyzingMatrixTables
The type for colors tables.
colors - Variable in class biggests.tables.TableSymbols
The set of colors.
colorsRedGreen_actionPerformed(ActionEvent) - Method in class biggests.gui.BiggestsFrame
 
colorsYellowBlue_actionPerformed(ActionEvent) - Method in class biggests.gui.BiggestsFrame
 
columnComparators - Variable in class biggests.tables.TableSorter
Hash map for the columns' comparators.
columnNames(boolean) - Static method in class biggests.tables.TableFunctionGroup
Returns the abbreviated names for the columns of this functions table.
COMPARABLE_COMPARATOR - Static variable in class biggests.tables.TableSorter
The comparator for specific comparable objects.
compare(Object, Object) - Method in class biggests.clustering.ClusterTreeNodeComparator
Compares two ClusterTreeNodes, o1 and o2.
COMPLETE_LINKAGE - Static variable in class biggests.clustering.HierarchicalClustering
Pairwise complete-linkage (clustering method).
completeColumnNames(boolean) - Static method in class biggests.tables.TableFunctionGroup
Returns the complete names of the columns of this functions table.
completeLinkageClustering(double[][]) - Method in class biggests.clustering.HierarchicalClustering
Performs clustering using pairwise complete-linkage on the given distance matrix.
computeBiclusters() - Method in class biggests.gui.ThreadBiclustering
Computes biclusters and GO frontend for function analysis.
computeDistance(double[][], double[][], int[][], int[][], double[], int, int, boolean, char) - Static method in class biggests.clustering.HierarchicalClustering
Calculates the distance between two genes/rows or two conditions/columns.
computeDistanceMatrix(double[][], int[][], double[], char, boolean) - Static method in class biggests.clustering.HierarchicalClustering
Calculates the distance matrix between genes/rows or conditions/columns using their measured gene expression data.
computeRanks(double[]) - Static method in class biggests.clustering.AbstractMetricClustering
Calculates the ranks of the elements in the array dataToRank.
computeRanks(ArrayList<Double>) - Static method in class biggests.clustering.AbstractMetricClustering
Calculates the ranks of the elements in the array dataToRank.
CONDITIONS_DIMENSION - Static variable in class biggests.clustering.AbstractMetricClustering
Clustering on conditions (columns) dimension (clustering dimension).
conditionsIndexes - Variable in class biggests.clustering.AbstractMetricClustering
The indexes of the conditions set by clustering method for file output.
conditionsNames - Variable in class biggests.clustering.AbstractMetricClustering
Conditions' names.
conditionsOrder - Variable in class biggests.clustering.AbstractMetricClustering
The order of the conditions in the data file.
conditionsWeights - Variable in class biggests.clustering.AbstractMetricClustering
The weights of the conditions.
constructColumnNames(NodeObjectInterface) - Static method in class biggests.tables.TableSymbols
Constructs the column names' array with symbolic data retrieved from the node object's symbolic matrix.
constructColumnNames(DiscretizedExpressionMatrix) - Static method in class biggests.tables.TableSymbolsWithMissingValues
Constructs the column names' array with symbolic data retrieved from the given discretized expression matrix.
constructColumnNames(NodeObjectInterface) - Static method in class biggests.tables.TableValues
Constructs the column names' array with data retrieved from the node object.
constructRowData(Biclustering, Hashtable<Integer, BiologicalRelevanceSummary>, boolean) - Static method in class biggests.tables.TableFunctionGroup
Constructs the row data matrix with data retrieved from the biclustering object.
constructRowData(GeneSetResult, boolean) - Static method in class biggests.tables.TableFunctionIndividual
Constructs the row data matrix with data retrieved from the bicluster object.
constructRowData(NodeObjectInterface) - Static method in class biggests.tables.TableSymbols
Constructs the row data matrix with symbolic data retrieved from the node object's symbolic matrix.
constructRowData(DiscretizedExpressionMatrix) - Static method in class biggests.tables.TableSymbolsWithMissingValues
Constructs the row data matrix with symbolic data retrieved from the node object's symbolic matrix.
constructRowData(NodeObjectInterface) - Static method in class biggests.tables.TableValues
Constructs the row data matrix with data retrieved from the node object.
convertDOTtoImage(String, String, String) - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
Converts a .dot file to an image file (png, gif, svg).
copy(File, File) - Static method in class biggests.gui.BiggestsIO
Copies a file to another location.
copyFunctionResultFilesForPostProcessedBiclusterGroup(TreePath) - Method in class biggests.gui.PanelPostProcessing
Copies the function result files for a post-processed biclusters' group.
createBiclusterChart(CategoryDataset, String, boolean, boolean, boolean) - Static method in class biggests.gui.PanelExpressionChart
 
createBiclusterDataset(Bicluster, boolean, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates an expression/pattern category dataset based on genes names, conditions names and expression values or pattern retrieved from the bicluster object.
createDefaultTableHeader() - Method in class biggests.tables.TableFunctionGroup
Overrides JTable's createDefaultTableHeader method.
createDefaultTableHeader() - Method in class biggests.tables.TableFunctionIndividual
Overrides JTable's createDefaultTableHeader method.
createDefaultTableHeader() - Method in class biggests.tables.TableValues
Overrides JTable's createDefaultTableHeader method.
createExpressionAllTimePointsChart(Bicluster, int, int, String, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a new panel holding an all time points expression chart, with expression data retrieved from bicluster and biclustering objects.
createExpressionAllTimePointsChart(Bicluster, String, int, int, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a new panel holding an all time points expression chart, with expression data retrieved from bicluster and biclustering objects.
createExpressionBiclusterPatternChart(CCC_Bicluster, int, int, String, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a new bicluster expression pattern chart panel for a given bicluster.
createExpressionBiclusterTimePointsChart(Bicluster, int, int, String, boolean, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a new time points expression chart panel for a given bicluster.
createExpressionBiclusterTimePointsChart(Bicluster, int, int, boolean, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a new time points expression chart panel for a given bicluster.
createExpressionChart(CategoryDataset, String, String, String, boolean, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a general expression chart from the given expressionDataset and with the given chartTitle, conditionsAxisName, expressionAxisName.
createExpressionDataset(Bicluster, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates an expression dataset for a bicluster.
createExpressionDataset(String[], String[], float[][], float, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a new expression category dataset with the given genesNames, conditionsNames and expressionValues.
createExpressionPatternChart(CategoryDataset, String, boolean, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a new pattern expression chart from a given expression patternDataset.
createGeneExpressionChart(CategoryDataset, String, boolean, boolean) - Static method in class biggests.gui.PanelExpressionChart
Creates a new gene expression chart from a given expressionDataset.
createPatternExpressionDataset(char[], char[], char, String[], int[]) - Static method in class biggests.gui.PanelExpressionChart
Creates an expression pattern dataset based on the given expression pattern (sequence of symbols) within the given alphabet (set of symbols that can appear in pattern).
createPatternExpressionDataset(CCC_Bicluster) - Static method in class biggests.gui.PanelExpressionChart
Creates a pattern expression dataset for the given bicluster.

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