Package biggests.gui

Class Summary
BiggestsApplication 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.
BiggestsFrame Title: BiGGEsTS Frame Description: The main frame of the application.
BiggestsFrame_this_componentAdapter  
BiggestsFrame_this_windowAdapter Title: Description:
BiggestsFrame_this_windowStateAdapter  
BiggestsFrame_tree_treeSelectionAdapter Title: Description:
BiggestsIO 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.
MyTreeViewApp 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.
PanelAnalyzingFunctionSignificanceGraph Title: Function Analysis - Significance Graph Panel Description: Displays a significance graph of a bicluster.
PanelAnalyzingFunctionSignificanceGraph_saveGraph_actionAdapter Title: Description:
PanelAnalyzingFunctionSignificanceGraph_zoomSlider_changeAdapter Title: Description:
PanelAnalyzingFunctionTable Title: Panel for Analyzing Tables of Functions Description: Displays a table of functions of a bicluster or group of biclusters.
PanelAnalyzingFunctionTable_applyButton_actionAdapter  
PanelAnalyzingFunctionTable_functionGroupTable_mouseAdapter  
PanelAnalyzingFunctionTable_recalculate_actionAdapter  
PanelAnalyzingMatrixDendrogram 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_applyButton_actionAdapter  
PanelAnalyzingMatrixDendrogram_clusterConditionsCheckBox_itemAdapter  
PanelAnalyzingMatrixDendrogram_clusterGenesCheckBox_itemAdapter  
PanelAnalyzingMatrixTables 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_biclustersNumberOption_itemAdapter Title: Description:
PanelBasicIOValidation Title: Panel with Basic Input/Output Validation Description: Extends JPanel class with some methods to perform basic validations over data input by the user.
PanelBiclustering Title: Biclustering Panel Description: Displays available biclustering techniques and allows for setting their corresponding parameters and apply them to the gene expression data.
PanelBiclustering_algorithmsList_listSelectionAdapter Title: Description:
PanelBiclustering_allowMissingsButton_mouseAdapter  
PanelBiclustering_applyButton_actionAdapter  
PanelBiclustering_geneShiftsCheckBox_itemAdapter Title: Description:
PanelBiclustering_restrictedErrorsECCCCheckBox_itemAdapter Title: Description:
PanelBiclustering_signChangesCheckBox_itemAdapter  
PanelBiclustering_timeLagsCheckBox_itemAdapter  
PanelExpression Title: Expression Panel Description: Displays expression charts.
PanelExpression_normalize_itemAdapter Title: Description:
PanelExpression_option_itemAdapter Title: Description:
PanelExpression_this_hierarchyBoundsAdapter  
PanelExpressionChart Title: Expression Chart Panel Description: A panel which holds an expression chart.
PanelFunctionAnalysis Title: Function Analysis Panel Description: This panel displays function analysis options to apply to a given bicluster or group of biclusters.
PanelFunctionAnalysis_browseGeneAssociationFilesPathButton_actionAdapter  
PanelFunctionAnalysis_browseGOFilesPathButton_actionAdapter Title: Description:
PanelFunctionAnalysis_downloadGeneAssociationFileButton_actionAdapter  
PanelFunctionAnalysis_downloadGeneOntologyFileButton_actionAdapter  
PanelFunctionAnalysis_goFrontEndCheckBox_itemAdapter  
PanelLoading 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_browseConversionFileButton_actionAdapter  
PanelLoading_browseDatasetFileButton_actionAdapter  
PanelLoading_datasetFileTextField_caretAdapter  
PanelLoading_datasetFileTextField_inputMethodAdapter  
PanelLoading_geneIDCheckBox_itemAdapter  
PanelLoading_loadButton_actionAdapter  
PanelPostProcessing Title: Post-Processing Panel Description: Displays options to select and apply post-processing techniques to groups of biclusters.
PanelPostProcessing_applyButton_actionAdapter Description: Action adapter for apply button.
PanelPostProcessing_filterCheckBox_itemAdapter Description: Item adapter for filter check box.
PanelPostProcessing_filterCriteriaList_listSelectionAdapter Description: List selection adapter for filter criteria list.
PanelPostProcessing_sortCheckBox_itemAdapter Description: Item adapter for sort check box.
PanelPostProcessing_sortCriteriaList_listSelectionAdapter Description: List selection adapter for sort criteria list.
PanelPreProcessing Title: Preprocessing Panel Description: Displays options to select and apply different preprocessing techniques on gene expression data matrices.
PanelPreProcessing_applyButton_actionAdapter  
PanelPreProcessing_discretizeCheckBox_itemAdapter  
PanelPreProcessing_discretizeComboBox_itemAdapter  
PanelPreProcessing_fillAverageRowButton_itemAdapter  
PanelPreProcessing_fillCheckBox_itemAdapter  
PanelPreProcessing_fillKNeighborsButton_itemAdapter  
PanelPreProcessing_fillValueButton_itemAdapter  
PanelPreProcessing_filterCheckBox_itemAdapter  
PanelPreProcessing_filterPercentGenesButton_itemAdapter  
PanelPreProcessing_normalizeByGeneButton_itemAdapter  
PanelPreProcessing_normalizeCheckBox_itemAdapter  
PanelPreProcessing_normalizeMean0Std1Button_itemAdapter  
PanelPreProcessing_normalizeMeanStdValuesButton_itemAdapter  
PanelPreProcessing_normalizeOverallButton_itemAdapter  
PanelPreProcessing_smoothCheckBox_itemAdapter  
SaveChartImageDialog 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_browseButton_actionAdapter  
SaveChartImageDialog_cancelButton_actionAdapter  
SaveChartImageDialog_displayedSizeRadioButton_itemAdapter  
SaveChartImageDialog_saveButton_actionAdapter  
ThreadBiclustering Title: Biclustering and function analysis thread.
ThreadDownloadGOFiles 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.
ThreadFunctionAnalysis Title: Function analysis thread.
ThreadHierarchicalClustering 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.
ThreadPostProcessing 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.