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A

AbstractMetricClustering - Class in biggests.clustering: Title: Abstract Metric Clustering Description: Defines an abstract class for clustering methods based on distance metrics.
AbstractMetricClustering(IMatrix) - Constructor for class biggests.clustering.AbstractMetricClustering: Creates a new AbstractClustering object to perform clustering over the set of gene expression data contained in expressionMatrix.
AbstractMetricClustering(int, int, double[], double[], double[], double[], int[], int[], String, String[], String[], String[], double[][], int[][]) - Constructor for class biggests.clustering.AbstractMetricClustering: Creates a new AbstractMetricClustering object to perform clustering over the given set of expression data.
accept(File) - Method in class biggests.utils.FileFilterDirectory: Checks if a certain file is acceptable under the filter conditions.
accept(File) - Method in class biggests.utils.FileFilterExtension: Checks if a certain file is acceptable under the filter conditions.
actionPerformed(ActionEvent) - Method in class biggests.gui.BiggestsFrame
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph_saveGraph_actionAdapter: Handles events fired by mouse click by the user.
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingFunctionTable_applyButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingFunctionTable_recalculate_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingMatrixDendrogram_applyButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelBiclustering_applyButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelFunctionAnalysis_browseGeneAssociationFilesPathButton_actionAdapter: Associates the specific handler of mouse clicks over browse gene association file path button with the overriden method mouseClicked.
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelFunctionAnalysis_browseGOFilesPathButton_actionAdapter: Associates the specific handler of mouse clicks over browse gene ontology file path button with the overriden method mouseClicked.
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelFunctionAnalysis_downloadGeneAssociationFileButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelFunctionAnalysis_downloadGeneOntologyFileButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelLoading_browseConversionFileButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelLoading_browseDatasetFileButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelLoading_loadButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelPostProcessing_applyButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.PanelPreProcessing_applyButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.SaveChartImageDialog_browseButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.SaveChartImageDialog_cancelButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.gui.SaveChartImageDialog_saveButton_actionAdapter
actionPerformed(ActionEvent) - Method in class biggests.utils.ProgressBarFrame_cancelButton_actionAdapter
addBiclusterGroupToDatasetTree(Biclustering, TreePath, GOFrontEnd) - Method in class biggests.gui.PanelBiclustering: Adds a bicluster group to the dataset tree.
addLoadedDataset(NodeInfo) - Method in class biggests.tree.DatasetTree: Adds the loaded dataset to the dataset tree and creates all additional nodes for preprocessed, discretized, biclustered and post-processed matrices of the dataset.
addLoadedDataset(NodeInfo, boolean) - Method in class biggests.tree.DatasetTree: Adds the loaded dataset to the dataset tree and creates all additional nodes for preprocessed, discretized, biclustered and post-processed matrices of the dataset.
addMessageToMessageHistory(String) - Method in class biggests.utils.ProgressBarFrame: Adds a new message to message history.
addNewNode(NodeInfo, TreePath) - Method in class biggests.tree.DatasetTree: Adds a new node to the datasets tree, associated with a node information object.
addNewNode(NodeInfo, TreePath, boolean) - Method in class biggests.tree.DatasetTree: Adds a new node to the datasets tree, associated with a node information object.
addPostProcessedBiclusterGroupToTree(Biclustering, ArrayList<String>, ArrayList<String>, TreePath) - Method in class biggests.gui.PanelPostProcessing: Adds a post-processed biclustering to the dataset tree.
addStylesToDocument(StyledDocument) - Method in class biggests.tree.NodeInfo: Adds a set of common styles to StyledDocument doc
algorithmsList_valueChanged(ListSelectionEvent) - Method in class biggests.gui.PanelBiclustering: Handles a selection change in algorithms' list.
ALL_TIME_POINTS - Static variable in class biggests.gui.PanelExpression: Constant which defines all time points expression chart type.
allowMissingsButton_mouseClicked(MouseEvent) - Method in class biggests.gui.PanelBiclustering
ALPHA - Static variable in class biggests.gui.PanelBiclustering: Name of the 'alpha' parameter (CC-TSB-biclustering).
alphabet - Variable in class biggests.tables.TableSymbols: The alphabet with all discretization symbols used in the discretization technique that gave rise to the set of discrete values that may appear in this symbols table.
ancestorResized(HierarchyEvent) - Method in class biggests.gui.PanelExpression_this_hierarchyBoundsAdapter
applyBiclusteringAlgorithm() - Method in class biggests.gui.PanelBiclustering: Applies biclustering algorithm.
applyButton() - Method in class biggests.gui.PanelPreProcessing: Returns apply preprocessing options button.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingFunctionTable: Handles the mouse event fired when the user clicks the apply button.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelAnalyzingMatrixDendrogram: Handles the event fired when the user clicks apply button.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelBiclustering: Handles the mouse event fired when the user clicks the apply button.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelPostProcessing: Applies the post-processing criteria to the current biclusters group.
applyButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelPreProcessing: Handles the mouse event fired when the user clicks on the apply button.
applyCCCBiclusteringAlgorithm() - Method in class biggests.gui.PanelBiclustering: Applies CCC-Biclustering algorithm.
applyCCTSBBiclusteringAlgorithm() - Method in class biggests.gui.PanelBiclustering: Applies CC-TSB-biclustering algorithm.
applyECCCBiclusteringAlgorithm() - Method in class biggests.gui.PanelBiclustering: Applies e-CCC-Biclustering algorithm.
Arrow - Class in biggests.utils: Title: Arrow Description: Class that implements an Icon.
Arrow(boolean, int, int) - Constructor for class biggests.utils.Arrow: Creates a new arrow for the given sorting status, with the given size and priority.
arrow - Variable in class biggests.utils.VerticalTextIconWithArrow
ASCENDING - Static variable in class biggests.tables.TableSorter: The status that indicates that a specific column is sorted in ascending order.
AVERAGE_LINKAGE - Static variable in class biggests.clustering.HierarchicalClustering: Pairwise average linkage (clustering method).
averageLinkageClustering(double[][]) - Method in class biggests.clustering.HierarchicalClustering: Performs clustering using pairwise average-linking on the given distance matrix.

B

BICLUSTER_GROUP - Static variable in class biggests.tree.NodeInfo: The bicluster group node object type.
BICLUSTER_SINGLE - Static variable in class biggests.tree.NodeInfo: The single bicluster node object type.
BICLUSTER_TIME_POINTS - Static variable in class biggests.gui.PanelExpression: Constant which defines bicluster time points expression chart type.
biclustering - Variable in class biggests.gui.ThreadPostProcessing: The bicluster group to post-process.
biclusteringError(String) - Method in class biggests.gui.ThreadBiclustering: Displays an error message when something went wrong with biclustering algorithm.
biclustersNumberOption_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelAnalyzingMatrixTables: Fired when the selected item of the biclusters' number combo box changes.
biggests.clustering - package biggests.clustering
biggests.gui - package biggests.gui
biggests.tables - package biggests.tables
biggests.tree - package biggests.tree
biggests.utils - package biggests.utils
BiggestsApplication - Class in biggests.gui: Title: BiGGEsTS - Biclustering Gene Expression Time Series Description: BiGGEsTS - Application Copyright: Copyright (C) 2007 Joana Gonçalves This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or any later version.
BiggestsApplication() - Constructor for class biggests.gui.BiggestsApplication: Starts the application.
BiggestsFrame - Class in biggests.gui: Title: BiGGEsTS Frame Description: The main frame of the application.
BiggestsFrame() - Constructor for class biggests.gui.BiggestsFrame: Application's main frame constructor.
BiggestsFrame_this_componentAdapter - Class in biggests.gui
BiggestsFrame_this_componentAdapter(BiggestsFrame) - Constructor for class biggests.gui.BiggestsFrame_this_componentAdapter
BiggestsFrame_this_windowAdapter - Class in biggests.gui: Title: Description:
BiggestsFrame_this_windowAdapter(BiggestsFrame) - Constructor for class biggests.gui.BiggestsFrame_this_windowAdapter
BiggestsFrame_this_windowStateAdapter - Class in biggests.gui
BiggestsFrame_this_windowStateAdapter(BiggestsFrame) - Constructor for class biggests.gui.BiggestsFrame_this_windowStateAdapter
BiggestsFrame_tree_treeSelectionAdapter - Class in biggests.gui: Title: Description:
BiggestsFrame_tree_treeSelectionAdapter(BiggestsFrame) - Constructor for class biggests.gui.BiggestsFrame_tree_treeSelectionAdapter
BiggestsInstall - Class in biggests.utils: Title: BiGGEsTS Install Description: Provides methods for installing the necessary files for BiGGEsTS to execute properly.
BiggestsInstall() - Constructor for class biggests.utils.BiggestsInstall
BiggestsInstall() - Method in class biggests.utils.BiggestsInstall: Creates a new instance of BiGGEsTS Install.
BiggestsIO - Class in biggests.gui: Title: BiGGEsTS's Input/Output Description: Provides methods for reading data from and writing data to files, for copying, deleting and creating directories and files.
BiggestsIO() - Constructor for class biggests.gui.BiggestsIO
browseButton_actionPerformed(ActionEvent) - Method in class biggests.gui.SaveChartImageDialog
browseConversionFileButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelLoading: Handles the mouse event fired by a user's click on browse conversion file button.
browseDatasetFileButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelLoading
browseGeneAssociationFilesPathButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelFunctionAnalysis: Handles event fired when the user clicks on browse gene association file path button.
browseGOFilesPathButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelFunctionAnalysis: Handles event fired when the user clicks browse gene ontology file path button.
BUF_SIZE - Static variable in class biggests.gui.BiggestsIO: The size of the buffer.

C

calcDimensions() - Method in class biggests.utils.VerticalTextIcon: Calculates the dimensions of the fComponent.
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.
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.
caretPositionChanged(InputMethodEvent) - Method in class biggests.gui.PanelLoading_datasetFileTextField_inputMethodAdapter
caretUpdate(CaretEvent) - Method in class biggests.gui.PanelLoading_datasetFileTextField_caretAdapter
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.
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
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.
componentResized(ComponentEvent) - Method in class biggests.gui.BiggestsFrame_this_componentAdapter
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, 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, 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.
createExpressionBiclusterPatternChart(CCC_Bicluster, int, int, 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, boolean, boolean) - Static method in class biggests.gui.PanelExpressionChart: Creates a new pattern expression chart from a given expression patternDataset.
createGeneExpressionChart(CategoryDataset, 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.

D

Dataset - Class in biggests.tree: Title: Dataset Description: Defines a dataset information object, which holds all the relevant information about a specific dataset loaded.
Dataset(int) - Constructor for class biggests.tree.Dataset: Constructs a new Dataset object with the given id.
datasetFileTextField_caretPositionChanged(InputMethodEvent) - Method in class biggests.gui.PanelLoading: Handles events fired by changes in caret position.
datasetFileTextField_caretUpdate(CaretEvent) - Method in class biggests.gui.PanelLoading: Handles an event fired when the caret position is updated.
datasetFileTextField_inputMethodTextChanged(InputMethodEvent) - Method in class biggests.gui.PanelLoading: Handles the event fired by a change in datasetFileTextField's text.
DatasetTree - Class in biggests.tree: Title: Dataset Tree Description: The dynamic tree which contains the gene expression datasets, matrices and biclusters.
DatasetTree() - Constructor for class biggests.tree.DatasetTree: Constructs a dataset tree with a single (mutable) tree node (called "Datasets").
DEFAULT_CJK - Static variable in class biggests.utils.VerticalTextIcon: Default CJK's rotation.
DEFAULT_MISSING_VALUE - Static variable in class biggests.gui.PanelLoading: Default value for missings.
DEFAULT_MUST_ROTATE - Static variable in class biggests.utils.VerticalTextIcon: Default must rotate rotation.
DEFAULT_ROMAN - Static variable in class biggests.utils.VerticalTextIcon: Default roman rotation.
deleteFolderContent(String) - Static method in class biggests.gui.BiggestsIO: Deletes a directory content.
deleteTempFilesAndDirectory() - Static method in class biggests.gui.PanelAnalyzingMatrixDendrogram
DELTA - Static variable in class biggests.gui.PanelBiclustering: Name of the 'delta' parameter (CC-TSB-biclustering).
DESCENDING - Static variable in class biggests.tables.TableSorter: The status that indicates that a specific column is sorted in descending order.
DISCRETIZE_ALPHA - Static variable in class biggests.gui.PanelPreProcessing: 'Alpha' discretization parameter name.
DISCRETIZE_PERCENT - Static variable in class biggests.gui.PanelPreProcessing: 'Percentage for discretization' parameter name.
DISCRETIZE_SYMBOLS - Static variable in class biggests.gui.PanelPreProcessing: 'Number of symbols' parameter name.
DISCRETIZE_THRESHOLD - Static variable in class biggests.gui.PanelPreProcessing: 'Threshold' discretization parameter name.
discretizeCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing: Handles the item state changed event fired when the user selects/deselects the discretize check box.
discretizeComboBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing: Handles the item state changed event fired when the user changes the selection in the discretize combo box.
DISCRETIZED - Static variable in class biggests.tree.NodeInfo: The discretized node object type.
displayedSizeRadioButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.SaveChartImageDialog: Handles the event fired when the state of the displayed size radio button changes.
displayFilteringErrorMessage(boolean) - Method in class biggests.gui.PanelPostProcessing: Displays a message when some problem occurs while performing filtering operations.
distanceMetrics - Static variable in class biggests.gui.PanelAnalyzingMatrixDendrogram: Similarity metrics (names to display).
distanceMetricsAlias - Static variable in class biggests.gui.PanelAnalyzingMatrixDendrogram: Similarity metrics alias (the arguments to pass to hierarchical methods).
divider - Variable in class biggests.tables.TableColors: Used to calculate the red or green component value of each colored matrix's cell.
doSaveAs() - Method in class biggests.gui.PanelExpressionChart
download(String, String, ProgressBarFrame, String) - Static method in class biggests.gui.BiggestsIO: Downloads the file from the Internet located in the specified address.
downloadGeneAssociationFile(String, String, String, ProgressBarFrame) - Static method in class biggests.gui.BiggestsIO: Downloads gene association file.
downloadGeneAssociationFileButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelFunctionAnalysis: Handles a mouse click event on download gene association file button.
downloadGeneOntologyFile(String, String, String, ProgressBarFrame) - Static method in class biggests.gui.BiggestsIO: Downloads gene ontology file.
downloadGeneOntologyFileButton_actionPerformed(ActionEvent) - Method in class biggests.gui.PanelFunctionAnalysis: Handles a mouse click event on download gene ontology file button.

E

E_CCC_BICLUSTERING - Static variable in class biggests.gui.PanelBiclustering: e-CCC-Biclustering algorithm name.
endProgram() - Method in class biggests.gui.MyTreeViewApp: Reimplements LinkedViewApp's endProgram method (the original method would call System.exit(0) and cause BiGGEsTS application to terminate, which we don't want to happen here).
endTreeViewApp() - Method in class biggests.gui.PanelAnalyzingMatrixDendrogram
equals(Object) - Method in class biggests.clustering.ClusterTreeNode: Overrides Object's equals method.
equals(Object) - Method in class biggests.clustering.ClusterTreeNodeComparator: Indicates whether some other object is "equal to" this Comparator.
EUCLIDEAN_DISTANCE - Static variable in class biggests.clustering.AbstractMetricClustering: Euclidean distance (distance metric).
euclideanDistance(double[][], double[][], int[][], int[][], double[], int, int, boolean) - Static method in class biggests.clustering.AbstractMetricClustering: Calculates the weighted Euclidean distance between two genes/rows or two conditions/columns.
EVEN_ROWS_COLOR - Static variable in class biggests.tables.TableFunctionGroup: Default color to user in even rows (when they are not selected).
EVEN_ROWS_COLOR - Static variable in class biggests.tables.TableFunctionIndividual: Default color for even rows.
exportComponentToImage(Component, String, String) - Static method in class biggests.gui.BiggestsIO: Exports a GUI component to an image file.
exportComponentToImage(Component, int, int, int, int, String, String) - Static method in class biggests.gui.BiggestsIO: Exports a GUI component to an image file.
exportToImage() - Method in class biggests.tables.TableColors: Exports this table to an image file.
exportToImage() - Method in class biggests.tables.TableSymbols: Exports this table to an image file.
expressionData - Variable in class biggests.clustering.AbstractMetricClustering: Expression data.

F

fCharHeight - Variable in class biggests.utils.VerticalTextIcon: The width and height of the label, character height and descent.
fCharStrings - Variable in class biggests.utils.VerticalTextIcon: The label parsed into one-char strings.
fCharWidths - Variable in class biggests.utils.VerticalTextIcon: The characters widths.
fComponent - Variable in class biggests.utils.VerticalTextIcon: The component in which the label will be drawn.
fDescent - Variable in class biggests.utils.VerticalTextIcon: The width and height of the label, character height and descent.
fHeight - Variable in class biggests.utils.VerticalTextIcon: The width and height of the label, character height and descent.
FileFilterDirectory - Class in biggests.utils: Title: File Filter with directory exclusion.
FileFilterDirectory(String[], String) - Constructor for class biggests.utils.FileFilterDirectory: Creates a new directory file filter, with a specific valid file extension and some invalid directory paths.
FileFilterExtension - Class in biggests.utils: Title: File Filter by extension.
FileFilterExtension(String) - Constructor for class biggests.utils.FileFilterExtension: Creates a new extension file filter, to filter files based on their extensions.
FILL_NEIGHBORS - Static variable in class biggests.gui.PanelPreProcessing: 'Number of neighbors' parameter name.
FILL_VALUE - Static variable in class biggests.gui.PanelPreProcessing: 'Value to fill missings' parameter name;
fillAverageRowButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing: Handles the item state changed event fired when the user selects the fill missings with average over the same row radio button.
fillCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
fillKNeighborsButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing: Handles the item state changed event fired when the user selects the fill missings with average over the k-neighbors radio button.
fillValueButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing: Handles the item state changed event fired when the user selects the fill missings with a given value radio button.
FILTER_ACV - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with an ACV value below a given threshold' option.
FILTER_ACV_ARV - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter trivial biclusters and biclusters with ACV and ARV values below given thresholds' option.
FILTER_ARV - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with an ARV value below a given threshold' option.
FILTER_CONDITIONS - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with less than a given number of conditions' option.
FILTER_CONDITIONS_GENES_ARV_ACV - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with less than given numbers of genes and conditions and with ARV and ACV values below given thresholds' option.
FILTER_CONDITIONS_GENES_ARV_ACV_MSR - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with less than given numbers of genes and conditions and with ARV, ACV and MSR values below given thresholds' option.
FILTER_CONSTANT_PATTERN - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with constant pattern' option.
filter_CONSTANT_PATTERN(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with a constant pattern and a % of overlapping conditions below two given thresholds.
FILTER_GENES - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with less than a given number of genes' option.
FILTER_GENES_CONDITIONS - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with less than a given number of genes and less than a given number of conditions' option.
FILTER_MSR - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with an MSR value below a given threshold' option.
FILTER_OVERLAPPING_GENES - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with a row similarity below a given threshold' option.
FILTER_OVERLAPPING_GENES_CONDITIONS - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters with row and column similarities below given thresholds' option.
FILTER_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT - Static variable in class biggests.gui.PanelPostProcessing
filter_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Filters the biclusters of the given biclusters' group (BiclusteringInDiscretizedMatrix) for which the pattern p-value with columns is not significant.
FILTER_PATTERN_PVALUE_NOT_SIGNIFICANT - Static variable in class biggests.gui.PanelPostProcessing
filter_PATTERN_PVALUE_NOT_SIGNIFICANT(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Filters the biclusters of the given biclusters' group (BiclusteringInDiscretizedMatrix) for which the pattern p-value is not significant.
FILTER_PERCENTAGE - Static variable in class biggests.gui.PanelPreProcessing: 'Percentage of genes to filter' parameter name.
FILTER_SIZE - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters smaller than a given size' option.
FILTER_SIZE_ARV_ACV - Static variable in class biggests.gui.PanelPostProcessing: The index of 'filter biclusters smaller than a given size and with ARV and ACV values below given thresholds' option.
FILTER_TRIVIAL - Static variable in class biggests.gui.PanelPostProcessing: The index of filter trivial biclusters option.
filter_TRIVIAL(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs trivial biclusters filtering algorithm.
filterBy_ACV_ARV_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with ACV and ARV below two given thresholds.
filterBy_ACV_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with an ACV below a given threshold.
filterBy_ARV_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with an ARV below a given threshold.
filterBy_MSR_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with a MSR below a given threshold.
filterBy_NR_CONDITIONS(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with less than a given number of conditions.
filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_MSR_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with a number of conditions, a number of genes, ACV, ARV and MSR below five given thresholds.
filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with a number of conditions, a number of genes, ACV and ARV below four given thresholds.
filterBy_NR_GENES(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with less than a given number of genes.
filterBy_NR_GENES_NR_CONDITIONS(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with less than a given number of genes and a given number of conditions.
filterBy_OVERLAPPING_GENES_CONDITIONS_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with a % of overlapping genes and a % of overlapping conditions below two given thresholds.
filterBy_OVERLAPPING_GENES_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with a % of overlapping genes below a given threshold.
filterBy_SIZE_ARV_ACV_Thresholds(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with size, ACV and ARV below three given thresholds.
filterBy_SIZE_Threshold(Biclustering, ArrayList<String>, ArrayList<String>) - Method in class biggests.gui.ThreadPostProcessing: Performs filtering of biclusters with size below a given threshold.
filterCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPostProcessing: Handles changes on filter check box selection.
filterCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing
filterCriteriaList_valueChanged(ListSelectionEvent) - Method in class biggests.gui.PanelPostProcessing: Handles a selection change on filter criteria list.
filterCriteriaList_valueChanged() - Method in class biggests.gui.PanelPostProcessing: Handles a selection change on filter criteria list.
filterPercentGenesButton_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelPreProcessing: Handles the item state changed event fired when the user selects the filter genes with more than a % of missing values radio button.
findAnnotationFileExtensionForOrganism(String) - Static method in class biggests.gui.PanelFunctionAnalysis: Finds and returns the corresponding annotation file extension for a given organism.
findBiclusterNodeByIDinSetOfBiclustersNodes(Enumeration, int) - Method in class biggests.tree.DatasetTree: Looks for a NodeInfo object of a bicluster or post-processed bicluster object with a specific id.
findClosestPair(int, double[][], int[], int[]) - Static method in class biggests.clustering.HierarchicalClustering: Searches the distance matrix to find the pair with the shortest distance between them.
findFileExtensionInDirectoryPath(String, String) - Static method in class biggests.gui.BiggestsIO: Finds the first file with a specific file extension in some specific directory.
findFileInDirectoryPath(String, String) - Static method in class biggests.gui.BiggestsIO: Finds for a specific filename in a specific directory path.
findGeneAssociationFileName(String, boolean) - Static method in class biggests.gui.PanelFunctionAnalysis: Finds a specific filename or extension for a given organism.
findInfoString(String) - Method in class biggests.tree.NodeInfo: Finds a specific information string.
finishTaskInLabelContext(String) - Method in class biggests.gui.BiggestsFrame
fLabel - Variable in class biggests.utils.VerticalTextIcon: The label to rotate.
formatter - Variable in class biggests.tables.TableFunctionGroup.FloatCellRenderer: The formatter which is used to format the float value.
formatter - Variable in class biggests.tables.TableFunctionIndividual.FloatCellRenderer: The formatter which is used to format the float value.
formatter - Variable in class biggests.tables.TableValues.FloatCellRenderer: The formatter which is used to format the float value.
fPosition - Variable in class biggests.utils.VerticalTextIcon: The position of the characters.
frame - Variable in class biggests.gui.ThreadHierarchicalClustering
fRotation - Variable in class biggests.utils.VerticalTextIcon: The rotation of the label.
functionGroupTable_mouseClicked(MouseEvent) - Method in class biggests.gui.PanelAnalyzingFunctionTable: Handles the event fired when the mouse is clicked on a function group table's row.
fWidth - Variable in class biggests.utils.VerticalTextIcon: The width and height of the label, character height and descent.

G

geneIDCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelLoading: Handles the event fired by a change in gene ID's check box selection.
generateNewDatasetId() - Method in class biggests.tree.DatasetTree: Generates a dataset id for a new Dataset object.
generateNewNodeInfoId(int, TreePath, boolean) - Method in class biggests.tree.DatasetTree: Returns the next id for a new NodeInfo object to be created in the dataset of the given selected path.
generateNewNodeObjectTypeId(int, boolean) - Method in class biggests.tree.Dataset: Generates a new id value (within this dataset) for a new node information object with the specified data type.
GENES_DIMENSION - Static variable in class biggests.clustering.AbstractMetricClustering: Clustering on genes (rows) dimension (clustering dimension).
geneShiftsCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelBiclustering: Handles a change in gene shifts check box state.
genesIndexes - Variable in class biggests.clustering.AbstractMetricClustering: The indexes of the genes set by clustering method for file output.
genesNames - Variable in class biggests.clustering.AbstractMetricClustering: Genes' names.
genesOrder - Variable in class biggests.clustering.AbstractMetricClustering: The order of the genes in the data file.
genesUniqueIDs - Variable in class biggests.clustering.AbstractMetricClustering: Genes' unique IDs.
genesWeights - Variable in class biggests.clustering.AbstractMetricClustering: The weights of the genes.
getActualColumnNames() - Method in class biggests.tables.TableFunctionIndividual: Returns the actual column names for this table.
getActualCompleteColumnNames() - Method in class biggests.tables.TableFunctionIndividual: Returns the actual complete, not abbreviated column names for this table.
getACVTextField() - Method in class biggests.gui.PanelPostProcessing: Returns ACV's threshold input text field.
getAlphabet() - Method in class biggests.tables.TableSymbols: Returns the alphabet with all discretization symbols used in the discretization technique that gave rise to the set of discrete values that may appear in this symbols table.
getApplyButton() - Method in class biggests.gui.PanelBiclustering: Returns apply button.
getARVTextField() - Method in class biggests.gui.PanelPostProcessing: Returns ARV's threshold input text field.
getAscendingButton() - Method in class biggests.gui.PanelPostProcessing: Returns ascending order option radio button.
getBackgroundHighlightColor() - Static method in class biggests.utils.HeatmapColorScheme
getBiclustering() - Method in class biggests.gui.PanelPostProcessing: Returns the group of biclusters that is being post-processed.
getBiclusteringAlgorithmsLabel() - Method in class biggests.gui.PanelBiclustering: Returns biclustering algorithms label.
getBiclusteringPanel() - Method in class biggests.gui.PanelBiclustering: Returns biclustering panel.
getBiclustersNumber() - Static method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the options presented to user about the number of tables that he/she wants to visualize.
getBoxLayout() - Method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the layout of this panel.
getBrowseGeneAssociationFilePathButton() - Method in class biggests.gui.PanelFunctionAnalysis: Returns browse gene association file path button.
getBrowseGeneOntologyFilePathButton() - Method in class biggests.gui.PanelFunctionAnalysis: Returns browse gene ontology file path button.
getChartHeight() - Method in class biggests.gui.PanelExpression: Returns the height of the displayed expression chart(s).
getChartWidth() - Method in class biggests.gui.PanelExpression: Returns the width of the displayed expression chart(s).
getColorAboveMean(int) - Static method in class biggests.utils.HeatmapColorScheme
getColorBelowMean(int) - Static method in class biggests.utils.HeatmapColorScheme
getColors() - Method in class biggests.tables.TableSymbols: Returns the set of colors used to color each of the table's cells.
getColumnClass(int) - Method in class biggests.tables.TableSorter: Returns the class of the column with index column.
getColumnClass(int) - Method in class biggests.tables.TableSorterFunctionGroup: Overrides TableSorter's getColumnClass method.
getColumnClass(int) - Method in class biggests.tables.TableSorterFunctionIndividual: Overrides TableSorter's getColumnClass method.
getColumnClass(int) - Method in class biggests.tables.TableSorterSymbols: Overrides TableSorterValues's getColumnClass method.
getColumnClass(int) - Method in class biggests.tables.TableSorterValues: Overrides TableSorter's getColumnClass method.
getColumnCount() - Method in class biggests.tables.TableSorter: Returns the number of columns in the table model.
getColumnName(int) - Method in class biggests.tables.TableSorter: Returns the name of the given column.
getColumnNames() - Static method in class biggests.tables.TableFunctionIndividual: Returns this table abbreviated columns names.
getComparator(int) - Method in class biggests.tables.TableSorter: Returns the appropriate comparator for the objects in the given column.
getComparator(int) - Method in class biggests.tables.TableSorterFunctionGroup: Overrides TableSorter's getComparator method.
getComparator(int) - Method in class biggests.tables.TableSorterFunctionIndividual: Overrides TableSorter's getComparator method.
getComparator(int) - Method in class biggests.tables.TableSorterSymbols: Overrides TableSorterValues's getComparator method.
getComparator(int) - Method in class biggests.tables.TableSorterValues: Overrides TableSorter's getComparator method.
getCompleteColumnNames() - Static method in class biggests.tables.TableFunctionIndividual: Returns this table complete columns names.
getConditionsNames() - Method in class biggests.gui.PanelExpressionChart: Returns the names of the conditions in the expression chart.
getConditionsTextField() - Method in class biggests.gui.PanelPostProcessing: Returns conditions' number threshold input text field.
getDataType() - Method in class biggests.tree.NodeInfo: Returns the node object data type value.
getDescendingButton() - Method in class biggests.gui.PanelPostProcessing: Returns descending order option radio button.
getDescription() - Method in class biggests.utils.FileFilterDirectory: Returns the description of this file filter.
getDescription() - Method in class biggests.utils.FileFilterExtension: Returns the description of this file filter.
getDiscretizeCheckBox() - Method in class biggests.gui.PanelPreProcessing: Returns discretize check box.
getDiscretizeComboBox() - Method in class biggests.gui.PanelPreProcessing: Returns discretize combo box.
getDiscretizeLabel() - Method in class biggests.gui.PanelPreProcessing: Returns discretize label.
getDiscretizeParameterLabel() - Method in class biggests.gui.PanelPreProcessing: Returns discretize parameter label.
getDiscretizeParameterTextField() - Method in class biggests.gui.PanelPreProcessing: Returns discretize parameter input text field.
getDistance() - Method in class biggests.clustering.ClusterTreeNode: Returns the distance between the left and the right elements/nodes (the sons of this node).
getDivider() - Method in class biggests.tables.TableColors: Returns the divider value for the float values in the table, that is, the value that will be used to divide the difference between the true float value of a cell and the meanValue to find the red or green color component to colorize the cell.
getErrorsNumberLabel() - Method in class biggests.gui.PanelBiclustering: Label for the number of errors allowed in e-CCC-Biclustering algorithm.
getErrorsNumberTextField() - Method in class biggests.gui.PanelBiclustering: Text field for the input of the number of errors allowed in e-CCC-Biclustering algorithm.
getEvenRowsColor() - Method in class biggests.tables.TableFunctionGroup: Returns the Color used to mark even rows that are not selected.
getEvenRowsColor() - Method in class biggests.tables.TableFunctionIndividual: Returns the Color used to mark even rows that are not selected.
getExpressionChart() - Method in class biggests.gui.PanelExpression: Returns single bicluster's expression chart that is being displayed in this panel.
getExpressionCharts() - Method in class biggests.gui.PanelExpression: Returns the expression charts of a set of biclusters (which belong to a specific group of biclusters).
getExpressionMatrix() - Method in class biggests.gui.PanelBiclustering: Returns the node object which contains the original, preprocessed or discretized matrix on which biclustering algorithm will be performed.
getExpressionMatrix() - Method in class biggests.gui.PanelPreProcessing: Returns the original or preprocessed expression matrix in which preprocessing techniques will be performed.
getExpressionType() - Method in class biggests.gui.PanelExpression: Returns the type of expression for this panel's chart.
getExpressionValues() - Method in class biggests.gui.PanelExpressionChart: Returns the expression values in the expression chart.
getFakeID() - Method in class biggests.tree.NodeInfo: Returns the ID of the post-processed bicluster.
getFilesFunctionAnalysisLabel() - Method in class biggests.gui.PanelFunctionAnalysis: Returns label of files to use on function analysis.
getFillAverageRowButton() - Method in class biggests.gui.PanelPreProcessing: Returns fill with average over the same row button.
getFillButtonGroup() - Method in class biggests.gui.PanelPreProcessing: Returns fill options button group.
getFillCheckBox() - Method in class biggests.gui.PanelPreProcessing: Returns fill check box.
getFillKNeighborsButton() - Method in class biggests.gui.PanelPreProcessing: Returns fill with average over the k-neighbors button.
getFillKNeighborsLabel() - Method in class biggests.gui.PanelPreProcessing: Returns fill with average over the k-neighbors label.
getFillKNeighborsTextField() - Method in class biggests.gui.PanelPreProcessing: Returns fill with average over the k-neighbors input text field.
getFillValueButton() - Method in class biggests.gui.PanelPreProcessing: Returns fill missings with a certain value button.
getFillValueTextField() - Method in class biggests.gui.PanelPreProcessing: Returns fill with a certain value input text field.
getFilterAllGenesButton() - Method in class biggests.gui.PanelPreProcessing: Returns filter all genes with missing values button.
getFilterButtonGroup() - Method in class biggests.gui.PanelPreProcessing: Returns the filter options button group.
getFilterCheckBox() - Method in class biggests.gui.PanelPostProcessing: Returns enabling/disabling filtering option check box.
getFilterCheckBox() - Method in class biggests.gui.PanelPreProcessing: Returns the filter check box.
getFilterCriteria() - Method in class biggests.gui.PanelPostProcessing
getFilterCriteriaLabel() - Method in class biggests.gui.PanelPostProcessing: Returns filtering criteria label.
getFilterCriteriaList() - Method in class biggests.gui.PanelPostProcessing: Returns filtering criteria list.
getFilterPanel() - Method in class biggests.gui.PanelPostProcessing: Returns the panel with filtering options.
getFilterPercentGenesButton() - Method in class biggests.gui.PanelPreProcessing: Returns filter genes with more than a % of missing values button.
getFilterPercentLabel() - Method in class biggests.gui.PanelPreProcessing: Returns filter percent label.
getFilterPercentTextField() - Method in class biggests.gui.PanelPreProcessing: Returns the filter percent input text field.
getForegroundHighlightColor() - Static method in class biggests.utils.HeatmapColorScheme
getFunctionAnalysisLabel() - Method in class biggests.gui.PanelFunctionAnalysis: Returns function analysis label.
getFunctionAnalysisPanel() - Method in class biggests.gui.PanelAnalyzingFunctionTable: Returns function analysis panel.
getGeneAssociationFilePathLabel() - Method in class biggests.gui.PanelFunctionAnalysis: Returns gene association file path label.
getGeneAssociationFilePathTextField() - Method in class biggests.gui.PanelFunctionAnalysis: Returns gene association file path text field.
getGeneAssociationFilesURL() - Method in class biggests.gui.BiggestsFrame: Returns gene association files URL.
getGeneOntologyFilePathLabel() - Method in class biggests.gui.PanelFunctionAnalysis: Returns gene ontology file path label.
getGeneOntologyFilePathTextField() - Method in class biggests.gui.PanelFunctionAnalysis: Returns gene ontology file path text field.
getGeneOntologyFilesURL() - Method in class biggests.gui.BiggestsFrame: Returns gene ontology files URL.
getGeneShiftsCheckBox() - Method in class biggests.gui.PanelBiclustering: Returns gene shifts for CCC-Biclustering and e-CCC-Biclustering algorithms check box.
getGenesNames() - Method in class biggests.gui.PanelExpressionChart: Returns the names of the genes in the expression chart.
getGenesTextField() - Method in class biggests.gui.PanelPostProcessing: Returns genes' number threshold input text field.
getGOFrontEndForSelectionPath(TreePath) - Method in class biggests.gui.PanelAnalyzingFunctionTable: Returns the GOFrontEnd for the given selectionPath, if it exists, otherwise returns null.
getGOFrontEndHashKeyForSelectionPath(TreePath) - Method in class biggests.gui.PanelAnalyzingFunctionTable: Returns the hashtable key for the GOFrontEnd of the given selectionPath.
getHeaderRendererIcon(int, int) - Method in class biggests.tables.TableSorter: Returns the Icon corresponding to the sorting status of the given column.
getHeatmapColorScheme() - Static method in class biggests.utils.HeatmapColorScheme
getHelp() - Method in class biggests.gui.BiggestsFrame: Returns the about menu.
getHighlySignificantColor() - Method in class biggests.tables.TableFunctionIndividual: Returns the Color used to mark highly significant terms.
getHighlySignificantColor(Color) - Method in class biggests.tables.TableFunctionIndividual: Sets a new color to mark highly significant terms.
getHighlySignificantPValueThreshold() - Method in class biggests.tables.TableFunctionIndividual: Returns the p-value threshold for highly significant gene ontology terms.
getIconHeight() - Method in class biggests.utils.Arrow: Returns the height of the arrow icon.
getIconHeight() - Method in class biggests.utils.VerticalTextIcon: Returns the icon's height.
getIconWidth() - Method in class biggests.utils.Arrow: Returns the width of the arrow icon.
getIconWidth() - Method in class biggests.utils.VerticalTextIcon: Returns the icon's width.
getId() - Method in class biggests.tree.Dataset: Returns the dataset id.
getId() - Method in class biggests.tree.NodeInfo: Returns the number id of the NodeInfo object.
getInfo() - Method in class biggests.tree.NodeInfo: Returns a styled document containing information about this node.
getInfoStrings() - Method in class biggests.tree.NodeInfo: Returns information strings.
getInfoStyles() - Method in class biggests.tree.NodeInfo: Returns information styles.
getInvalidDirectoryPaths() - Method in class biggests.utils.FileFilterDirectory: Returns this file filter invalid directory paths.
getLabelContext() - Method in class biggests.gui.BiggestsFrame: Returns the context label, which displays tips about functionality options to user.
getLastBiclusterGroupId() - Method in class biggests.tree.Dataset: Returns the last id given to a bicluster group node information object within the current dataset.
getLastDiscretizedId() - Method in class biggests.tree.Dataset: Returns the last id given to a discretized node information object within the current dataset.
getLastPostprocessedGroupId() - Method in class biggests.tree.Dataset: Returns the last id given to a post-processed group node information object within the current dataset.
getLastPreprocessedId() - Method in class biggests.tree.Dataset: Returns the last id given to a preprocessed node information object within the current dataset.
getLeft() - Method in class biggests.clustering.ClusterTreeNode: Returns the index of the left element or node (left son).
getMainFrame() - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph: Returns the application's main frame.
getMainFrame() - Method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the application's main frame.
getMainFrame() - Method in class biggests.gui.PanelBiclustering: Returns the application's main frame.
getMainFrame() - Method in class biggests.gui.PanelExpression: Returns the application's main frame, where this panel is being displayed.
getMainFrame() - Method in class biggests.gui.PanelFunctionAnalysis: Returns the application's main frame.
getMainFrame() - Method in class biggests.gui.PanelPostProcessing: Returns the frame of the application.
getMainFrame() - Method in class biggests.gui.PanelPreProcessing: Returns the application's main frame.
getMarkovChainOrderFilterTextField() - Method in class biggests.gui.PanelPostProcessing: Returns Markov chain order input text field.
getMarkovChainOrderSortTextField() - Method in class biggests.gui.PanelPostProcessing: Returns Markov chain order input text field.
getMeanValue() - Method in class biggests.tables.TableColors: Returns the mean value of the float values in the table.
getMeanValueColor() - Static method in class biggests.utils.HeatmapColorScheme
getMenu() - Method in class biggests.gui.BiggestsFrame: Returns the application's menu bar.
getMessageHistory() - Method in class biggests.utils.ProgressBarFrame: Returns message history.
getMissingValue() - Method in class biggests.tables.TableColorsWithMissingValues: Returns the value used to mark cells which correspond to missing values on the original gene expression data.
getMissingValueColor() - Static method in class biggests.utils.HeatmapColorScheme
getMSRTextField() - Method in class biggests.gui.PanelPostProcessing: Returns MSR threshold input text field.
getName() - Method in class biggests.tree.Dataset: Returns the name of this dataset.
getName() - Method in class biggests.tree.NodeInfo: Returns the name of this node information object.
getNeighborsECCCLabel() - Method in class biggests.gui.PanelBiclustering: Label for the number of neighbors on e-CCC-Biclustering algorithm.
getNeighborsECCCTextField() - Method in class biggests.gui.PanelBiclustering: Text field for the input of number of neighbors for e-CCC-Biclustering algorithm.
getNodeInfo() - Method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the node information object containing the object with the data to display in the table.
getNodeObject() - Method in class biggests.gui.PanelAnalyzingFunctionTable: Returns the bicluster group that is being processed.
getNodeObject() - Method in class biggests.tree.NodeInfo: Returns the node object associated with the current node information object.
getNodeObjectType() - Method in class biggests.tree.NodeInfo: Returns the node object type.
getNormalize() - Method in class biggests.gui.PanelExpression: Returns the check box which allows the user to choose between an expression chart with original or normalized data.
getNormalizeButtonGroup() - Method in class biggests.gui.PanelPreProcessing: Returns normalize options button group.
getNormalizeByGeneButton() - Method in class biggests.gui.PanelPreProcessing: Returns normalize by gene button.
getNormalizeCheckBox() - Method in class biggests.gui.PanelPreProcessing: Returns normalize check box.
getNormalizeMean0Std1Button() - Method in class biggests.gui.PanelPreProcessing: Returns normalize to mean 0 and std 1 button.
getNormalizeMeanStdButtonGroup() - Method in class biggests.gui.PanelPreProcessing: Returns normalize to mean and std options button group.
getNormalizeMeanStdValuesButton() - Method in class biggests.gui.PanelPreProcessing: Returns normalize by mean and std values button.
getNormalizeMeanStdValuesLabel() - Method in class biggests.gui.PanelPreProcessing: Returns normalize to mean and std values label.
getNormalizeMeanValueTextField() - Method in class biggests.gui.PanelPreProcessing: Return normalize mean input text field.
getNormalizeOverallButton() - Method in class biggests.gui.PanelPreProcessing: Returns normalize overall values button.
getNormalizeStdValueTextField() - Method in class biggests.gui.PanelPreProcessing: Returns normalize std input text field.
getNumberOfDendrograms() - Static method in class biggests.gui.PanelAnalyzingMatrixDendrogram
getOddRowsColor() - Method in class biggests.tables.TableFunctionGroup: Returns the Color used to mark odd rows that are not selected.
getOddRowsColor() - Method in class biggests.tables.TableFunctionIndividual: Returns the Color used to mark odd rows that are not selected.
getOption() - Method in class biggests.gui.PanelExpression: Returns the combo box for the user to choose the number of biclusters to display.
getOrganism() - Method in class biggests.gui.PanelFunctionAnalysis: Returns the organism related with this function analysis.
getOrganismLabel() - Method in class biggests.gui.PanelFunctionAnalysis: Returns the organism label.
getPanelAnalyzingExpressionAllTimePoints() - Method in class biggests.gui.BiggestsFrame: Returns the expression analysis by all time points chart panel.
getPanelAnalyzingFunctionSignificanceGraph() - Method in class biggests.gui.BiggestsFrame: Returns the function analysis - significance graph panel.
getPanelAnalyzingFunctionTable() - Method in class biggests.gui.BiggestsFrame: Returns the function analysis - table panel.
getPanelAnalyzingMatrixColors() - Method in class biggests.gui.BiggestsFrame: Returns the matrix analysis by colors panel.
getPanelAnalyzingMatrixDendrogram() - Method in class biggests.gui.BiggestsFrame: Returns the matrix analysis by dendrogram panel.
getPanelAnalyzingMatrixSymbols() - Method in class biggests.gui.BiggestsFrame: Returns the matrix analysis by symbols panel.
getPanelAnalyzingMatrixValues() - Method in class biggests.gui.BiggestsFrame: Returns the matrix analysis by values panel.
getPanelBiclustering() - Method in class biggests.gui.BiggestsFrame: Returns biclustering panel.
getPanelContent() - Method in class biggests.gui.BiggestsFrame: Returns this frames' content panel.
getPanelExpressionBiclusterPattern() - Method in class biggests.gui.BiggestsFrame: Returns the expression analysis by bicluster pattern chart panel.
getPanelExpressionBiclusterTimePoints() - Method in class biggests.gui.BiggestsFrame: Returns the expression analysis by bicluster time points chart panel.
getPanelLoading() - Method in class biggests.gui.BiggestsFrame: Returns the loading panel.
getPanelPreProcessing() - Method in class biggests.gui.BiggestsFrame: Returns preprocessing panel.
getPanelRight() - Method in class biggests.gui.BiggestsFrame: Returns the panel on the right, which holds the tabs and visualization panels.
getPanels() - Method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the set of panels which holds the tables and their headers, which are displayed in this panel (for COLORS and SYMBOLS tableTypes only).
getParentNodeInfo() - Method in class biggests.tree.NodeInfo: Returns parent node information object.
getPathsToFolders() - Method in class biggests.gui.BiggestsFrame: Returns the paths to function results, gene ontology files and sessions.
getPathToDatasets() - Method in class biggests.gui.BiggestsFrame: Returns the path to the directory with dataset files.
getPathToDOT() - Method in class biggests.gui.BiggestsFrame: Returns the path to dot binary file.
getPathToFunctionResults() - Method in class biggests.gui.BiggestsFrame: Returns the path to function results' folder/directory.
getPathToGO_Files() - Method in class biggests.gui.BiggestsFrame: Returns the path to gene ontology files folder/directory.
getPathToImage() - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph: Returns the path to image.
getPathToSessions() - Method in class biggests.gui.BiggestsFrame: Returns the path to stored session files folder/directory.
getPathToSvg() - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph: Returns the path to svg.
getProgressBar() - Method in class biggests.utils.ProgressBarFrame: Returns the progress bar.
getPvalueLabel() - Method in class biggests.gui.PanelFunctionAnalysis: Returns p-value label.
getPvalueTextField() - Method in class biggests.gui.PanelFunctionAnalysis: Returns text field for the input of a p-value.
getRestrictedErrorsECCCCheckBox() - Method in class biggests.gui.PanelBiclustering: Returns restricted errors for e-CCC-Biclustering algorithm check box.
getRight() - Method in class biggests.clustering.ClusterTreeNode: Returns the index of the right element or node (right son).
getRoot() - Method in class biggests.tree.DatasetTree: Returns the root node of the dataset tree.
getRowCount() - Method in class biggests.tables.TableSorter: Returns the number of rows in the table model.
getScrollAnalyzingExpressionAllTimePoints() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which holds the expression analysis - all time points chart panel.
getScrollAnalyzingExpressionBiclusterPattern() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which holds the expression analysis - bicluster pattern chart panel.
getScrollAnalyzingExpressionBiclusterTimePoints() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which holds the expression analysis - bicluster time points chart panel.
getScrollAnalyzingFunctionSignificanceGraph() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which holds the function analysis - significance graph panel.
getScrollAnalyzingFunctionTable() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which holds the function analysis - table of functions panel.
getScrollAnalyzingMatrixColors() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which holds the matrix analysis by colors panel.
getScrollAnalyzingMatrixSymbols() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which holds the matrix analysis by symbols panel.
getScrollAnalyzingMatrixValues() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which holds the matrix analysis by values panel.
getScrollBiclustering() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which scrolls biclustering panel.
getScrollInfo() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which scrolls information text pane.
getScrollLoading() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which scrolls loading panel.
getScrollPreProcessing() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which scrolls preprocessing panel.
getScrolls() - Method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the array with the scroll panes that hold the tables to be displayed (for VALUES tableType only).
getScrollTree() - Method in class biggests.gui.BiggestsFrame: Returns the scroll pane which scrolls the dataset tree.
getSelectionPath() - Method in class biggests.gui.PanelAnalyzingFunctionTable: Returns the tree selection path that corresponds to the bicluster or bicluster group that is being processed.
getSelectionPath() - Method in class biggests.gui.PanelBiclustering: Returns the dataset tree selected path which corresponds to the path of the dataset which in turn leads to the node with the matrix on which biclustering algorithm will be performed.
getSelectionPath() - Method in class biggests.gui.PanelFunctionAnalysis: Returns the dataset tree selected path which corresponds to the path of the dataset which in turn leads to the node with the matrix on which biclustering algorithm will be performed.
getSelectionPath() - Method in class biggests.gui.PanelPostProcessing: Rreturns the selected path in the dataset tree.
getSelectionPath() - Method in class biggests.gui.PanelPreProcessing: Returns the path selected on the dataset tree.
getSetOfBiclusters() - Method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the set of biclusters from which the set of tables is constructed.
getSetOfBiclusters() - Method in class biggests.gui.PanelExpression: Returns the set of biclusters retrieved from the group of biclusters to display.
getShiftsLabel() - Method in class biggests.gui.PanelBiclustering: Returns the label for number of shifts for CCC-Biclustering and e-CCC-Biclustering algorithms.
getShiftsTextField() - Method in class biggests.gui.PanelBiclustering: Returns the text field for the input of CCC-Biclustering and e-CCC-Biclustering algorithms number of shifts.
getSignificantColor() - Method in class biggests.tables.TableFunctionGroup: Returns the Color used to mark significant terms.
getSignificantColor() - Method in class biggests.tables.TableFunctionIndividual: Returns the Color used to mark significant terms.
getSignificantPValueThreshold() - Method in class biggests.tables.TableFunctionIndividual: Returns the p-value threshold for significant gene ontology terms.
getSimilarityTextField() - Method in class biggests.gui.PanelPostProcessing: Returns the similarity threshold input text field.
getSizeTextField() - Method in class biggests.gui.PanelPostProcessing: Returns the size threshold input text field.
getSmoothCheckBox() - Method in class biggests.gui.PanelPreProcessing: Returns smooth check box.
getSmoothWindowLabel() - Method in class biggests.gui.PanelPreProcessing: Returns smooth window label.
getSmoothWindowTextField() - Method in class biggests.gui.PanelPreProcessing: Returns smooth window input text field.
getSortCheckBox() - Method in class biggests.gui.PanelPostProcessing: Returns enabling/disabling sorting option check box.
getSortCriteria() - Method in class biggests.gui.PanelPostProcessing
getSortCriteriaLabel() - Method in class biggests.gui.PanelPostProcessing: Returns the sorting criteria label.
getSortCriteriaList() - Method in class biggests.gui.PanelPostProcessing: Returns sorting criteria list.
getSortingStatus(int) - Method in class biggests.tables.TableSorter: Returns the sorting status of the given column: DESCENDING NOT_SORTED ASCENDING
getSortPanel() - Method in class biggests.gui.PanelPostProcessing: Returns the panel with the sorting options.
getSplitLeftRight() - Method in class biggests.gui.BiggestsFrame: Returns the left-right split pane.
getSplitTopBottom() - Method in class biggests.gui.BiggestsFrame: Returns the top-bottom split pane.
getSpringLayout() - Method in class biggests.gui.PanelBiclustering: Returns the layout of this panel.
getSpringLayout() - Method in class biggests.gui.PanelPreProcessing: Returns the layout of this panel.
getStop() - Static method in class biggests.gui.BiggestsIO: Returns the value of stop flag.
getString() - Method in class biggests.utils.ProgressBarFrame: Returns the message displayed by the progress bar.
getSvgGraph() - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph: Returns the swing-based component which holds the svg graph.
getTabbedPane() - Method in class biggests.gui.BiggestsFrame: Returns the main tabbed pane.
getTabbedPaneAnalyzing() - Method in class biggests.gui.BiggestsFrame: Returns the analysis tabbed pane.
getTabbedPaneAnalyzingExpression() - Method in class biggests.gui.BiggestsFrame: Returns the expression analysis tabbed pane.
getTabbedPaneAnalyzingFunction() - Method in class biggests.gui.BiggestsFrame: Returns the function analysis tabbed pane.
getTabbedPaneAnalyzingMatrix() - Method in class biggests.gui.BiggestsFrame: Returns the matrix analysis tabbed pane.
getTableHeader() - Method in class biggests.tables.TableSorter: Returns the table header.
getTableModel() - Method in class biggests.tables.TableSorter: Returns the table model.
getTables() - Method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the array which contains the tables to be displayed (may contain TableValuess, TableColorss and TableSymbolss, depending on the tableType).
getTableType() - Method in class biggests.gui.PanelAnalyzingMatrixTables: Returns the type of the tables presented in the panel.
getTextPaneInfo() - Method in class biggests.gui.BiggestsFrame: Returns the information text pane, which displays informations about the selected datasets, matrices or biclusters in the tree.
getToolTipText(MouseEvent) - Method in class biggests.tables.TableColorsWithMissingValues: Overrides TableValues's getToolTipText method in order to allow the renderer's tips to be used if they have text set.
getToolTipText(MouseEvent) - Method in class biggests.tables.TableFunctionGroup: Overrides JTable's getToolTipText method in order to allow the renderer's tips to be used if they have text set.
getToolTipText(MouseEvent) - Method in class biggests.tables.TableFunctionIndividual: Overrides JTable's getToolTipText method in order to allow the renderer's tips to be used if they have text set.
getToolTipText(MouseEvent) - Method in class biggests.tables.TableHeader: Overrides JTableHeader's getToolTipText method.
getToolTipText(MouseEvent) - Method in class biggests.tables.TableHeaderFunction: Overrides JTableHeader's getToolTipText method.
getToolTipText(MouseEvent) - Method in class biggests.tables.TableValues: Overrides JTable's getToolTipText method in order to allow the renderer's tips to be used if they have text set.
getToolTipText(MouseEvent) - Method in class biggests.tables.TableValuesWithMissingValues: Overrides TableValues's getToolTipText method in order to allow the renderer's tips to be used if they have text set.
getTree() - Method in class biggests.gui.BiggestsFrame: Returns the dataset tree object.
getValidFileExtension() - Method in class biggests.utils.FileFilterDirectory: Returns this file filter valid file extension.
getValidFileExtension() - Method in class biggests.utils.FileFilterExtension: Returns this file filter valid file extension.
getValueAt(int, int) - Method in class biggests.tables.TableSorter: Returns the element in the cell at row and column indexes.
getVisualizationOption() - Method in class biggests.gui.PanelExpression: Returns visualization options (number of biclusters to be displayed) to include in a combo box when the expression type is either BICLUSTER_TIME_POINTS or PATTERN and the corresponding object is a group of biclusters.
getZoom() - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph: Returns the current zoom scale factor.
getZoomSlider() - Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph: Returns the zoom slider.
GIF - Static variable in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph: GIF image type.
goFrontEnd - Variable in class biggests.tables.TableValues
goFrontEndCheckBox_itemStateChanged(ItemEvent) - Method in class biggests.gui.PanelFunctionAnalysis
goProperties - Variable in class biggests.tables.TableValues
gunzipFile(File, File) - Static method in class biggests.gui.BiggestsIO: Gunzips the input archive.




H

HeatmapColorScheme - Class in biggests.utils
Title: 

 Description: 

 Copyright: Copyright (c) 2006

 Company: 
HeatmapColorScheme() - 
Constructor for class biggests.utils.HeatmapColorScheme
 
helpAbout_actionPerformed(ActionEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks Help -> About item menu.
HierarchicalClustering - Class in biggests.clustering
Title: Hierarchical Clustering

 Description: This class implements Hierarchical Clustering over
                 expression data.
HierarchicalClustering(IMatrix) - 
Constructor for class biggests.clustering.HierarchicalClustering
Creates a new HierarchicalClustering object to
 perform hierarchical clustering over the set of gene expression
 data contained in expressionMatrix.
HierarchicalClustering(int, int, double[], double[], double[], double[], int[], int[], String, String[], String[], String[], double[][], int[][]) - 
Constructor for class biggests.clustering.HierarchicalClustering
Creates a new HierarchicalClustering object to
 perform hierarchical clustering over the given set of
 expression data.
hierarchicalClusteringTempFilesDirectoryPath - 
Static variable in class biggests.gui.PanelAnalyzingMatrixDendrogram
 
hierarchicalClusteringWithFileOutput(char, char, char, String) - 
Method in class biggests.clustering.HierarchicalClustering
Performs hierarchical clustering over this set of data and writes
 output information in corresponding files (.GTR, .ATR, .CDT).
hierarchicalClusteringWithTreeOutput(double[][], int[][], double[], boolean, char, char, double[][]) - 
Method in class biggests.clustering.HierarchicalClustering
Performs hierarchical clustering using pairwise single-, maximum-,
 centroid-, or average-linkage, as defined by
 clusteringMethod, on a given set of gene expression
 data, using the distance metric given by distanceMetric.
HIGHLY_SIGNIFICANT_COLOR - 
Static variable in class biggests.tables.TableFunctionIndividual
Default color for highly significant terms.



I

initDOT() - 
Static method in class biggests.utils.BiggestsInstall
Sets the path to Graphviz dot file executable.
initializeColors() - 
Method in class biggests.tables.TableSymbols
Initializes the array of colors to be used by prepareRenderer to
 color cells, when the table has to be displayed.
initializeFolders(String[]) - 
Static method in class biggests.gui.BiggestsIO
Creates a set of directories with the specified paths.
initializeGOFrontEnds() - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
 
inputMethodTextChanged(InputMethodEvent) - 
Method in class biggests.gui.PanelLoading_datasetFileTextField_inputMethodAdapter
 
installDOT() - 
Static method in class biggests.utils.BiggestsInstall
Initializes the path to dot binary file, according
 to the operating system BiGGEsTS is running on.
InvalidNodeObjectTypeException - Exception in biggests.utils
Title: 

 Description: 

 Copyright:   Copyright (C) 2007  Joana Gonçalves
                 This program is free software; you can redistribute
                 it and/or modify it under the terms of the GNU General
                 Public License as published by the Free Software
                 Foundation; either version 3 of the License, or
                 any later version.
InvalidNodeObjectTypeException() - 
Constructor for exception biggests.utils.InvalidNodeObjectTypeException
Constructs a new instance of InvalidNodeObjectTypeException.
InvalidNodeObjectTypeException(String) - 
Constructor for exception biggests.utils.InvalidNodeObjectTypeException
Constructs a new instance of InvalidDataTypeException
 with the given information message.
isCellEditable(int, int) - 
Method in class biggests.tables.TableSorter
Checks if the cell with the given row and
 column indexes is editable.
isGeneID() - 
Method in class biggests.tree.NodeInfo
Returns genes' names type.
isSorting() - 
Method in class biggests.tables.TableSorter
Checks if the table is sorting.
isSvgBuilded() - 
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
Checks if the gvt tree for the svg document is already built.
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelAnalyzingMatrixDendrogram_clusterConditionsCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelAnalyzingMatrixDendrogram_clusterGenesCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelAnalyzingMatrixTables_biclustersNumberOption_itemAdapter
Associates the specific handler for the item state event fired by
 the user's selection on the biclusters number option combo box with
 the general item state changed event handler.
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelBiclustering_geneShiftsCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelBiclustering_restrictedErrorsECCCCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelBiclustering_signChangesCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelBiclustering_timeLagsCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelExpression_normalize_itemAdapter
Handles the event fired by the selection in the normalize check box.
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelExpression_option_itemAdapter
Handles the event fired by the selection in the option combo box.
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelFunctionAnalysis_goFrontEndCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelLoading_geneIDCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPostProcessing_filterCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPostProcessing_sortCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_discretizeCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_discretizeComboBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_fillAverageRowButton_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_fillCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_fillKNeighborsButton_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_fillValueButton_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_filterCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_filterPercentGenesButton_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_normalizeByGeneButton_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_normalizeCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_normalizeMean0Std1Button_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_normalizeMeanStdValuesButton_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_normalizeOverallButton_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing_smoothCheckBox_itemAdapter
 
itemStateChanged(ItemEvent) - 
Method in class biggests.gui.SaveChartImageDialog_displayedSizeRadioButton_itemAdapter
 



J

jbInit() - 
Method in class biggests.gui.SaveChartImageDialog
Initializes GUI components.
JPG - 
Static variable in class biggests.gui.BiggestsIO
Image format: JPG
JVMInfo - Class in biggests.utils
Title: JVM Info

 Description: Provides methods to get information about the JVM in
                 which this code is being executed.
JVMInfo() - 
Constructor for class biggests.utils.JVMInfo
 



K

kBufferSpace - 
Static variable in class biggests.utils.VerticalTextIcon
Buffer size.
KENDALL_TAU_CORRELATION - 
Static variable in class biggests.clustering.AbstractMetricClustering
Kendall's tau correlation (distance metric).
kendallsTauCorrelation(double[][], double[][], int[][], int[][], double[], int, int, boolean) - 
Static method in class biggests.clustering.AbstractMetricClustering
Computes Kendall's Tau distance between two rows or two columns.



L

LEGAL_MUST_ROTATE - 
Static variable in class biggests.utils.VerticalTextIcon
Valid must rotate rotations.
LEGAL_ROMAN - 
Static variable in class biggests.utils.VerticalTextIcon
Valid roman's rotations.
LEXICAL_COMPARATOR - 
Static variable in class biggests.tables.TableSorter
The lexical comparator.
loadButton_actionPerformed(ActionEvent) - 
Method in class biggests.gui.PanelLoading
Handles the mouse event fired by a user's click on load button.



M

main(String[]) - 
Static method in class biggests.gui.BiggestsApplication
Application entry point.
main(String[]) - 
Static method in class biggests.utils.BiggestsInstall
Installs Graphviz dot executable or checks and sets the given
 dot filepath.
main(String[]) - 
Static method in class biggests.utils.JVMInfo
The main method.
mainFrame - 
Variable in class biggests.gui.PanelAnalyzingMatrixTables
The application's main frame.
mainFrame - 
Variable in class biggests.gui.PanelExpression
The application's main frame, where this panel is being displayed.
MAX_HEIGHT - 
Static variable in class biggests.gui.BiggestsIO
Maximum image height.
MAX_ITERATIONS - 
Static variable in class biggests.gui.PanelBiclustering
Name of the 'maximum number of iterations' parameter
 (CC-TSB-biclustering).
MAX_TIME_LAG - 
Static variable in class biggests.gui.PanelBiclustering
Maximum time lag.
MAX_WIDTH - 
Static variable in class biggests.gui.BiggestsIO
Maximum image width.
meanValue - 
Variable in class biggests.tables.TableColors
The mean of the node object matrix's values.
missingsMask - 
Variable in class biggests.clustering.AbstractMetricClustering
Missing values mask.
missingValue - 
Variable in class biggests.tables.TableValuesWithMissingValues
The value used to fill missing values.
modelIndex(int) - 
Method in class biggests.tables.TableSorter
Returns the model index for a given viewIndex.
mouseClicked(MouseEvent) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable_functionGroupTable_mouseAdapter
 
mouseClicked(MouseEvent) - 
Method in class biggests.gui.PanelBiclustering_allowMissingsButton_mouseAdapter
 
mouseClicked(MouseEvent) - 
Method in class biggests.tables.TableFunctionIndividual_this_mouseAdapter
 
mouseClicked(MouseEvent) - 
Method in class biggests.tables.TableValues_this_mouseAdapter
 
mouseListener - 
Variable in class biggests.tables.TableSorter
The mouse listener of the table.
MyTreeViewApp - Class in biggests.gui
Title: 

 Description: 

 Copyright:   Copyright (C) 2007  Joana Gonçalves
                 This program is free software; you can redistribute
                 it and/or modify it under the terms of the GNU General
                 Public License as published by the Free Software
                 Foundation; either version 2 of the License, or
                 any later version.
MyTreeViewApp() - 
Constructor for class biggests.gui.MyTreeViewApp
Creates a new MyTreeViewApp to present results of
 hierarchical clustering over a set of expression data.
MyTreeViewApp(XmlConfig) - 
Constructor for class biggests.gui.MyTreeViewApp
Constructor for MyTreeViewApp object.



N

NEIGHBORS - 
Static variable in class biggests.gui.PanelBiclustering
Name of the 'neighbors' parameter (e-CCC-Biclustering).
NINETY_DEGREES - 
Static variable in class biggests.utils.VerticalTextIcon
Ninety degrees rotation.
NO_CLUSTERING - 
Static variable in class biggests.clustering.AbstractMetricClustering
No clustering (distance metric).
NodeInfo - Class in biggests.tree
Title: Node Information Object

 Description: Contains information about the content of a
                 specific node in the dataset tree.
NodeInfo(NodeObjectInterface, int, TreePath, DatasetTree, NodeInfo, ArrayList<String>, ArrayList<String>, int) - 
Constructor for class biggests.tree.NodeInfo
Constructs an object of type NodeInfo (with all the information about
 a certain node, including a pointer for the node object itself.
NodeInfo(NodeObjectInterface, int, TreePath, DatasetTree, NodeInfo, ArrayList<String>, ArrayList<String>) - 
Constructor for class biggests.tree.NodeInfo
Constructs an object of type NodeInfo (with all the information about
 a certain node, including a pointer for the node object itself.
normalize_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelExpression
Checks the option selected by the user in the normalize check box.
NORMALIZE_MEAN - 
Static variable in class biggests.gui.PanelPreProcessing
'Mean value to normalize expression data' parameter name.
NORMALIZE_STD - 
Static variable in class biggests.gui.PanelPreProcessing
'Std value to normalize expression data' parameter name.
normalizeByGeneButton_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects
 the normalize by gene radio button.
normalizeCheckBox_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user
 selects/deselects the normalize check box.
normalizeMean0Std1Button_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects
 the normalize by mean 0 and std 1 radio button.
normalizeMeanStdValuesButton_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects
 the normalize by mean and std values radio button.
normalizeOverallButton_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user selects
 the normalize overall values radio button.
NOT_SORTED - 
Static variable in class biggests.tables.TableSorter
The status that indicates that a specific column is not sorted.
NUMBER_OF_BICLUSTERS - 
Static variable in class biggests.gui.PanelBiclustering
Name of the 'number of biclusters' parameter (CC-TSB-biclustering).
NUMBER_OF_ERRORS - 
Static variable in class biggests.gui.PanelBiclustering
Name of the 'number of errors' parameter (e-CCC-Biclustering).
numberOfConditions - 
Variable in class biggests.clustering.AbstractMetricClustering
The number of conditions (microarrays) in the experiment.
numberOfGenes - 
Variable in class biggests.clustering.AbstractMetricClustering
The number of genes in the experiment.



O

ODD_ROWS_COLOR - 
Static variable in class biggests.tables.TableFunctionGroup
Default color to user in odd rows (when they are not selected).
ODD_ROWS_COLOR - 
Static variable in class biggests.tables.TableFunctionIndividual
Default color for odd rows.
OLIGO - 
Static variable in class biggests.gui.PanelLoading
Type of gene expression data: oligonucleotides.
option_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelExpression
Checks the option selected by the user in the "number of
 biclusters to display" combo box.
organisms - 
Static variable in class biggests.gui.PanelFunctionAnalysis
Set of organisms to display in organism combo box.
ORIGINAL - 
Static variable in class biggests.tree.NodeInfo
The original node object type.



P

paint(Bicluster, TreePath) - 
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
Paints this panel with a table of functions for the genes
 in bicluster.
paint(IMatrix, TreePath) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Paints a table of functions with data retrieved from the given
 expressionMatrix.
paint(GeneSetResult, GOFrontEnd, String[], float) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Paints a function table with the GO terms annotated for all the
 genes of the experiment.
paint(Bicluster, GeneSetResult, float, TreePath) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Paints the functions table in this panel, with data retrieved from
 bicluster object.
paint(Biclustering, TreePath, Hashtable<Integer, BiologicalRelevanceSummary>) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Paints this panel with a table of faunctions for the given
 biclustering (biclusters' group).
paint(IMatrix) - 
Method in class biggests.gui.PanelAnalyzingMatrixDendrogram
Paints this panel to perform hierarchical clustering over
 an expression matrix.
paint(NodeInfo, TreePath) - 
Method in class biggests.gui.PanelAnalyzingMatrixTables
Creates and displays the tables with data retrieved from the
 node object associated with the given node info object.
paint(DiscretizedExpressionMatrix, TreePath) - 
Method in class biggests.gui.PanelBiclustering
Paints this biclustering panel with options to perform biclustering
 on the discretizedExpressionMatrix and options to
 perform function analysis.
paint(TreePath) - 
Method in class biggests.gui.PanelFunctionAnalysis
Paints the panel with information from the given
 selectionPath.
paint(Biclustering, TreePath) - 
Method in class biggests.gui.PanelPostProcessing
Paints post-processing panel with post-processing options for a
 specific biclusters group and tree selection path.
paint(ExpressionMatrix, TreePath) - 
Method in class biggests.gui.PanelPreProcessing
Paints this preprocessing panel with the preprocessing options
 related with a given expressionMatrix.
paintAgain() - 
Method in class biggests.gui.PanelAnalyzingMatrixTables
 
paintAllTimePointsChart(NodeInfo, NodeInfo) - 
Method in class biggests.gui.PanelExpression
Paints an expression chart which data consists of the gene expression
 values for the genes in a specific nodeInfo matrix object
 under all conditions of a specific parentNodeInfo matrix
 object.
paintBasic() - 
Method in class biggests.gui.PanelPostProcessing
 
paintBiclusteringAlgorithmPanelWithCCC() - 
Method in class biggests.gui.PanelBiclustering
Paints biclustering algorithm panel with CCC-Biclustering algorithm.
paintBiclusteringAlgorithmPanelWithCCTSB() - 
Method in class biggests.gui.PanelBiclustering
Paints biclustering algorithm panel with CC-TSB-Biclustering algorithm.
paintBiclusteringAlgorithmPanelWithECCC() - 
Method in class biggests.gui.PanelBiclustering
Paints biclustering algorithm panel with E-CCC-Biclustering algorithm.
paintBiclusterPatternCharts(NodeInfo) - 
Method in class biggests.gui.PanelExpression
Paints one bicluster / set of bicluster pattern charts.
paintBiclusterTimePointsCharts(NodeInfo) - 
Method in class biggests.gui.PanelExpression
Paints one or a set of bicluster time points charts.
paintDiscrete() - 
Method in class biggests.gui.PanelPostProcessing
Paints post-processing object for biclusters groups with discrete data.
paintFloat() - 
Method in class biggests.gui.PanelPostProcessing
 
paintIcon(Component, Graphics, int, int) - 
Method in class biggests.utils.Arrow
Paints the arrow.
paintIcon(Component, Graphics, int, int) - 
Method in class biggests.utils.VerticalTextIcon
Draws the icon at the specified location.
paintIcon(Component, Graphics, int, int) - 
Method in class biggests.utils.VerticalTextIconWithArrow
Draws the icon at the specified location.
PanelAnalyzingFunctionSignificanceGraph - Class in biggests.gui
Title: Function Analysis - Significance Graph Panel

 Description: Displays a significance graph of a bicluster.
PanelAnalyzingFunctionSignificanceGraph(BiggestsFrame) - 
Constructor for class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
Creates a new function analysis - significance graph panel.
PanelAnalyzingFunctionSignificanceGraph_saveGraph_actionAdapter - Class in biggests.gui
Title: 

 Description: 
PanelAnalyzingFunctionSignificanceGraph_saveGraph_actionAdapter(PanelAnalyzingFunctionSignificanceGraph) - 
Constructor for class biggests.gui.PanelAnalyzingFunctionSignificanceGraph_saveGraph_actionAdapter
 
PanelAnalyzingFunctionSignificanceGraph_zoomSlider_changeAdapter - Class in biggests.gui
Title: 

 Description: 
PanelAnalyzingFunctionSignificanceGraph_zoomSlider_changeAdapter(PanelAnalyzingFunctionSignificanceGraph) - 
Constructor for class biggests.gui.PanelAnalyzingFunctionSignificanceGraph_zoomSlider_changeAdapter
 
PanelAnalyzingFunctionTable - Class in biggests.gui
Title: Panel for Analyzing Tables of Functions

 Description: Displays a table of functions of a bicluster
                 or group of biclusters.
PanelAnalyzingFunctionTable(BiggestsFrame) - 
Constructor for class biggests.gui.PanelAnalyzingFunctionTable
Creates a new PanelAnalyzingFunctionTable.
PanelAnalyzingFunctionTable_applyButton_actionAdapter - Class in biggests.gui
 
PanelAnalyzingFunctionTable_applyButton_actionAdapter(PanelAnalyzingFunctionTable) - 
Constructor for class biggests.gui.PanelAnalyzingFunctionTable_applyButton_actionAdapter
 
PanelAnalyzingFunctionTable_functionGroupTable_mouseAdapter - Class in biggests.gui
 
PanelAnalyzingFunctionTable_functionGroupTable_mouseAdapter(PanelAnalyzingFunctionTable) - 
Constructor for class biggests.gui.PanelAnalyzingFunctionTable_functionGroupTable_mouseAdapter
 
PanelAnalyzingFunctionTable_recalculate_actionAdapter - Class in biggests.gui
 
PanelAnalyzingFunctionTable_recalculate_actionAdapter(PanelAnalyzingFunctionTable) - 
Constructor for class biggests.gui.PanelAnalyzingFunctionTable_recalculate_actionAdapter
 
PanelAnalyzingMatrixDendrogram - Class in biggests.gui
Title: Panel for Analyzing Matrix Dendrograms

 Description: Allows the user to parameterize and apply
                 hierarchical clustering algorithms to obtain a
                 hierarchical representation of the gene expression
                 data, a dendrogram.
PanelAnalyzingMatrixDendrogram(BiggestsFrame) - 
Constructor for class biggests.gui.PanelAnalyzingMatrixDendrogram
Creates a new PanelAnalyzingMatrixDendrogram with options
 to perform hierarchical clustering over a set of expression
 data.
PanelAnalyzingMatrixDendrogram_applyButton_actionAdapter - Class in biggests.gui
 
PanelAnalyzingMatrixDendrogram_applyButton_actionAdapter(PanelAnalyzingMatrixDendrogram) - 
Constructor for class biggests.gui.PanelAnalyzingMatrixDendrogram_applyButton_actionAdapter
 
PanelAnalyzingMatrixDendrogram_clusterConditionsCheckBox_itemAdapter - Class in biggests.gui
 
PanelAnalyzingMatrixDendrogram_clusterConditionsCheckBox_itemAdapter(PanelAnalyzingMatrixDendrogram) - 
Constructor for class biggests.gui.PanelAnalyzingMatrixDendrogram_clusterConditionsCheckBox_itemAdapter
 
PanelAnalyzingMatrixDendrogram_clusterGenesCheckBox_itemAdapter - Class in biggests.gui
 
PanelAnalyzingMatrixDendrogram_clusterGenesCheckBox_itemAdapter(PanelAnalyzingMatrixDendrogram) - 
Constructor for class biggests.gui.PanelAnalyzingMatrixDendrogram_clusterGenesCheckBox_itemAdapter
 
PanelAnalyzingMatrixTables - Class in biggests.gui
Title: Matrix Analysis Tables Panel

 Description: Displays tables of real values, tables of colors
                 or tables of symbols for matrices, biclusters or
                 groups of biclusters.
PanelAnalyzingMatrixTables(BiggestsFrame, int) - 
Constructor for class biggests.gui.PanelAnalyzingMatrixTables
Creates a new panel to display tables.
PanelAnalyzingMatrixTables_biclustersNumberOption_itemAdapter - Class in biggests.gui
Title: 

 Description: 
PanelAnalyzingMatrixTables_biclustersNumberOption_itemAdapter(PanelAnalyzingMatrixTables) - 
Constructor for class biggests.gui.PanelAnalyzingMatrixTables_biclustersNumberOption_itemAdapter
 
PanelBasicIOValidation - Class in biggests.gui
Title: Panel with Basic Input/Output Validation

 Description: Extends JPanel class with some methods to
                 perform basic validations over data input by the user.
PanelBasicIOValidation() - 
Constructor for class biggests.gui.PanelBasicIOValidation
 
PanelBiclustering - Class in biggests.gui
Title: Biclustering Panel

 Description: Displays available biclustering techniques
                 and allows for setting their corresponding
                 parameters and apply them to the gene
                 expression data.
PanelBiclustering(BiggestsFrame) - 
Constructor for class biggests.gui.PanelBiclustering
Creates a new biclustering panel, with biclustering algorithms
 options.
PanelBiclustering_algorithmsList_listSelectionAdapter - Class in biggests.gui
Title: 

 Description: 
PanelBiclustering_algorithmsList_listSelectionAdapter(PanelBiclustering) - 
Constructor for class biggests.gui.PanelBiclustering_algorithmsList_listSelectionAdapter
 
PanelBiclustering_allowMissingsButton_mouseAdapter - Class in biggests.gui
 
PanelBiclustering_allowMissingsButton_mouseAdapter(PanelBiclustering) - 
Constructor for class biggests.gui.PanelBiclustering_allowMissingsButton_mouseAdapter
 
PanelBiclustering_applyButton_actionAdapter - Class in biggests.gui
 
PanelBiclustering_applyButton_actionAdapter(PanelBiclustering) - 
Constructor for class biggests.gui.PanelBiclustering_applyButton_actionAdapter
 
PanelBiclustering_geneShiftsCheckBox_itemAdapter - Class in biggests.gui
Title: 

 Description: 
PanelBiclustering_geneShiftsCheckBox_itemAdapter(PanelBiclustering) - 
Constructor for class biggests.gui.PanelBiclustering_geneShiftsCheckBox_itemAdapter
 
PanelBiclustering_restrictedErrorsECCCCheckBox_itemAdapter - Class in biggests.gui
Title: 

 Description: 
PanelBiclustering_restrictedErrorsECCCCheckBox_itemAdapter(PanelBiclustering) - 
Constructor for class biggests.gui.PanelBiclustering_restrictedErrorsECCCCheckBox_itemAdapter
 
PanelBiclustering_signChangesCheckBox_itemAdapter - Class in biggests.gui
 
PanelBiclustering_signChangesCheckBox_itemAdapter(PanelBiclustering) - 
Constructor for class biggests.gui.PanelBiclustering_signChangesCheckBox_itemAdapter
 
PanelBiclustering_timeLagsCheckBox_itemAdapter - Class in biggests.gui
 
PanelBiclustering_timeLagsCheckBox_itemAdapter(PanelBiclustering) - 
Constructor for class biggests.gui.PanelBiclustering_timeLagsCheckBox_itemAdapter
 
PanelExpression - Class in biggests.gui
Title: Expression Panel

 Description: Displays expression charts.
PanelExpression(BiggestsFrame, int) - 
Constructor for class biggests.gui.PanelExpression
Creates a new panel to display expression charts.
PanelExpression_normalize_itemAdapter - Class in biggests.gui
Title: 

 Description: 
PanelExpression_normalize_itemAdapter(PanelExpression) - 
Constructor for class biggests.gui.PanelExpression_normalize_itemAdapter
 
PanelExpression_option_itemAdapter - Class in biggests.gui
Title: 

 Description: 
PanelExpression_option_itemAdapter(PanelExpression) - 
Constructor for class biggests.gui.PanelExpression_option_itemAdapter
 
PanelExpression_this_hierarchyBoundsAdapter - Class in biggests.gui
 
PanelExpression_this_hierarchyBoundsAdapter(PanelExpression) - 
Constructor for class biggests.gui.PanelExpression_this_hierarchyBoundsAdapter
 
PanelExpressionChart - Class in biggests.gui
Title: Expression Chart Panel

 Description: A panel which holds an expression chart.
PanelExpressionChart(Bicluster, boolean, int, int, int, int, int, int, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - 
Constructor for class biggests.gui.PanelExpressionChart
Constructs a gene or pattern expression chart with the genes names,
 conditions names and gene expression data retrieved from the given
 bicluster.
PanelExpressionChart(String[], String[], float[][], float, int, int, int, int, int, int, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - 
Constructor for class biggests.gui.PanelExpressionChart
Constructs a gene expression chart with the given
 genesNames, conditionsNames and respective
 expressionValues
PanelExpressionChart(char[], char[], char, String[], int[], int, int, int, int, int, int, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - 
Constructor for class biggests.gui.PanelExpressionChart
Constructs a pattern expression chart based on the given
 expression pattern (sequence of symbols) within
 the given alphabet (set of symbols that can appear
 in pattern).
PanelFunctionAnalysis - Class in biggests.gui
Title: Function Analysis Panel

 Description: This panel displays function analysis options to
                 apply to a given bicluster or group of biclusters.
PanelFunctionAnalysis(BiggestsFrame) - 
Constructor for class biggests.gui.PanelFunctionAnalysis
Creates a new PanelFunctionAnalysis.
PanelFunctionAnalysis_browseGeneAssociationFilesPathButton_actionAdapter - Class in biggests.gui
 
PanelFunctionAnalysis_browseGeneAssociationFilesPathButton_actionAdapter(PanelFunctionAnalysis) - 
Constructor for class biggests.gui.PanelFunctionAnalysis_browseGeneAssociationFilesPathButton_actionAdapter
 
PanelFunctionAnalysis_browseGOFilesPathButton_actionAdapter - Class in biggests.gui
Title: 

 Description: 
PanelFunctionAnalysis_browseGOFilesPathButton_actionAdapter(PanelFunctionAnalysis) - 
Constructor for class biggests.gui.PanelFunctionAnalysis_browseGOFilesPathButton_actionAdapter
 
PanelFunctionAnalysis_downloadGeneAssociationFileButton_actionAdapter - Class in biggests.gui
 
PanelFunctionAnalysis_downloadGeneAssociationFileButton_actionAdapter(PanelFunctionAnalysis) - 
Constructor for class biggests.gui.PanelFunctionAnalysis_downloadGeneAssociationFileButton_actionAdapter
 
PanelFunctionAnalysis_downloadGeneOntologyFileButton_actionAdapter - Class in biggests.gui
 
PanelFunctionAnalysis_downloadGeneOntologyFileButton_actionAdapter(PanelFunctionAnalysis) - 
Constructor for class biggests.gui.PanelFunctionAnalysis_downloadGeneOntologyFileButton_actionAdapter
 
PanelFunctionAnalysis_goFrontEndCheckBox_itemAdapter - Class in biggests.gui
 
PanelFunctionAnalysis_goFrontEndCheckBox_itemAdapter(PanelFunctionAnalysis) - 
Constructor for class biggests.gui.PanelFunctionAnalysis_goFrontEndCheckBox_itemAdapter
 
PanelLoading - Class in biggests.gui
Title: Loading Panel

 Description: This panel displays options to load a
                 gene expression dataset, performs all the
                 necessary validation operations of the input and
                 loads the required data, adding the corresponding
                 nodes to the datasettree.
PanelLoading(BiggestsFrame) - 
Constructor for class biggests.gui.PanelLoading
Creates a new loading panel.
PanelLoading_browseConversionFileButton_actionAdapter - Class in biggests.gui
 
PanelLoading_browseConversionFileButton_actionAdapter(PanelLoading) - 
Constructor for class biggests.gui.PanelLoading_browseConversionFileButton_actionAdapter
 
PanelLoading_browseDatasetFileButton_actionAdapter - Class in biggests.gui
 
PanelLoading_browseDatasetFileButton_actionAdapter(PanelLoading) - 
Constructor for class biggests.gui.PanelLoading_browseDatasetFileButton_actionAdapter
 
PanelLoading_datasetFileTextField_caretAdapter - Class in biggests.gui
 
PanelLoading_datasetFileTextField_caretAdapter(PanelLoading) - 
Constructor for class biggests.gui.PanelLoading_datasetFileTextField_caretAdapter
 
PanelLoading_datasetFileTextField_inputMethodAdapter - Class in biggests.gui
 
PanelLoading_datasetFileTextField_inputMethodAdapter(PanelLoading) - 
Constructor for class biggests.gui.PanelLoading_datasetFileTextField_inputMethodAdapter
 
PanelLoading_geneIDCheckBox_itemAdapter - Class in biggests.gui
 
PanelLoading_geneIDCheckBox_itemAdapter(PanelLoading) - 
Constructor for class biggests.gui.PanelLoading_geneIDCheckBox_itemAdapter
 
PanelLoading_loadButton_actionAdapter - Class in biggests.gui
 
PanelLoading_loadButton_actionAdapter(PanelLoading) - 
Constructor for class biggests.gui.PanelLoading_loadButton_actionAdapter
 
PanelPostProcessing - Class in biggests.gui
Title: Post-Processing Panel

 Description: Displays options to select and apply post-processing
                 techniques to groups of biclusters.
PanelPostProcessing(BiggestsFrame) - 
Constructor for class biggests.gui.PanelPostProcessing
Creates a new post-processing panel.
PanelPostProcessing_applyButton_actionAdapter - Class in biggests.gui
Description: Action adapter for apply button.
PanelPostProcessing_applyButton_actionAdapter(PanelPostProcessing) - 
Constructor for class biggests.gui.PanelPostProcessing_applyButton_actionAdapter
 
PanelPostProcessing_filterCheckBox_itemAdapter - Class in biggests.gui
Description: Item adapter for filter check box.
PanelPostProcessing_filterCheckBox_itemAdapter(PanelPostProcessing) - 
Constructor for class biggests.gui.PanelPostProcessing_filterCheckBox_itemAdapter
 
PanelPostProcessing_filterCriteriaList_listSelectionAdapter - Class in biggests.gui
Description: List selection adapter for filter criteria list.
PanelPostProcessing_filterCriteriaList_listSelectionAdapter(PanelPostProcessing) - 
Constructor for class biggests.gui.PanelPostProcessing_filterCriteriaList_listSelectionAdapter
 
PanelPostProcessing_sortCheckBox_itemAdapter - Class in biggests.gui
Description: Item adapter for sort check box.
PanelPostProcessing_sortCheckBox_itemAdapter(PanelPostProcessing) - 
Constructor for class biggests.gui.PanelPostProcessing_sortCheckBox_itemAdapter
 
PanelPostProcessing_sortCriteriaList_listSelectionAdapter - Class in biggests.gui
Description: List selection adapter for sort criteria list.
PanelPostProcessing_sortCriteriaList_listSelectionAdapter(PanelPostProcessing) - 
Constructor for class biggests.gui.PanelPostProcessing_sortCriteriaList_listSelectionAdapter
 
PanelPreProcessing - Class in biggests.gui
Title: Preprocessing Panel

 Description: Displays options to select and apply different
                 preprocessing techniques on gene expression
                 data matrices.
PanelPreProcessing(BiggestsFrame) - 
Constructor for class biggests.gui.PanelPreProcessing
Creates a new preprocessing panel.
PanelPreProcessing_applyButton_actionAdapter - Class in biggests.gui
 
PanelPreProcessing_applyButton_actionAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_applyButton_actionAdapter
 
PanelPreProcessing_discretizeCheckBox_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_discretizeCheckBox_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_discretizeCheckBox_itemAdapter
 
PanelPreProcessing_discretizeComboBox_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_discretizeComboBox_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_discretizeComboBox_itemAdapter
 
PanelPreProcessing_fillAverageRowButton_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_fillAverageRowButton_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_fillAverageRowButton_itemAdapter
 
PanelPreProcessing_fillCheckBox_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_fillCheckBox_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_fillCheckBox_itemAdapter
 
PanelPreProcessing_fillKNeighborsButton_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_fillKNeighborsButton_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_fillKNeighborsButton_itemAdapter
 
PanelPreProcessing_fillValueButton_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_fillValueButton_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_fillValueButton_itemAdapter
 
PanelPreProcessing_filterCheckBox_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_filterCheckBox_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_filterCheckBox_itemAdapter
 
PanelPreProcessing_filterPercentGenesButton_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_filterPercentGenesButton_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_filterPercentGenesButton_itemAdapter
 
PanelPreProcessing_normalizeByGeneButton_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_normalizeByGeneButton_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_normalizeByGeneButton_itemAdapter
 
PanelPreProcessing_normalizeCheckBox_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_normalizeCheckBox_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_normalizeCheckBox_itemAdapter
 
PanelPreProcessing_normalizeMean0Std1Button_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_normalizeMean0Std1Button_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_normalizeMean0Std1Button_itemAdapter
 
PanelPreProcessing_normalizeMeanStdValuesButton_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_normalizeMeanStdValuesButton_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_normalizeMeanStdValuesButton_itemAdapter
 
PanelPreProcessing_normalizeOverallButton_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_normalizeOverallButton_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_normalizeOverallButton_itemAdapter
 
PanelPreProcessing_smoothCheckBox_itemAdapter - Class in biggests.gui
 
PanelPreProcessing_smoothCheckBox_itemAdapter(PanelPreProcessing) - 
Constructor for class biggests.gui.PanelPreProcessing_smoothCheckBox_itemAdapter
 
PARAMETER_ACV - 
Static variable in class biggests.gui.PanelPostProcessing
Average column variance parameter name.
PARAMETER_ARV - 
Static variable in class biggests.gui.PanelPostProcessing
Average row variance parameter name.
PARAMETER_CONDITIONS - 
Static variable in class biggests.gui.PanelPostProcessing
Number of conditions parameter name.
PARAMETER_GENES - 
Static variable in class biggests.gui.PanelPostProcessing
Number of genes parameter name.
PARAMETER_MARKOV_FILTER - 
Static variable in class biggests.gui.PanelPostProcessing
Markov chain order parameter name.
PARAMETER_MARKOV_SORT - 
Static variable in class biggests.gui.PanelPostProcessing
 
PARAMETER_MSR - 
Static variable in class biggests.gui.PanelPostProcessing
Mean squared residue parameter name.
PARAMETER_PVALUE - 
Static variable in class biggests.gui.PanelPostProcessing
 
PARAMETER_SIMILARITY - 
Static variable in class biggests.gui.PanelPostProcessing
Similarity parameter name.
PARAMETER_SIZE - 
Static variable in class biggests.gui.PanelPostProcessing
Size parameter name.
parent - 
Variable in class biggests.tables.TableValues
 
PATTERN - 
Static variable in class biggests.gui.PanelExpression
Constant which defines pattern expression chart type.
PDF - 
Static variable in class biggests.gui.SaveChartImageDialog
PDF document file extension.
PEARSON_ABS_CORRELATION - 
Static variable in class biggests.clustering.AbstractMetricClustering
Pearson's absolute correlation (distance metric).
PEARSON_CORRELATION - 
Static variable in class biggests.clustering.AbstractMetricClustering
Pearson's correlation (distance metric).
pearsonsAbsoluteCorrelation(double[][], double[][], int[][], int[][], double[], int, int, boolean) - 
Static method in class biggests.clustering.AbstractMetricClustering
Calculates the weighted Pearson distance between two
 genes/rows or conditions/columns, using the absolute
 value of the correlation.
pearsonsCorrelation(double[][], double[][], int[][], int[][], double[], int, int, boolean) - 
Static method in class biggests.clustering.AbstractMetricClustering
Calculates the weighted Pearson distance between two
 genes/rows or conditions/columns in a matrix.
PNG - 
Static variable in class biggests.gui.BiggestsIO
Image format: PNG
PNG - 
Static variable in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
PNG image type.
PNG - 
Static variable in class biggests.gui.SaveChartImageDialog
PNG document file extension.
POSITION_FAR_TOP_RIGHT - 
Static variable in class biggests.utils.VerticalTextIcon
The far top right position.
POSITION_NORMAL - 
Static variable in class biggests.utils.VerticalTextIcon
The normal position.
POSITION_TOP_RIGHT - 
Static variable in class biggests.utils.VerticalTextIcon
The top right position.
POSTPROCESSED_GROUP - 
Static variable in class biggests.tree.NodeInfo
The post-processed group node object type.
POSTPROCESSED_SINGLE - 
Static variable in class biggests.tree.NodeInfo
The post-processed single node object type.
postProcessingPanel - 
Variable in class biggests.gui.ThreadPostProcessing
The post-processing panel which makes the user interface
 for post-processing options.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TableColors
Overrides TableValues's prepareRenderer method.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TableColorsWithMissingValues
Overrides TableColors's prepareRenderer method.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TableFunctionGroup
Overrides JTable's prepareRenderer method.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TableFunctionIndividual
Overrides JTable's prepareRenderer method.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TablePreview
Overrides JTable's prepareRenderer method.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TableSymbols
Overrides TableValues's prepareRenderer method.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TableSymbolsWithMissingValues
Overrides TableValues's prepareRenderer method.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TableValues
Overrides JTable's prepareRenderer method.
prepareRenderer(TableCellRenderer, int, int) - 
Method in class biggests.tables.TableValuesWithMissingValues
Overrides TableValues's prepareRenderer method.
PREPROCESSED - 
Static variable in class biggests.tree.NodeInfo
The preprocessed node object type.
ProgressBarFrame - Class in biggests.utils
Title: Progress Bar Frame

 Description: Dialog for displaying an indeterminate progress bar.
ProgressBarFrame(Frame, Thread, String, boolean) - 
Constructor for class biggests.utils.ProgressBarFrame
Creates a new ProgressBarFrame dialog.
ProgressBarFrame_cancelButton_actionAdapter - Class in biggests.utils
Title: 

 Description: 
ProgressBarFrame_cancelButton_actionAdapter(ProgressBarFrame) - 
Constructor for class biggests.utils.ProgressBarFrame_cancelButton_actionAdapter
 
ProgressBarFrame_this_windowAdapter - Class in biggests.utils
 
ProgressBarFrame_this_windowAdapter(ProgressBarFrame) - 
Constructor for class biggests.utils.ProgressBarFrame_this_windowAdapter
 
progressFrame - 
Variable in class biggests.gui.ThreadPostProcessing
The frame which holds the bar that displays information
 about the post-processing algorithms application progress.
propertyChange(PropertyChangeEvent) - 
Method in class biggests.utils.VerticalTextIcon
Checks for changes to the font on the fComponent
 so that it can invalidate the layout if the size changes.
putGOFrontEnd(TreePath, GOFrontEnd) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Puts a new GO frontend in the GO frontends hashtable.



R

readConversionEntriesFromFileTXT(String, char) - 
Static method in class biggests.gui.BiggestsIO
Reads conversion file entries from a text file.
readExpressionDataFromFileTXT(String, char, float) - 
Static method in class biggests.gui.BiggestsIO
Reads gene expression data from a txt file.
readHeightInput() - 
Method in class biggests.gui.SaveChartImageDialog
Reads the height input from the corresponding text field.
readParameter(String) - 
Method in class biggests.gui.PanelBasicIOValidation
Abstract method.
readParameter(String) - 
Method in class biggests.gui.PanelBiclustering
Reads a parameter from its input text field box.
readParameter(String) - 
Method in class biggests.gui.PanelPostProcessing
Reads a filtering/sorting parameter from its input text field box.
readParameter(String) - 
Method in class biggests.gui.PanelPreProcessing
Reads the parameter string for its input parameter text field.
readParameterDouble(String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user and converts
 it to a floating point (double) value.
readParameterDouble(double, double, String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user, converts
 it to a floating point value (double and checks if
 the resulting value is in [min, max] range.
readParameterDouble(double, String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user, converts
 it to a floating point value (double) and checks if
 the resulting value is above min value.
readParameterFloat(String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user and converts
 it to a floating point (float) value.
readParameterFloat(float, float, String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user, converts
 it to a floating point value (float and checks if
 the resulting value is in [min, max] range.
readParameterFloat(float, String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user, converts
 it to a floating point value (float) and checks if
 the resulting value is above min value.
readParameterInteger(String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user and converts
 it to an integer value.
readParameterInteger(int, int, String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user, converts
 it to an integer value and checks if the resulting value is in
 [min, max] range.
readParameterInteger(int, String) - 
Method in class biggests.gui.PanelBasicIOValidation
Reads parameterToRead entered by the user, converts
 it to an integer value and checks if the resulting value is above
 min value.
readParameterInteger(int, int, String) - 
Method in class biggests.gui.PanelBiclustering
 
readWidthInput() - 
Method in class biggests.gui.SaveChartImageDialog
Reads the width input from the corresponding textfield.
recalcDimensions() - 
Method in class biggests.utils.VerticalTextIcon
Recalculates the dimensions.
recalculate_actionPerformed(ActionEvent) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Handles the mouse event fired when the user clicks on
 recalculate functions button.
RED_GREEN_SCHEME - 
Static variable in class biggests.utils.HeatmapColorScheme
 
reload() - 
Method in class biggests.tree.DatasetTree
Reloads the tree model, so all (new) nodes get visible.
repaintPanelAnalyzingFunctionTable(GeneSetResult, float) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Repaints function analysis panel after recalculating
 biological relevance of a bicluster.
repaintPanelAnalyzingFunctionTable(Hashtable<Integer, BiologicalRelevanceSummary>) - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Repaints function analysis panel after recalculating
 biological relevance of a biclusters' group.
repaintPanelAnalyzingFunctionTable() - 
Method in class biggests.gui.PanelAnalyzingFunctionTable
Repaints function analysis panel after recalculating
 biological relevance of an expression matrix (original,
 preprocessed or discretized one).
repaintTimePointsChart(int, int, boolean) - 
Method in class biggests.gui.PanelExpressionChart
Returns a new time points (bicluster or all time points)
 chart panel, repainted from the the current one.
restoreSession(BiggestsFrame, String) - 
Static method in class biggests.gui.BiggestsIO
Restores a session from a .zip archive file.
restoreSession2(BiggestsFrame, String) - 
Static method in class biggests.gui.BiggestsIO
Restores a session from a .zip archive file.
restrictedErrorsECCCCheckBox_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelBiclustering
Handles the item state changed event fired when the user
 selects/deselects restricted errors for e-CCC-Biclustering
 algorithm check box.
ROTATE_DEFAULT - 
Static variable in class biggests.utils.VerticalTextIcon
The default rotation.
ROTATE_LEFT - 
Static variable in class biggests.utils.VerticalTextIcon
The left rotation option.
ROTATE_NONE - 
Static variable in class biggests.utils.VerticalTextIcon
The no rotation option.
ROTATE_RIGHT - 
Static variable in class biggests.utils.VerticalTextIcon
The right rotation option.
run() - 
Method in class biggests.gui.ThreadBiclustering
Overrides Thread's  run method.
run() - 
Method in class biggests.gui.ThreadDownloadGOFiles
Overrides Thread's  run method.
run() - 
Method in class biggests.gui.ThreadFunctionAnalysis
Overrides Thread's  run method.
run() - 
Method in class biggests.gui.ThreadHierarchicalClustering
 
run() - 
Method in class biggests.gui.ThreadPostProcessing
Overrides Thread's run method.



S

saveButton_actionPerformed(ActionEvent) - 
Method in class biggests.gui.SaveChartImageDialog
Handles the event fired when the user clicks save button.
saveChartAsPDF(File, JFreeChart, int, int, FontMapper) - 
Static method in class biggests.gui.SaveChartImageDialog
Saves a chart to a PDF file.
saveChartAsSVG(File, JFreeChart, int, int) - 
Static method in class biggests.gui.SaveChartImageDialog
Saves a chart as a SVG document.
SaveChartImageDialog - Class in biggests.gui
Title: Save Chart Image Dialog

 Description: Dialog suited for prompting the user to provide the
                 width, height and file format to export a chart as
                 an image.
SaveChartImageDialog(Frame, Component, String, boolean, int, int) - 
Constructor for class biggests.gui.SaveChartImageDialog
Creates a save chart image dialog.
SaveChartImageDialog_browseButton_actionAdapter - Class in biggests.gui
 
SaveChartImageDialog_browseButton_actionAdapter(SaveChartImageDialog) - 
Constructor for class biggests.gui.SaveChartImageDialog_browseButton_actionAdapter
 
SaveChartImageDialog_cancelButton_actionAdapter - Class in biggests.gui
 
SaveChartImageDialog_cancelButton_actionAdapter(SaveChartImageDialog) - 
Constructor for class biggests.gui.SaveChartImageDialog_cancelButton_actionAdapter
 
SaveChartImageDialog_displayedSizeRadioButton_itemAdapter - Class in biggests.gui
 
SaveChartImageDialog_displayedSizeRadioButton_itemAdapter(SaveChartImageDialog) - 
Constructor for class biggests.gui.SaveChartImageDialog_displayedSizeRadioButton_itemAdapter
 
SaveChartImageDialog_saveButton_actionAdapter - Class in biggests.gui
 
SaveChartImageDialog_saveButton_actionAdapter(SaveChartImageDialog) - 
Constructor for class biggests.gui.SaveChartImageDialog_saveButton_actionAdapter
 
saveCurrentSession(boolean) - 
Method in class biggests.gui.BiggestsFrame
Saves current session to a zip archive file.
saveGraph_actionPerformed(ActionEvent) - 
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
Handles the user click on the save graph button.
saveSession(DatasetTree, String, String) - 
Static method in class biggests.gui.BiggestsIO
Saves a session to a .zip archive file.
saveSession2(DatasetTree, String, String) - 
Static method in class biggests.gui.BiggestsIO
Saves a session to a .zip archive file.
SCROLL_BAR_INCREMENT - 
Static variable in class biggests.gui.BiggestsFrame
 
selectionPath - 
Variable in class biggests.gui.ThreadPostProcessing
The selected path in the dataset tree, holding the bicluster
 group object to post-process.
SEMICOLON - 
Static variable in class biggests.gui.PanelLoading
Data delimiter: semicolon.
serialVersionUID - 
Static variable in class biggests.tree.Dataset
 
serialVersionUID - 
Static variable in class biggests.tree.DatasetTree
 
serialVersionUID - 
Static variable in class biggests.tree.NodeInfo
 
sessionExit_actionPerformed(ActionEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks Session -> Exit item menu.
sessionLoadDataset_actionPerformed(ActionEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks the menu item Session ->
 Load Dataset.
sessionLoadSession_actionPerformed(ActionEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks the menu item Session ->
 Load Session.
sessionSaveSession_actionPerformed(ActionEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user clicks the menu item Session ->
 Save Session.
setBackAndForegroundHighlightColors(JComponent) - 
Static method in class biggests.utils.HeatmapColorScheme
 
setColumnComparator(Class, Comparator) - 
Method in class biggests.tables.TableSorter
Sets the given comparator for the given objects'
 type.
setDiscretizeCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelPreProcessing
Sets the discretize check box selected/deselected, enabling/disabling
 the corresponding discretize options.
setDistance(double) - 
Method in class biggests.clustering.ClusterTreeNode
Sets the distance between left and right sons.
setEvenRowsColor(Color) - 
Method in class biggests.tables.TableFunctionGroup
Sets a new color to mark even rows that are not selected.
setEvenRowsColor(Color) - 
Method in class biggests.tables.TableFunctionIndividual
Sets a new color to mark even rows that are not selected.
setFilterCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelPostProcessing
Sets filter check box selected/deselected.
setFilterCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelPreProcessing
Sets the filter check box selected/deselected, enabling/disabling
 the corresponding filter options.
setGeneIDCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelLoading
Sets gene ID check box selected/deselected.
setGeneShiftsCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelBiclustering
Sets gene shifts check box selected/deselected, along with
 the corresponding enabling/disabling of shifts label and
 input text field.
setHeatmapColorScheme(int) - 
Static method in class biggests.utils.HeatmapColorScheme
 
setInfoStrings(ArrayList<String>) - 
Method in class biggests.tree.NodeInfo
Sets information strings.
setInfoStyles(ArrayList<String>) - 
Method in class biggests.tree.NodeInfo
Sets information styles.
setLabel(String) - 
Method in class biggests.utils.VerticalTextIcon
Sets the fLabel to the given label string,
 updating the orientation as needed and invalidating the layout if
 the size changes.
setLeft(int) - 
Method in class biggests.clustering.ClusterTreeNode
Sets the index for left son.
setNormalizeCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelPreProcessing
Sets the normalize check box selected/deselected, enabling/disabling
 the corresponding normalize options.
setNumberOfDendrograms(int) - 
Static method in class biggests.gui.PanelAnalyzingMatrixDendrogram
 
setOddRowsColor(Color) - 
Method in class biggests.tables.TableFunctionGroup
Sets a new color to mark odd rows that are not selected.
setOddRowsColor(Color) - 
Method in class biggests.tables.TableFunctionIndividual
Sets a new color to mark odd rows that are not selected.
setPathToDOT(String) - 
Static method in class biggests.gui.BiggestsFrame
 
setPreviewEnabled(boolean) - 
Method in class biggests.gui.PanelLoading
Sets preview option enabled/disabled.
setRestrictedErrorsECCCCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelBiclustering
Sets restricted errors for e-CCC-Biclustering algorithm check
 box selected/deselected, along with the corresponding
 enabling/disabling of neighbors label and text field.
setRight(int) - 
Method in class biggests.clustering.ClusterTreeNode
Sets the index for right son.
setSignificantColor(Color) - 
Method in class biggests.tables.TableFunctionGroup
Sets a new color to mark significant terms.
setSignificantColor(Color) - 
Method in class biggests.tables.TableFunctionIndividual
Sets a new color to mark significant terms.
setSmoothCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelPreProcessing
Sets the smooth check box selected/deselected, enabling/disabling
 the corresponding smooth options.
setSortCheckBoxSelected(boolean) - 
Method in class biggests.gui.PanelPostProcessing
Sets sort check box selected/deselected.
setSortingStatus(int, int) - 
Method in class biggests.tables.TableSorter
Sets the sorting status for a given column.
setStop(boolean) - 
Static method in class biggests.gui.BiggestsIO
Sets stop flag.
setString(String) - 
Method in class biggests.utils.ProgressBarFrame
Sets the message displayed by the progress bar.
setStringsAndStyles(Biclustering) - 
Method in class biggests.gui.PanelBiclustering
Sets strings and styles attributes according to
 the type and parameters of biclustering object.
setStringsAndStylesCCC(CCC_Biclustering) - 
Method in class biggests.gui.PanelBiclustering
Sets strings and styles attributes according to the
 parameters of the CCC_Biclustering object.
setStringsAndStylesCCTSB(CC_TSB_Biclustering) - 
Method in class biggests.gui.PanelBiclustering
Sets strings and styles attributes according to the
 parameters of the CC_TSB_Biclustering object.
setStringsAndStylesECCC(E_CCC_Biclustering) - 
Method in class biggests.gui.PanelBiclustering
Sets strings and styles attributes according to the
 parameters of the E_CCC_Biclustering object.
setTabbedPaneAnalyzingEnabledTabs(boolean, boolean, boolean) - 
Method in class biggests.gui.BiggestsFrame
Enables/disables tabs on the analyzing tabbed pane.
setTabbedPaneAnalyzingMatrixEnabledTabs(boolean, boolean, boolean, boolean) - 
Method in class biggests.gui.BiggestsFrame
Enables/disables tabs on the matrix analysis tabbed pane.
setTabbedPaneEnabledTabs(boolean, boolean, boolean, boolean, boolean, boolean) - 
Method in class biggests.gui.BiggestsFrame
Enables/disables tabs on the main tabbed pane.
setTableHeader(JTableHeader) - 
Method in class biggests.tables.TableSorter
Sets the table header.
setTableHeader(JTableHeader) - 
Method in class biggests.tables.TableSorterVerticalHeader
 
setTableModel(TableModel) - 
Method in class biggests.tables.TableSorter
Sets the table model.
setTree(DatasetTree) - 
Method in class biggests.gui.BiggestsFrame
Sets a new dataset tree.
setValue(Object) - 
Method in class biggests.tables.TableFunctionGroup.FloatCellRenderer
Overrides DefaultTableCellRenderer's
 setValue method.
setValue(Object) - 
Method in class biggests.tables.TableFunctionIndividual.FloatCellRenderer
Overrides DefaultTableCellRenderer's
 setValue method.
setValue(Object) - 
Method in class biggests.tables.TableValues.FloatCellRenderer
Overrides DefaultTableCellRenderer's
 setValue method.
setValueAt(Object, int, int) - 
Method in class biggests.tables.TableSorter
Sets the element of the cell with row and
 column) indexes.
SHIFTS - 
Static variable in class biggests.gui.PanelBiclustering
Name of the 'shifts' parameter for CCC-Biclustering
 and e-CCC-Biclustering algorithms.
showDendrogram(String, String) - 
Method in class biggests.gui.PanelAnalyzingMatrixDendrogram
 
showDiscretizeErrorMessage(String) - 
Method in class biggests.gui.PanelPreProcessing
Shows the discretization error message.
signChangesCheckBox_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelBiclustering
 
SIGNIFICANT_COLOR - 
Static variable in class biggests.tables.TableFunctionGroup
Default color to mark rows that contain biclusters with significant terms.
SIGNIFICANT_COLOR - 
Static variable in class biggests.tables.TableFunctionIndividual
Default color for significant terms.
SINGLE_LINKAGE - 
Static variable in class biggests.clustering.HierarchicalClustering
Pairwise single-linkage (clustering method).
singleLinkageClustering(double[][], int[][], double[], double[][], char, boolean) - 
Method in class biggests.clustering.HierarchicalClustering
Performs single-linkage hierarchical clustering, using either
 the distance matrix directly, if available, or by calculating the
 distances from the expression data matrix.
SMOOTH_WINDOW - 
Static variable in class biggests.gui.PanelPreProcessing
'Smoothing window' parameter name.
smoothCheckBox_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPreProcessing
Handles the item state changed event fired when the user
 selects/deselects the smooth check box.
SORT_ACV - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their ACV values' option.
SORT_ARV - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their ARV values' option.
SORT_ARV_ACV_DIFF - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by the differences between
 their ARV and ACV values' option.
SORT_ARV_MSR_DIFF - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by the differences between
 their ARV and MSR values' option.
SORT_BEST_GO_BONFERRONI_PVALUE - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their best GO Bonferroni
 corrected p-value' option.
SORT_BEST_GO_PVALUE - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their best GO p-value' option.
SORT_CONDITIONS - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their number of conditions' option.
SORT_GENES - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their number of genes' option.
SORT_MSR - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their MSR values' option.
SORT_PATTERN_COLUMNS_PVALUE - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by the p-value for their pattern
 with columns' option.
SORT_PATTERN_PVALUE - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their pattern p-value' option.
SORT_SIZE - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their size' option.
SORT_VARIANCE - 
Static variable in class biggests.gui.PanelPostProcessing
The index of 'sort biclusters by their variance' option.
sortBy_ACV(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their ACV.
sortBy_ARV(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their ARV.
sortBy_ARV_ACV_DIFF(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by the difference of their ARV
 and ACV (ARV-ACV).
sortBy_ARV_MSR_DIFF(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by the difference of their ARV
 and MSR (ARV-MSR).
sortBy_BEST_GO_BONFERRONI_PVALUE(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their best GO Bonferroni
 corrected p-values in ascending order.
sortBy_BEST_GO_PVALUE(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their best GO p-values
 in ascending order.
sortBy_MSR(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their MSR.
sortBy_NR_CONDITIONS(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their number of conditions.
sortBy_NR_GENES(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their number of genes.
sortBy_PATTERN_PVALUE(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their pattern p-value
 in ascending order.
sortBy_PATTERN_WITH_COLUMNS_PVALUE(BiclusteringInDiscretizedMatrix, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their pattern with
 columns p-value in ascending order.
sortBy_SIZE(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their sizes.
sortBy_VARIANCE(Biclustering, ArrayList<String>, ArrayList<String>) - 
Method in class biggests.gui.ThreadPostProcessing
Performs sorting of biclusters by their variances.
sortCheckBox_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelPostProcessing
Handles changes on sort check box selection.
sortClusteringTree(boolean, double[], double[], int[], ClusterTreeNode[]) - 
Method in class biggests.clustering.HierarchicalClustering
Sorts the nodes of the tree based on the
 tree's structure.
sortCriteriaList_valueChanged(ListSelectionEvent) - 
Method in class biggests.gui.PanelPostProcessing
Handles a selection change on sort criteria list.
sortCriteriaList_valueChanged() - 
Method in class biggests.gui.PanelPostProcessing
Handles a selection change on sort criteria list.
sortIndexes(double[], int[]) - 
Static method in class biggests.clustering.AbstractMetricClustering
Sets up an index table given the data, such that data[indexes[i]],
 with i = 0, ..., data.length is in increasing order.
SPACE - 
Static variable in class biggests.gui.PanelLoading
Data delimiter: space.
SPEARMAN_RANK_CORRELATION - 
Static variable in class biggests.clustering.AbstractMetricClustering
Spearman's rank correlation (distance metric).
spearmansRankCorrelation(double[][], double[][], int[][], int[][], double[], int, int, boolean) - 
Static method in class biggests.clustering.AbstractMetricClustering
Calculates the Spearman distance between two genes/rows or
 conditions/columns.
springLayout() - 
Method in class biggests.gui.PanelFunctionAnalysis
Returns the layout for this panel.
startTaskInLabelContext(String) - 
Method in class biggests.gui.BiggestsFrame
 
stateChanged(ChangeEvent) - 
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph_zoomSlider_changeAdapter
Handles the events of changing in the state of certain components.
SVG - 
Static variable in class biggests.gui.BiggestsIO
Image format: SVG
SVG - 
Static variable in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
SVG image type.
SVG - 
Static variable in class biggests.gui.SaveChartImageDialog
SVG document file extension.
SYMBOLS - 
Static variable in class biggests.gui.PanelAnalyzingMatrixTables
The type for symbols tables.
SYMBOLS - 
Static variable in class biggests.tree.NodeInfo
The symbol values matrix data type.



T

TAB - 
Static variable in class biggests.gui.PanelLoading
Data delimiter: tab.
TableColors - Class in biggests.tables
Title: Colors Table

 Description:
                 Defines a table of colors with the following data:

                 - header -> conditions' names (more widely, Strings)

                 - first column -> genes' names (more widely, Strings)

                 - all other columns' cells -> gene expression values
                 (more widely, float values)

                 A table of colors has a vertical text header and each
                 of its cells is colored according to the float value that
                 holds in it.
TableColors(NodeObjectInterface, GOFrontEnd, Component) - 
Constructor for class biggests.tables.TableColors
Creates a new colored table with data from the the given node object's
 matrix.
TableColors(NodeObjectInterface) - 
Constructor for class biggests.tables.TableColors
Creates a new colored table with data from the the given node object's
 matrix.
TableColors(Object[][], Object[], boolean) - 
Constructor for class biggests.tables.TableColors
Creates a new colored table with the given row data and columns' names.
TableColorsWithMissingValues - Class in biggests.tables
Title: Table of colors with missing values

 Description:
                 Defines a table of colors with the following data:

                 - header -> conditions' names (more widely, Strings)

                 - first column -> genes' names (more widely, Strings)

                 - all other columns' cells -> gene expression values
                 (more widely, float values)

                 A table of colors has a vertical text header and each
                 of its cells is colored according to the float value it
                 holds.
TableColorsWithMissingValues(AbstractExpressionMatrix, GOFrontEnd, Component) - 
Constructor for class biggests.tables.TableColorsWithMissingValues
Creates a new colored table with data from the given expression matrix
 with missing values.
TableColorsWithMissingValues(AbstractExpressionMatrix) - 
Constructor for class biggests.tables.TableColorsWithMissingValues
Creates a new colored table with data from the given expression matrix
 with missing values.
TableFunctionGroup - Class in biggests.tables
Title: Table of Functions for a Group of Biclusters

 Description: Defines a table for displaying data of function
                 analysis performed on a given a group of biclusters.
TableFunctionGroup(Biclustering, Hashtable<Integer, BiologicalRelevanceSummary>, boolean) - 
Constructor for class biggests.tables.TableFunctionGroup
Creates a new function table from the data of a biclusters group object.
TableFunctionGroup(Object[][], Object[], boolean) - 
Constructor for class biggests.tables.TableFunctionGroup
Creates a new function table from the data of a biclusters group object.
TableFunctionGroup(TableSorterFunctionGroup) - 
Constructor for class biggests.tables.TableFunctionGroup
Creates a new function table from the data of a biclusters group object.
TableFunctionGroup.FloatCellRenderer - Class in biggests.tables
Title: FloatCellRenderer: A renderer for cells which
           contain float numbers.
TableFunctionGroup.FloatCellRenderer() - 
Constructor for class biggests.tables.TableFunctionGroup.FloatCellRenderer
Constructs a new FloatCellRenderer.
TableFunctionGroup.NumberCellRenderer - Class in biggests.tables
Title: NumberCellRenderer: A renderer for cells which
           contain numbers.
TableFunctionGroup.NumberCellRenderer() - 
Constructor for class biggests.tables.TableFunctionGroup.NumberCellRenderer
Constructs a new NumberCellRenderer for a cell.
TableFunctionIndividual - Class in biggests.tables
Title: Function Table for an Individual Bicluster

 Description: Contains data about function analysis performed on
                 a given bicluster.
TableFunctionIndividual(Bicluster, GeneSetResult, GOFrontEnd, float, Component) - 
Constructor for class biggests.tables.TableFunctionIndividual

 Creates a new table of functions from the data of a bicluster object.
TableFunctionIndividual(IMatrix, GOFrontEnd) - 
Constructor for class biggests.tables.TableFunctionIndividual
Creates a new function table from the GO terms infotmation
 in matrix.
TableFunctionIndividual(GeneSetResult, GOFrontEnd, String[], float) - 
Constructor for class biggests.tables.TableFunctionIndividual
Creates a new function table from the given GO terms.
TableFunctionIndividual(GeneSetResult, GOFrontEnd, String[]) - 
Constructor for class biggests.tables.TableFunctionIndividual
Creates a new function table from the given GO terms.
TableFunctionIndividual(Object[][], Object[], GOFrontEnd, float, float) - 
Constructor for class biggests.tables.TableFunctionIndividual
Creates a new table of functions with GO terms and p-values data.
TableFunctionIndividual(TableSorterFunctionIndividual, GOFrontEnd, float) - 
Constructor for class biggests.tables.TableFunctionIndividual
Creates a new table of functions from the given
 tableSorterModel.
TableFunctionIndividual(TableSorterFunctionIndividual, GOFrontEnd, float, float) - 
Constructor for class biggests.tables.TableFunctionIndividual
Creates a new table of functions for the given tableSorterModel.
TableFunctionIndividual.FloatCellRenderer - Class in biggests.tables
Title: FloatCellRenderer: A renderer for cells which
           contain float numbers.
TableFunctionIndividual.FloatCellRenderer() - 
Constructor for class biggests.tables.TableFunctionIndividual.FloatCellRenderer
Constructs a new FloatCellRenderer.
TableFunctionIndividual.NumberCellRenderer - Class in biggests.tables
Title: NumberCellRenderer: A renderer for cells which
           contain numbers.
TableFunctionIndividual.NumberCellRenderer() - 
Constructor for class biggests.tables.TableFunctionIndividual.NumberCellRenderer
Constructs a new NumberCellRenderer for a cell.
TableFunctionIndividual_this_mouseAdapter - Class in biggests.tables
Title: 

 Description: 

 Copyright:   Copyright (C) 2007  Joana Gonçalves
                 This program is free software; you can redistribute
                 it and/or modify it under the terms of the GNU General
                 Public License as published by the Free Software
                 Foundation; either version 2 of the License, or
                 any later version.
TableFunctionIndividual_this_mouseAdapter(TableFunctionIndividual) - 
Constructor for class biggests.tables.TableFunctionIndividual_this_mouseAdapter
 
TableHeader - Class in biggests.tables
Title: Header for Tables

 Description: Defines a header for generic tables.
TableHeader() - 
Constructor for class biggests.tables.TableHeader
Overrides JTableHeader's constructor.
TableHeader(TableColumnModel) - 
Constructor for class biggests.tables.TableHeader
Overrides JTableHeader's constructor.
tableHeader - 
Variable in class biggests.tables.TableSorter
The header of the table.
TableHeaderFunction - Class in biggests.tables
Title: Header for Tables of Functions

 Description: Defines a header for tables of functions.
TableHeaderFunction() - 
Constructor for class biggests.tables.TableHeaderFunction
Overrides JTableHeader's constructor.
TableHeaderFunction(TableColumnModel) - 
Constructor for class biggests.tables.TableHeaderFunction
Overrides JTableHeader's constructor.
tableModel - 
Variable in class biggests.tables.TableSorter
The table model.
TablePreview - Class in biggests.tables
Title: Preview Table

 Description:  A preview table displays: names of genes in the
                  first column, names of conditions in the header
                  (first row) and gene expression values in remaining
                  cells.
TablePreview(Object[][], Object[], ArrayList<Integer>, ArrayList<Integer>) - 
Constructor for class biggests.tables.TablePreview
Creates a new preview table with the given row data and column names.
TablePreview(TableModel, ArrayList<Integer>, ArrayList<Integer>) - 
Constructor for class biggests.tables.TablePreview
Creates a new preview table with the given row data and column names.
TableSorter - Class in biggests.tables
Title: Table Sorter - a model for sorting tables

 Description:  TableSorter is a decorator for TableModels adding
                  sorting functionality to a supplied TableModel.
TableSorter() - 
Constructor for class biggests.tables.TableSorter
Creates a new TableSorter with default mouse and
 table model listeners.
TableSorter(TableModel) - 
Constructor for class biggests.tables.TableSorter
Creates a new TableSorter with the given table model.
TableSorter(TableModel, JTableHeader) - 
Constructor for class biggests.tables.TableSorter
Creates a new TableSorter with the given table
 model and header.
TableSorterFunctionGroup - Class in biggests.tables
Title: Table Sorter for Tables of Functions of Biclusters' Groups

 Description: A table model which allows for column sorting.
TableSorterFunctionGroup(boolean) - 
Constructor for class biggests.tables.TableSorterFunctionGroup
Constructs a new TableSorterFunctionGroup model.
TableSorterFunctionGroup(TableModel, boolean) - 
Constructor for class biggests.tables.TableSorterFunctionGroup
Constructs a new TableSorterFunctionGroup model.
TableSorterFunctionGroup(TableModel, TableHeader, boolean) - 
Constructor for class biggests.tables.TableSorterFunctionGroup
Constructs a new TableSorterFunctionGroup model.
TableSorterFunctionIndividual - Class in biggests.tables
Title: Table Sorter for Tables of Functions of Biclusters

 Description: A table model which allows for column sorting.
TableSorterFunctionIndividual() - 
Constructor for class biggests.tables.TableSorterFunctionIndividual
Constructs a new TableSorterFunctionIndividual model.
TableSorterFunctionIndividual(TableModel) - 
Constructor for class biggests.tables.TableSorterFunctionIndividual
Constructs a new TableSorterFunctionIndividual model.
TableSorterFunctionIndividual(TableModel, TableHeader) - 
Constructor for class biggests.tables.TableSorterFunctionIndividual
Constructs a new TableSorterFunctionIndividual model.
TableSorterSymbols - Class in biggests.tables
Title: Table Sorter for Tables with Discrete Values

 Description: A table model which allows for column sorting.
TableSorterSymbols() - 
Constructor for class biggests.tables.TableSorterSymbols
Constructs a new TableSorterSymbols model.
TableSorterSymbols(TableModel) - 
Constructor for class biggests.tables.TableSorterSymbols
Constructs a new TableSorterSymbols model from a
 plain table model.
TableSorterSymbols(TableModel, TableHeader) - 
Constructor for class biggests.tables.TableSorterSymbols
Constructs a new TableSorterSymbols model from a plain table
 model and a given table header.
TableSorterValues - Class in biggests.tables
Title: Table Sorter for Tables with Float Values

 Description: A table model which allows for column sorting.
TableSorterValues() - 
Constructor for class biggests.tables.TableSorterValues
Constructs a new TableSorterValues model.
TableSorterValues(TableModel) - 
Constructor for class biggests.tables.TableSorterValues
Constructs a new TableSorterValues model.
TableSorterValues(TableModel, TableHeader) - 
Constructor for class biggests.tables.TableSorterValues
Constructs a new TableSorterValues model.
TableSorterVerticalHeader - Class in biggests.tables
Title: TableSorterVerticalHeader model

 Description: This table model implements table sorting and also a table
                 header model which writes vertical oriented column names.
TableSorterVerticalHeader() - 
Constructor for class biggests.tables.TableSorterVerticalHeader
Constructs a new ColorsTableSorter model.
TableSorterVerticalHeader(TableModel) - 
Constructor for class biggests.tables.TableSorterVerticalHeader
Constructs a new TableSorterVerticalHeader model from a
 plain table model.
TableSorterVerticalHeader(TableModel, TableHeader) - 
Constructor for class biggests.tables.TableSorterVerticalHeader
Constructs a new TableSorterVerticalHeader model from a plain table
 model and a given table header.
TableSymbols - Class in biggests.tables
Title: Table of Symbols

 Description:
                 Defines a table of symbols with the following data:

                 - header -> conditions' names (more widely, Strings)

                 - first column -> genes' names (more widely, Strings)

                 - all other columns' cells -> gene expression symbols
                 (more widely, characters)

                 A table of symbols has a vertical text header and each
                 of its cells is colored according to the symbol that
                 holds in it.
TableSymbols(NodeObjectInterface, GOFrontEnd, Component) - 
Constructor for class biggests.tables.TableSymbols
Creates a new table of symbols with data from the the given node object's
 matrix.
TableSymbols(NodeObjectInterface) - 
Constructor for class biggests.tables.TableSymbols
Creates a new table of symbols with data from the the given node object's
 matrix.
TableSymbols(Object[][], Object[]) - 
Constructor for class biggests.tables.TableSymbols
Creates a new table of symbols with data from the the given node object's
 matrix.
TableSymbolsWithMissingValues - Class in biggests.tables
Title: Table of Symbols with Missing Values

 Description:
                 Defines a table of symbols with the following data:

                 - header -> conditions' names (more widely, Strings)

                 - first column -> genes' names (more widely, Strings)

                 - all other columns' cells -> gene expression symbols
                 (more widely, characters)

                 A table of symbols has a vertical text header and each
                 of its cells is colored according to the symbol that
                 holds in it.
TableSymbolsWithMissingValues(DiscretizedExpressionMatrix, GOFrontEnd, Component) - 
Constructor for class biggests.tables.TableSymbolsWithMissingValues
Creates a new table of symbols with data from the the given
 discretized expression matrix.
TableSymbolsWithMissingValues(DiscretizedExpressionMatrix) - 
Constructor for class biggests.tables.TableSymbolsWithMissingValues
Creates a new table of symbols with data from the the given
 discretized expression matrix.
TableValues - Class in biggests.tables
Title: Table of Values

 Description:
                 Defines a table of values with the following data:

                 - header -> conditions' names (more widely, Strings)

                 - first column -> genes' names (more widely, Strings)

                 - all other columns' cells -> gene expression values
                 (more widely, float values)

                 This is a simple table that shows the raw values that
                 are assigned when using one of the constructors and
                 implements sorting functionality on the columns, i.e.,
                 allows the reordering of the rows, sorting them by a
                 specific column's cells values in ascending or descending
                 order.
TableValues(NodeObjectInterface, GOFrontEnd, Component) - 
Constructor for class biggests.tables.TableValues
Creates a new values table from the data of a node object.
TableValues(NodeObjectInterface) - 
Constructor for class biggests.tables.TableValues
Creates a new values table from the data of a node object.
TableValues(Object[][], Object[]) - 
Constructor for class biggests.tables.TableValues
Creates a new values table with the given row data and column names.
TableValues.FloatCellRenderer - Class in biggests.tables
Title: FloatCellRenderer: A renderer for cells which
           contain float numbers.
TableValues.FloatCellRenderer() - 
Constructor for class biggests.tables.TableValues.FloatCellRenderer
Constructs a new FloatCellRenderer.
TableValues.NumberCellRenderer - Class in biggests.tables
Title: NumberCellRenderer: A renderer for cells which
           contain numbers.
TableValues.NumberCellRenderer() - 
Constructor for class biggests.tables.TableValues.NumberCellRenderer
Constructs a new NumberCellRenderer for a cell.
TableValues_this_mouseAdapter - Class in biggests.tables
 
TableValues_this_mouseAdapter(TableValues) - 
Constructor for class biggests.tables.TableValues_this_mouseAdapter
 
TableValuesWithMissingValues - Class in biggests.tables
Title: Table of values with missing values

 Description:
                 Defines a table of values with the following data:

                 - header -> conditions' names (more widely, Strings)

                 - first column -> genes' names (more widely, Strings)

                 - all other columns' cells -> gene expression values
                 (more widely, float values)

                 This is a simple table that shows the raw values that
                 are assigned when using one of the constructors and
                 implements sorting functionality on the columns, i.e.,
                 allows the reordering of the rows, sorting them by the
                 values of a specific column in ascending or descending
                 order.
TableValuesWithMissingValues(IMatrix, GOFrontEnd, Component) - 
Constructor for class biggests.tables.TableValuesWithMissingValues
Creates a new values table from the data of an expression matrix with
 missing values.
TableValuesWithMissingValues(IMatrix) - 
Constructor for class biggests.tables.TableValuesWithMissingValues
Creates a new values table from the data of an expression matrix with
 missing values.
testDatasetFilePath() - 
Method in class biggests.gui.PanelLoading
Tests dataset file path in datasetFileTextField.
this_ancestorResized(HierarchyEvent) - 
Method in class biggests.gui.PanelExpression
 
this_componentResized(ComponentEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles the event fired when the user resizes the main window.
this_mouseClicked(MouseEvent) - 
Method in class biggests.tables.TableColors
Handles a mouse click in this table of colors.
this_mouseClicked(MouseEvent) - 
Method in class biggests.tables.TableFunctionIndividual
Handles the event fired when the user clicks a row of this table.
this_mouseClicked(MouseEvent) - 
Method in class biggests.tables.TableSymbols
Handles a mouse click in this table of colors.
this_mouseClicked(MouseEvent) - 
Method in class biggests.tables.TableValues
 
this_windowClosing(WindowEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles the event fired when the main window of the
 application is closing.
this_windowClosing(WindowEvent) - 
Method in class biggests.utils.ProgressBarFrame
 
this_windowStateChanged(WindowEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles the event fired when the state of the main window changes.
ThreadBiclustering - Class in biggests.gui
Title: Biclustering and function analysis thread.
ThreadBiclustering(BiggestsFrame, Biclustering, TreePath) - 
Constructor for class biggests.gui.ThreadBiclustering
Creates a new ThreadBiclusteringFunctionAnalysis
ThreadDownloadGOFiles - Class in biggests.gui
Title: Download gene ontology files thread

 Description: Thread to download gene ontology files from
                 www.geneontology.org (long time consuming task)
                 while displaying a progress bar dialog to the user.
ThreadDownloadGOFiles(BiggestsFrame, PanelFunctionAnalysis, String) - 
Constructor for class biggests.gui.ThreadDownloadGOFiles
Creates a new thread to download a gene ontology/association file.
ThreadFunctionAnalysis - Class in biggests.gui
Title: Function analysis thread.
ThreadFunctionAnalysis(BiggestsFrame, Biclustering, TreePath, File[], File, float) - 
Constructor for class biggests.gui.ThreadFunctionAnalysis
Creates a new ThreadFunctionAnalysis.
ThreadFunctionAnalysis(BiggestsFrame, Biclustering, TreePath, String, String, File, float) - 
Constructor for class biggests.gui.ThreadFunctionAnalysis
Creates a new ThreadFunctionAnalysis.
ThreadFunctionAnalysis(BiggestsFrame, IMatrix, TreePath, File[], File, String, float) - 
Constructor for class biggests.gui.ThreadFunctionAnalysis
Creates a new Function Analysis Thread to perform function
 analysis over a matrix.
ThreadFunctionAnalysis(BiggestsFrame, IMatrix, TreePath, String, String, File, String, float) - 
Constructor for class biggests.gui.ThreadFunctionAnalysis
Creates a new Function Analysis Thread to perform function
 analysis over a matrix.
ThreadFunctionAnalysis(BiggestsFrame, Bicluster, TreePath, String, String, String, float) - 
Constructor for class biggests.gui.ThreadFunctionAnalysis
Creates a new Function Analysis Thread to perform function
 analysis on a bicluster.
ThreadHierarchicalClustering - Class in biggests.gui
Title: 

 Description: 

 Copyright:   Copyright (C) 2007  Joana Gonçalves
                 This program is free software; you can redistribute
                 it and/or modify it under the terms of the GNU General
                 Public License as published by the Free Software
                 Foundation; either version 3 of the License, or
                 any later version.
ThreadHierarchicalClustering(BiggestsFrame, HierarchicalClustering, char, char, char, String, String) - 
Constructor for class biggests.gui.ThreadHierarchicalClustering
 
ThreadPostProcessing - Class in biggests.gui
Title: Post-Processing Thread

 Description: Implements a thread to apply post-processing algorithms,
                 such as filtering and sorting of biclusters based on
                 well known metrics.
ThreadPostProcessing(Biclustering, TreePath, PanelPostProcessing) - 
Constructor for class biggests.gui.ThreadPostProcessing
Creates a new post-processing thread, to post-process a
 group of biclusters.
timeLagsCheckBox_itemStateChanged(ItemEvent) - 
Method in class biggests.gui.PanelBiclustering
 
toString() - 
Method in class biggests.tree.Dataset
Overrides toString() method from class Object.
toString() - 
Method in class biggests.tree.NodeInfo
Overrides the default toString method.
tree_valueChanged(TreeSelectionEvent) - 
Method in class biggests.gui.BiggestsFrame
Handles a change in dataset tree's selection.



U

UNCENTERED_ABS_CORRELATION - 
Static variable in class biggests.clustering.AbstractMetricClustering
Uncentered absolute correlation (distance metric).
UNCENTERED_CORRELATION - 
Static variable in class biggests.clustering.AbstractMetricClustering
Uncentered correlation (distance metric).
uncenteredAbsoluteCorrelation(double[][], double[][], int[][], int[][], double[], int, int, boolean) - 
Static method in class biggests.clustering.AbstractMetricClustering
Calculates the weighted Pearson distance between two
 genes/rows or conditions/columns, using the absolute
 value of the uncentered version of the Pearson correlation.
uncenteredCorrelation(double[][], double[][], int[][], int[][], double[], int, int, boolean) - 
Static method in class biggests.clustering.AbstractMetricClustering
Calculates the weighted Pearson distance between two
 genes/rows or conditions/columns, using the uncentered
 version of the Pearson correlation.
uniqueID - 
Variable in class biggests.clustering.AbstractMetricClustering
The name of the unique ID used to identify genes in the data file.
useGOFrontEnd() - 
Method in class biggests.gui.PanelFunctionAnalysis
Check if GO frontend can be used for function analysis.



V

valueChanged(TreeSelectionEvent) - 
Method in class biggests.gui.BiggestsFrame_tree_treeSelectionAdapter
 
valueChanged(ListSelectionEvent) - 
Method in class biggests.gui.PanelBiclustering_algorithmsList_listSelectionAdapter
 
valueChanged(ListSelectionEvent) - 
Method in class biggests.gui.PanelPostProcessing_filterCriteriaList_listSelectionAdapter
 
valueChanged(ListSelectionEvent) - 
Method in class biggests.gui.PanelPostProcessing_sortCriteriaList_listSelectionAdapter
 
VALUES - 
Static variable in class biggests.gui.PanelAnalyzingMatrixTables
The type for values tables.
VALUES - 
Static variable in class biggests.tree.NodeInfo
The float values matrix data type.
verifyRotation(String, int) - 
Static method in class biggests.utils.VerticalTextIcon
Returns the best rotation for the string:

 - ROTATE_NONE

 - ROTATE_LEFT

 - ROTATE_RIGHT


 This is public static so you can use it to test a string without
 creating a VerticalTextIcon.
VerticalTextIcon - Class in biggests.utils
Title: Vertical Text Icon

 Description: VerticalTextIcon is an Icon implementation which draws
                 a short string vertically.
VerticalTextIcon(Component, String) - 
Constructor for class biggests.utils.VerticalTextIcon
Creates a VerticalTextIcon for the specified
 component with the specified label.
VerticalTextIcon(Component, String, int) - 
Constructor for class biggests.utils.VerticalTextIcon
Creates a VerticalTextIcon for the specified
 component with the specified label.
VerticalTextIconWithArrow - Class in biggests.utils
Title: Vertical Text Icon With Arrow

 Description: Implements an icon with vertical text and an arrow.
VerticalTextIconWithArrow(Icon, Component, String) - 
Constructor for class biggests.utils.VerticalTextIconWithArrow
 
VerticalTextIconWithArrow(Icon, Component, String, int) - 
Constructor for class biggests.utils.VerticalTextIconWithArrow
 



W

windowClosed(WindowEvent) - 
Method in class biggests.gui.MyTreeViewApp
Overrides LinkedViewApp's windowClosed
 method.
windowClosing(WindowEvent) - 
Method in class biggests.gui.BiggestsFrame_this_windowAdapter
 
windowClosing(WindowEvent) - 
Method in class biggests.utils.ProgressBarFrame_this_windowAdapter
 
windowStateChanged(WindowEvent) - 
Method in class biggests.gui.BiggestsFrame_this_windowStateAdapter
 
writeChartAsPDF(OutputStream, JFreeChart, int, int, FontMapper) - 
Static method in class biggests.gui.SaveChartImageDialog
Writes a chart to an output stream in PDF format.
writeChartAsSVG(Writer, JFreeChart, int, int) - 
Static method in class biggests.gui.SaveChartImageDialog
Writes a chart to an output stream in SVG document format.
writeJVMBitsToFile() - 
Static method in class biggests.utils.JVMInfo
Writes the number of bits of the JVM to a text file
 named bits.txt in the current directory.



Y

YELLOW_BLUE_SCHEME - 
Static variable in class biggests.utils.HeatmapColorScheme
 



Z

zoomSlider_stateChanged(ChangeEvent) - 
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
Handles changes on the zoom slider.


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