|
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. |