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 |
Modifier and Type | Method and 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.
|
Constructor and Description |
---|
MyDistMaxListener(AbstractAlignmentJmol parent) |
Modifier and Type | Method and Description |
---|---|
void |
AligPanel.setAlignmentJmol(AbstractAlignmentJmol jmol) |
void |
MultipleAligPanel.setStructureAlignmentJmol(AbstractAlignmentJmol jmol) |
Constructor and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
MultipleAlignmentJmol
A class that provides a 3D visualization Frame in Jmol for
MultipleAlignment s. |
class |
StructureAlignmentJmol
A class that provides a simple GUI for Jmol
|
Modifier and Type | Method and 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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