All Classes
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All Classes Interface Summary Class Summary Enum Summary Class Description AboutDialog AbstractAlignmentJmol An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.AFPChainCoordManager AFPFromFasta Demo displaying a structural alignment from a FASTA file usingFastaAFPChainConverter.AlignedPosition AlignmentCalc A class that obtains two structures via DAS and aligns them This is done in a separate thread.AlignmentCalc A class that obtains two structures via DAS and aligns them This is done in a separate thread.AlignmentCalculationRunnable AlignmentGui A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload.AlignmentGuiDemo Get an instance of the two alignment GUIs.AlignmentPositionListener AlignmentTextPanel AligPanel A JPanel that can display an AFPChain in a nice way and interact with Jmol.AligPanelMouseMotionListener AligUIManager AlternativeAlignmentFrame a frame showing the alternative alignments, which are the result of a structure superimpositionAtomInfo This class uniquely describes an atomAtomInfoParser AutoSuggestProvider A class that provides auto-completion suggestions for JAutoSuggestBiojavaJmol A class that provides a simple GUI for JmolBrowserOpener ChooseDirAction Ask the user to provide a directory containting PDB files.ColorConverter ColorInterpolator ColorUtils ConfigPDBInstallPanel ConfigXMLHandler XML content handler for serialisation of RegistryConfiguration classContinuousColorMapper Provides a mapping between real numbers and Colors.ContinuousColorMapperTransform Maps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering.CookBook CoordManager a class that manages the conversion of sequence coordinate system to JPanel drawing coordinatesDefaultAutoSuggestProvider DefaultMatrixMapper Color Mapper which mimics the default coloring of JMatrixPanel pixels.DemoAlignmentFromFasta Demo of how to use theFastaStructureParserclass to read protein structures from a FASTA file.DemoCE DemoCeSymm Quick demo of how to call CE-Symm programmatically.DemoFATCAT DemoMultipleMC Demo for running the CEMC Algorithm on a protein family and visualizing the results.DemoNWALignment DemoQuatSymmetryJmol This demo shows how to display theQuatSymmetryResultsof a structure.DemoRotationAxis A demo for how to useRotationAxisto display the rotation for an alignment.DemoShowBiolAssembly DemoShowCATHDomain DemoShowLargeAssembly DemoStructureFromFasta Demo of how to use theFastaStructureParserclass to read protein structures from a FASTA file.DemoSW3DAligner DisplayAFP A utility class for visualistion of structure alignmentsDotPlotPanel Displays the dot plot trace for an alignment.GradientMapper Maps a set of real values onto a gradient.GradientPanel HelpDialog HSVColorSpace JAutoSuggest A JTextField that can make suggestions for auto-complete.JMatrixPanel a JPanel that can display a difference of distance matrix and paths that have been taken for the alignmentJmolAlignedPositionListener JmolPanel JmolPanel.JmolLoggerAdapter JmolSymmetryScriptGenerator JmolSymmetryScriptGeneratorC1 JmolSymmetryScriptGeneratorCn JmolSymmetryScriptGeneratorDn JmolSymmetryScriptGeneratorH JmolSymmetryScriptGeneratorI JmolSymmetryScriptGeneratorO JmolSymmetryScriptGeneratorPointGroup JmolSymmetryScriptGeneratorT JmolTools JmolViewerImpl JNLPProxy JPrintPanel LinearColorInterpolator LinearColorInterpolator.InterpolationDirection LogColorMapper Performs a log10 transform on input before passing the values off to another colorMapper.MemoryMonitor Tracks Memory allocated & used, displayed in graph form.MenuCreator Create the menus for structure alignment GUI windows (JFrames).MenuCreator Create the menu for BiojavaJmolMenuCreator.DotPlotListener Creates a frame to display a DotPlotPanel.MultipleAlignmentCalc A class that obtains structures via DAS and aligns them.MultipleAlignmentCoordManager Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.MultipleAlignmentGUI A JFrame that allows to trigger a multiple structure alignment, either from files in a directory or after manual upload.MultipleAlignmentJmol A class that provides a 3D visualization Frame in Jmol forMultipleAlignments.MultipleAlignmentJmolDisplay Utility Class that provides helper methods for the visualization ofMultipleAlignments.MultipleAligPanel A JPanel that can display the sequence alignment of aMultipleAlignmentin a nice way and interact with Jmol by selecting the aligned atoms of the sequence selection.MultipleAligPanelMouseMotionListener Mouse Motion Listener for theMultipleAligPanel, which provides methods to obtain positions of the mouse and connect them to the sequence alignment positions using the information inMultipleAlignmentCoordManager.MultipleStatusDisplay This class provides information of the selected positions in theMultipleAligPanel.MyAlignmentLoadListener Loads an alignment in an XML format and displays its content in a new Jmol panel.MyDistMaxListener Shows the interatomic Distance Matrices of all the Structures aligned in different Frames.MyExportListener MyJmolStatusListener MyOpenPdbFileListener MySaveFileListener Save an alignment to a specified File by the user.MyTableRowSorter ParameterGUI UI forConfigStrucAligParams, for the AlignmentGUI.PDBDirPanel A class to define where a structure for the alignment is coming fromPDBServerPanel A class to define where a structure for the alignment is coming fromPDBUploadPanel A JPanel to upload 2 custom PDB files.RasmolCommandListener a utility class that listens to Ramsol script commands in the @linkBiojavaJmolclassRenderStyle ScaleableMatrixPanel A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm.SCOPAutoSuggestProvider ScopInstallationInstance ScopSelectPanel Selection SelectionImpl SelectMultiplePanel A Text Panel that allows the user to specify multiple structure identifiers, space separated.SelectPDBPanel A Panel that allows user to specify PDB & chain ID, as well as sub-rangesSequenceDisplay A sequence display that can show the results of a protein structure alignment.SequenceMouseListener a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate SequenceListener and FeatureListener eventsSequenceScalePanel A class that draws a Sequence as a rectangle, a scale display over it.ShowPDBIDListener ShowStructureInJmol Demo how to load and display a structure in JmolSqrtColorMapper Performs a sqrt transform on input before passing the values off to another colorMapper.StatusDisplay StructureAlignmentDisplay StructureAlignmentJmol A class that provides a simple GUI for JmolStructureLoaderThread StructurePairSelector To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.StructureViewer SymmetryCalc Calculates a symmetry analysis and displays the results.SymmetryDisplay Class that provides visualizations methods for symmetry alignments.SymmetryGui A JFrame that allows to trigger a symmetry analysis, either from files in a directory or after manual upload Adapted from the AlignmentGui class in biojava.SymmetryListener Action Listener for the symmetry menu.SystemInfo WebStartClientDemo WebStartMain WrapLayout FlowLayout subclass that fully supports wrapping of components.