public JalviewJmolBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
public JalviewJmolBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- viewer = theViewer;
- viewer.setJmolStatusListener(this);
- viewer.addSelectionListener(this);
+ jmolViewer = theViewer;
+ jmolViewer.setJmolStatusListener(this);
+ jmolViewer.addSelectionListener(this);
{
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getStructureFiles());
{
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getStructureFiles());
public String superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, HiddenColumns[] _hiddenCols)
{
public String superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, HiddenColumns[] _hiddenCols)
{
}
// TODO: verify atomIndex is selecting correct model.
// return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
}
// TODO: verify atomIndex is selecting correct model.
// return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
// Then, construct pass a reader for the string to Jmol.
// ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
// fileName, null, reader, false, null, null, 0);
// Then, construct pass a reader for the string to Jmol.
// ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
// fileName, null, reader, false, null, null, 0);
// calculate essential attributes for the pdb data imported inline.
// prolly need to resolve modelnumber properly - for now just use our
// 'best guess'
// calculate essential attributes for the pdb data imported inline.
// prolly need to resolve modelnumber properly - for now just use our
// 'best guess'
"" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
}
// search pdbentries and sequences to find correct pdbentry for this
"" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
}
// search pdbentries and sequences to find correct pdbentry for this
// this is a foreign pdb file that jalview doesn't know about - add
// it to the dataset and try to find a home - either on a matching
// sequence or as a new sequence.
// this is a foreign pdb file that jalview doesn't know about - add
// it to the dataset and try to find a home - either on a matching
// sequence or as a new sequence.
"PDB");
// parse pdb file into a chain, etc.
// locate best match for pdb in associated views and add mapping to
"PDB");
// parse pdb file into a chain, etc.
// locate best match for pdb in associated views and add mapping to
"model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
"model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
(jmolfileio ? new SmarterJmolAdapter() : null),
htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
(jmolfileio ? new SmarterJmolAdapter() : null),
htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
console = createJmolConsole(consolePanel, buttonsToShow);
if (consolePanel != null)
console = createJmolConsole(consolePanel, buttonsToShow);
if (consolePanel != null)