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. AlignmentCalcDB 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 DBResultTable DBSearchGUI DisplayAFPA utility class for visualistion of structure alignments DotPlotPanelDisplays the dot plot trace for an alignment. GUIAlignmentProgressListenera GUI that allows to watch progress as multiple alignments are being processed. GUIFarmJobRunnable 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