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

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(DiscretizedExpressionMatrix, 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.
TableColorsWithMissingValues(DiscretizedExpressionMatrix) - Constructor for class biggests.tables.TableColorsWithMissingValues
Creates a new colored table with data from the given expression matrix with missing values.
TableColorsWithMissingValues(Bicluster, GOFrontEnd, Component) - Constructor for class biggests.tables.TableColorsWithMissingValues
Creates a new colored table with data from the given bicluster with missing values.
TableColorsWithMissingValues(Bicluster) - Constructor for class biggests.tables.TableColorsWithMissingValues
Creates a new colored table with data from the given bicluster 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) - Constructor for class biggests.tables.TableFunctionIndividual
Creates a new table of functions with terms and p-values data.
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(Object[][], Object[], GOFrontEnd) - Constructor for class biggests.tables.TableFunctionIndividual
Creates a new table of functions from the given rowData and columnNames 1st column - GO Term ID
2nd column - GO Term Name
3rd column - Number of Genes in Population Annotated with the Term
GO Term IDGO Term Name#Ann.
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(TableSorterFunctionIndividual, GOFrontEnd) - 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.
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.
TableSymbolsWithMissingValues(CCC_Bicluster, GOFrontEnd, Component) - Constructor for class biggests.tables.TableSymbolsWithMissingValues
Creates a new table of symbols with data from the the given bicluster.
TableSymbolsWithMissingValues(CCC_Bicluster) - Constructor for class biggests.tables.TableSymbolsWithMissingValues
Creates a new table of symbols with data from the given bicluster's 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(TableSorterValues) - 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.
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.
TableValuesWithMissingValues(Bicluster, GOFrontEnd, Component) - Constructor for class biggests.tables.TableValuesWithMissingValues
Creates a new values table from the data of a bicluster with missing values.
TableValuesWithMissingValues(Bicluster) - Constructor for class biggests.tables.TableValuesWithMissingValues
Creates a new values table from the data of a bicluster 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, GOFrontEnd, 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, IMatrix, TreePath, GOFrontEnd, File, String, float) - Constructor for class biggests.gui.ThreadFunctionAnalysis
Creates a new Function Analysis Thread to perform function analysis on a matrix.
ThreadFunctionAnalysis(BiggestsFrame, Bicluster, TreePath, File[], File, float) - Constructor for class biggests.gui.ThreadFunctionAnalysis
Creates a new Function Analysis Thread to perform function analysis on a bicluster.
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.
ThreadFunctionAnalysis(BiggestsFrame, Bicluster, TreePath, GOFrontEnd, File, float) - Constructor for class biggests.gui.ThreadFunctionAnalysis
Creates a new ThreadFunctionAnalysis.
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_mouseClicked(MouseEvent) - Method in class biggests.gui.BiggestsFrame
Handles a mouse click in this table of colors.
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