import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
SequenceI[][] seqs)
{
createProgressBar();
- // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
- String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
- ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
- null);
+ ap.getStructureSelectionManager(), pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
if (pdbentrys.length > 1)
}
/**
- * Retrieve chains for sequences by inspecting their PDB refs. The hope is
- * that the first will be to the sequence's own chain. Really need a more
- * managed way of doing this.
- *
- * @param seqs
- * @return
- */
- protected String[][] extractChains(SequenceI[][] seqs)
- {
- String[][] chains = new String[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
- {
- chains[i] = new String[seqs[i].length];
- int seqno = 0;
- for (SequenceI seq : seqs[i])
- {
- String chain = null;
- if (seq.getDatasetSequence() != null)
- {
- Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
- .getAllPDBEntries();
- if (pdbrefs != null && pdbrefs.size() > 0)
- {
- // FIXME: SequenceI.PDBEntry[0] chain mapping used for
- // ChimeraViewFrame. Is this even used ???
-
- chain = pdbrefs.get(0).getChainCode();
- }
- }
- chains[i][seqno++] = chain;
- }
- }
- return chains;
- }
-
- /**
* Create a new viewer from saved session state data including Chimera session
* file
*
*/
void initChimera()
{
- jalview.gui.Desktop.addInternalFrame(this,
- jmb.getViewerTitle("Chimera", true), getBounds().width,
- getBounds().height);
+ Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
+ getBounds().width, getBounds().height);
if (!jmb.launchChimera())
{
*
* @param chainNames
*/
+ @Override
void setChainMenuItems(List<String> chainNames)
{
chainMenu.removeAll();
/**
* Show only the selected chain(s) in the viewer
*/
+ @Override
void showSelectedChains()
{
List<String> toshow = new ArrayList<String>();
List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
List<Integer> filePDBpos = new ArrayList<Integer>();
PDBEntry thePdbEntry = null;
+ StructureFile pdb = null;
try
{
String[] curfiles = jmb.getPdbFile(); // files currently in viewer
}
}
int num = -1;
-
for (PDBEntry pe : filePDB)
{
num++;
stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
jmb.getChains()[pos], pe.getFile(), protocol);
+ stashFoundChains(pdb, pe.getFile());
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
}
}
+ jmb.refreshGUI();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
* @return
* @throws Exception
*/
+
+ private void stashFoundChains(StructureFile pdb, String file)
+ {
+ for (int i = 0; i < pdb.getChains().size(); i++)
+ {
+ String chid = new String(pdb.getId() + ":"
+ + pdb.getChains().elementAt(i).id);
+ jmb.getChainNames().add(chid);
+ jmb.getChainFile().put(chid, file);
+ }
+ }
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
// FIXME: this is duplicated code with Jmol frame ?