Uses of Class
org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
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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 -
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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)
Creates a new Frame with the MultipleAlignment Sequence Panel.Constructors in org.biojava.nbio.structure.align.gui with parameters of type AbstractAlignmentJmol Constructor Description MyDistMaxListener(AbstractAlignmentJmol parent)
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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 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 forMultipleAlignment
s.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.
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