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

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.
getDefaultDOTPath() - Static method in class biggests.utils.BiggestsInstall
 
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.FileFilterDirectoryChooser
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.
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.
getSelectedNode() - Method in class biggests.tree.DatasetTree
 
getSelectedNodeComponent() - Method in class biggests.tree.DatasetTree
 
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
 
gunzipFile(File, File) - Static method in class biggests.gui.BiggestsIO
Gunzips the input archive.

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