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. |
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. |
PanelAnalyzingFunctionSignificanceGraph |
Title: Function Analysis - Significance Graph Panel
Description: Displays a significance graph of a bicluster. |
PanelAnalyzingFunctionTable |
Title: Panel for Analyzing Tables of Functions
Description: Displays a table of functions of a bicluster
or group of biclusters. |
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. |
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. |
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. |
PanelExpression |
Title: Expression Panel
Description: Displays expression charts. |
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. |
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. |
PanelPostProcessing |
Title: Post-Processing Panel
Description: Displays options to select and apply post-processing
techniques to groups of biclusters. |
PanelPreProcessing |
Title: Preprocessing Panel
Description: Displays options to select and apply different
preprocessing techniques on gene expression
data matrices. |
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. |
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. |