All Classes and Interfaces
Class
Description
An Abstract Class to generalize the visualization of AFP and
MultipleAlignment structure alignments in Jmol.
Demo displaying a structural alignment from a FASTA file using
FastaAFPChainConverter.A class that obtains two structures via DAS and aligns them
This is done in a separate thread.
A class that obtains two structures via DAS and aligns them
This is done in a separate thread.
A JFrame that allows to trigger a pairwise structure alignment,
either from files in a directory,
or after manual upload.
Get an instance of the two alignment GUIs.
A JPanel that can display an AFPChain in a nice way and interact with Jmol.
a frame showing the alternative alignments, which are the result of a structure superimposition
This class uniquely describes an atom
A class that provides auto-completion suggestions for JAutoSuggest
A class that provides a simple GUI for Jmol
Ask the user to provide a directory containting PDB files.
XML content handler for serialisation of RegistryConfiguration class
Provides a mapping between real numbers and Colors.
Maps colors by performing a transform of the input data and then passing
the transformed value to a ContinuousColorMapper for rendering.
a class that manages the conversion of sequence coordinate system to
JPanel drawing coordinates
Color Mapper which mimics the default coloring of JMatrixPanel pixels.
Demo of how to use the
FastaStructureParser class to read protein
structures from a FASTA file.Quick demo of how to call CE-Symm programmatically.
Demo for running the CEMC Algorithm on a protein family and
visualizing the results.
This demo shows how to display the
QuatSymmetryResults of a
structure.A demo for how to use
RotationAxis to display the rotation for an
alignment.Demo of how to use the
FastaStructureParser class to read protein
structures from a FASTA file.A utility class for visualistion of structure alignments
Displays the dot plot trace for an alignment.
Maps a set of real values onto a gradient.
A JTextField that can make suggestions for auto-complete.
a JPanel that can display a difference of distance matrix and paths that have been
taken for the alignment
Performs a log10 transform on input before passing the values off to another
colorMapper.
Tracks Memory allocated invalid input: '&' used, displayed in graph form.
Create the menus for structure alignment GUI windows (JFrames).
Create the menu for BiojavaJmol
Creates a frame to display a DotPlotPanel.
A class that obtains structures via DAS and aligns them.
Generalization of the Coodinate Manager to include an arbitrary number of
sequences (lines) for MultipleAlignment visualization.
A JFrame that allows to trigger a multiple structure alignment,
either from files in a directory or after manual upload.
A class that provides a 3D visualization Frame in Jmol for
MultipleAlignments.Utility Class that provides helper methods for the visualization of
MultipleAlignments.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.Mouse Motion Listener for the
MultipleAligPanel,
which provides methods to obtain positions of the mouse
and connect them to the sequence alignment positions using
the information in MultipleAlignmentCoordManager.This class provides information of the selected positions in the
MultipleAligPanel.Loads an alignment in an XML format and displays its content in a
new Jmol panel.
Shows the interatomic Distance Matrices of all the Structures aligned in different Frames.
Save an alignment to a specified File by the user.
UI for
ConfigStrucAligParams, for the AlignmentGUI.A class to define where a structure for the alignment is coming from
A class to define where a structure for the alignment is coming from
A JPanel to upload 2 custom PDB files.
a utility class that listens to Ramsol script commands in the @link
BiojavaJmol classA JPanel that can display the underlying distance matrix
data of the protein structure alignment algorithm.
A Text Panel that allows the user to specify multiple structure
identifiers, space separated.
A Panel that allows user to specify PDB invalid input: '&' chain ID, as well as sub-ranges
A sequence display that can show the results of a protein structure alignment.
a mouse listener for the AbstractChainRenderer class
it listens to all mouse events and triggeres appropriate
SequenceListener and FeatureListener events
A class that draws a Sequence as a rectangle, a scale display over it.
Demo how to load and display a structure in Jmol
Performs a sqrt transform on input before passing the values off to another
colorMapper.
A class that provides a simple GUI for Jmol
To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
Calculates a symmetry analysis and displays the results.
Class that provides visualizations methods for symmetry alignments.
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.
Action Listener for the symmetry menu.
FlowLayout subclass that fully supports wrapping of components.