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 using FastaAFPChainConverter.
|
| 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.
|
| AlignmentCalcDB |
|
| 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 superimposition
|
| AtomInfo |
This class uniquely describes an atom
|
| AtomInfoParser |
|
| AutoSuggestProvider |
A class that provides auto-completion suggestions for JAutoSuggest
|
| BiojavaJmol |
A class that provides a simple GUI for Jmol
|
| BrowserOpener |
|
| ChooseDirAction |
Ask the user to provide a directory containting PDB files.
|
| ColorConverter |
|
| ColorInterpolator |
|
| ColorUtils |
|
| ConfigPDBInstallPanel |
|
| ConfigXMLHandler |
XML content handler for serialisation of RegistryConfiguration class
|
| ContinuousColorMapper |
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 coordinates
|
| DBResultTable |
|
| DBSearchGUI |
|
| DefaultAutoSuggestProvider |
|
| DefaultMatrixMapper |
Color Mapper which mimics the default coloring of JMatrixPanel pixels.
|
| DemoAlignmentFromFasta |
Demo of how to use the FastaStructureParser class 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 the QuatSymmetryResults of a
structure.
|
| DemoRotationAxis |
A demo for how to use RotationAxis to display the rotation for an
alignment.
|
| DemoShowBiolAssembly |
|
| DemoShowCATHDomain |
|
| DemoShowLargeAssembly |
|
| DemoShowValidationResults |
|
| DemoStructureFromFasta |
Demo of how to use the FastaStructureParser class to read protein
structures from a FASTA file.
|
| DemoSW3DAligner |
|
| DisplayAFP |
A utility class for visualistion of structure alignments
|
| DotPlotPanel |
Displays the dot plot trace for an alignment.
|
| GradientMapper |
Maps a set of real values onto a gradient.
|
| GradientPanel |
|
| GUIAlignmentProgressListener |
a GUI that allows to watch progress as multiple alignments are being processed.
|
| GUIFarmJobRunnable |
|
| 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 alignment
|
| JmolAlignedPositionListener |
|
| 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 BiojavaJmol
|
| MenuCreator.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 for
MultipleAlignments.
|
| MultipleAlignmentJmolDisplay |
Utility Class that provides helper methods for the visualization of
MultipleAlignments.
|
| MultipleAligPanel |
A JPanel that can display the sequence alignment of a
MultipleAlignment in a nice way and interact with Jmol by
selecting the aligned atoms of the sequence selection.
|
| MultipleAligPanelMouseMotionListener |
|
| MultipleStatusDisplay |
|
| 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 for ConfigStrucAligParams, for the AlignmentGUI.
|
| PDBDirPanel |
A class to define where a structure for the alignment is coming from
|
| PDBServerPanel |
A class to define where a structure for the alignment is coming from
|
| PDBUploadPanel |
A JPanel to upload 2 custom PDB files.
|
| RasmolCommandListener |
a utility class that listens to Ramsol script commands in the @link BiojavaJmol class |
| RenderStyle |
|
| 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-ranges
|
| SequenceDisplay |
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 events
|
| SequenceScalePanel |
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 Jmol
|
| SqrtColorMapper |
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 Jmol
|
| StructureLoaderThread |
|
| 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 |
|
| WebStartDBSearch |
A Web Start wrapper for a FarmJobRunnable.
|
| WebStartDBSearchResults |
|
| WebStartMain |
|
| WrapLayout |
FlowLayout subclass that fully supports wrapping of components.
|