Interface Summary Interface Description AlignmentCalculationRunnable
Class Summary Class Description AboutDialog AlignmentCalcA class that obtains two structures via DAS and aligns them This is done in a separate thread. AlignmentGuiA JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload. AlignmentTextPanel ChooseDirActionAsk the user to provide a directory containting PDB files. ConfigPDBInstallPanel DisplayAFPA utility class for visualistion of structure alignments DotPlotPanelDisplays the dot plot trace for an alignment. HelpDialog JPrintPanel MemoryMonitorTracks Memory allocated & used, displayed in graph form. MenuCreatorCreate the menus for structure alignment GUI windows (JFrames). MenuCreator.DotPlotListenerCreates a frame to display a DotPlotPanel. MultipleAlignmentCalcA class that obtains structures via DAS and aligns them. MultipleAlignmentGUIA JFrame that allows to trigger a multiple structure alignment, either from files in a directory or after manual upload. MultipleAlignmentJmolDisplayUtility Class that provides helper methods for the visualization of
MyAlignmentLoadListenerLoads an alignment in an XML format and displays its content in a new Jmol panel. MyDistMaxListenerShows the interatomic Distance Matrices of all the Structures aligned in different Frames. MyExportListener MyOpenPdbFileListener MySaveFileListenerSave an alignment to a specified File by the user. MyTableRowSorter ParameterGUIUI for
ConfigStrucAligParams, for the AlignmentGUI.
SelectPDBPanelA Panel that allows user to specify PDB & chain ID, as well as sub-ranges ShowPDBIDListener StructureAlignmentDisplay StructureLoaderThread SystemInfo