Package IMPACT

Class Summary

AlignmentEditor	Implementation of methods and data structures for GUIAlignmentEditor.
ConTestTask	Implementation of background task for ConTest execution.
CSVTableModel	Implementation of specific Table Model for Comma Separated Values files.
FileFormatConverter	Implementation of functions to read/write several formats of MSA files.
GenericJarTask	Implementation of background task to run any java (jar) program file. Used for A Tree Viewer (ATV) and Jmol programs.
GUI	Implementation of IMPACT, main.
GUIAboutBox	Implementation of an About box for menu Help.
GUIAlignmentEditor	Implementation of MSA Editor / Viewer, also topology (re)estimation through PhyML.
GUIConfPreferences	Implementation of IMPACT Preferences. Configuration and management of several paths.
GUIDialogs	Implementation of several dialog messages.
GUIFileChooser	Implementation of a File Chooser.
GUIFileFormatConverter	Implementation of MSA File Format Converter. Supports conversion between formats like Mase, Fasta, Clustal and Phylip
GUIInitializationBox	Implementation of a user debbuging box, for GUI initialization.
GUIPhyMLOptions	Implementation of PhyML Options selection.
GUIProgExecOutput	Implementation of external program execution output viewer.
GUIResultsSummary	Implementation of options to provide for producing summary of results.
GUIResultsView	Implementation of Comma Separated Values (CSV) format files viewer.
MSAColumnColorRenderer	Implementation of specific Table Cell Renderer for presenting selected columns in MSA table.
MSATableModel	Implementation of specific Table Model for Multiple Sequence Alignments.
PhyMLTask	Implementation of a background task for PhyML execution.
ResultsSummary	Implementation of several methods to present a summary of results. These are based in R output file, MSA file, and 3D location (created by user).
ResultsView	Implementation of several methods to allow reading Comma Separating Values (CSV) files.
RSoftwareTask	Implementation of background task to run R scripts.
Utilities	Implementation of various methods and data structures needed across IMPACT package.
ViewerTask	Implementation of background task to run PDF/PS viewer.