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

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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(AbstractExpressionMatrix, TreePath) - Method in class biggests.gui.PanelBiclustering
Paints this biclustering panel with options to perform biclustering and function analysis on AbstractExpressionMatrix objects (ExpressionMatrix and PreProcessedExpressionMatrix).
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.
paint(PreProcessedExpressionMatrix, 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.
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.
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.
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.
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.
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.
PanelExpressionChart - Class in biggests.gui
Title: Expression Chart Panel Description: A panel which holds an expression chart.
PanelExpressionChart(Bicluster, boolean, int, int, String, 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, String, 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, String, 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.
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.
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.
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.
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.BiggestsIO
Image format: PDF
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.
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.
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.

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