Uses of Class
org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Packages that use AbstractAlignmentJmol

Package	Description
org.biojava.nbio.structure.align.gui
org.biojava.nbio.structure.align.gui.aligpanel
org.biojava.nbio.structure.align.gui.jmol	Utility methods for better interaction with Jmol.
org.biojava.nbio.structure.symmetry.gui

Uses of AbstractAlignmentJmol in org.biojava.nbio.structure.align.gui

Methods in org.biojava.nbio.structure.align.gui with parameters of type AbstractAlignmentJmol

Modifier and Type	Method	Description
static JMenuItem	MenuCreator.getExportPDBMenuItem(AbstractAlignmentJmol parent)
static JMenuBar	MenuCreator.initJmolMenu(JFrame frame, AbstractAlignmentJmol parent, AFPChain afpChain, MultipleAlignment msa)	Provide a JMenuBar that can be added to a JFrame containing a JmolPanel.
static void	DisplayAFP.showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)
static void	MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol)	Deprecated. Replace with
static void	MultipleAlignmentJmolDisplay.showMultipleAlignmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol)	Creates a new Frame with the MultipleAlignment Sequence Panel.

Constructors in org.biojava.nbio.structure.align.gui with parameters of type AbstractAlignmentJmol

Modifier	Constructor	Description
	MyDistMaxListener(AbstractAlignmentJmol parent)

Uses of AbstractAlignmentJmol in org.biojava.nbio.structure.align.gui.aligpanel

Methods in org.biojava.nbio.structure.align.gui.aligpanel with parameters of type AbstractAlignmentJmol

Modifier and Type	Method	Description
void	AligPanel.setAlignmentJmol(AbstractAlignmentJmol jmol)
void	MultipleAligPanel.setStructureAlignmentJmol(AbstractAlignmentJmol jmol)

Constructors in org.biojava.nbio.structure.align.gui.aligpanel with parameters of type AbstractAlignmentJmol

Modifier	Constructor	Description
	MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)	Constructor using an afpChain and the atom arrays for pairwise alignments.
	MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm)	Constructor using a MultipleAlignment.

Uses of AbstractAlignmentJmol in org.biojava.nbio.structure.align.gui.jmol

Subclasses of AbstractAlignmentJmol in org.biojava.nbio.structure.align.gui.jmol

Modifier and Type	Class	Description
class	MultipleAlignmentJmol	A class that provides a 3D visualization Frame in Jmol for MultipleAlignments.
class	StructureAlignmentJmol	A class that provides a simple GUI for Jmol

Uses of AbstractAlignmentJmol in org.biojava.nbio.structure.symmetry.gui

Methods in org.biojava.nbio.structure.symmetry.gui that return AbstractAlignmentJmol

Modifier and Type	Method	Description
static AbstractAlignmentJmol	SymmetryDisplay.display(CeSymmResult symmResult)	Displays a single structure in a cartoon representation with each symmetric repeat colored differently.