/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.io.*;
import jalview.jbgui.GStructureViewer;
+import jalview.api.AlignmentViewPanel;
import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
import jalview.datamodel.*;
}
IProgressIndicator progressBar = null;
+ /**
+ * add a single PDB structure to a new or existing Jmol view
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
+ final AlignmentPanel ap)
{
progressBar = ap.alignFrame;
// ////////////////////////////////
if (option == JOptionPane.YES_OPTION)
{
+ // TODO : Fix multiple seq to one chain issue here.
ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped,
AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
{
if (frames[i] instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol) frames[i]);
+ final AppJmol topJmol = ((AppJmol) frames[i]);
// JBPNOTE: this looks like a binding routine, rather than a gui
// routine
for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
{
topJmol.jmb.addSequence(pe, seq);
topJmol.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
topJmol.buildJmolActionMenu();
+ ap.getStructureSelectionManager().sequenceColoursChanged(ap);
break;
}
}
}
}
// /////////////////////////////////
-
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, null, null);
+ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ }
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
+ boolean promptUser=pdbentrys.length==1;
+ progressBar = ap.alignFrame;
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+ if (pdbentrys.length>1)
+ {
+ alignAddedStructures=true;
+ useAlignmentPanelForSuperposition(ap);
+ }
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
-
- if (pdbentry.getFile() != null)
- {
- initJmol("load \"" + pdbentry.getFile() + "\"");
- }
- else
+ worker=null;
+ String filelist="";
+// for (PDBEntry pe: pdbentrys)
+// {
+// if (pe.getFile()==null)
+ {
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+// break;
+ }
+// filelist+=" \""+pe.getFile()+"\"";
+
+/* }
+ if (worker==null)
{
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
+ initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
}
-
+*/
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
}
/**
+ * create a new Jmol containing several structures superimposed using the given alignPanel.
+ * @param ap
+ * @param pe
+ * @param seqs
+ */
+ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+ {
+ openNewJmol(ap, pe, seqs);
+ }
+
+ /**
* list of sequenceSet ids associated with the view
*/
ArrayList<String> _aps = new ArrayList();
"Couldn't load file", JOptionPane.ERROR_MESSAGE);
}
+ long lastnotify = jmb.getLoadNotifiesHandled();
if (files.length() > 0)
{
if (!addingStructures)
cmd.append("\nloadingJalviewdata=null");
final String command = cmd.toString();
cmd = null;
- long lastnotify = jmb.getLoadNotifiesHandled();
+ lastnotify = jmb.getLoadNotifiesHandled();
+
try
{
jmb.evalStateCommand(command);
{
Cache.log.error("Couldn't add files to Jmol viewer!", ex);
}
- // need to wait around until script has finished
- while (lastnotify >= jmb.getLoadNotifiesHandled())
- ;
+ }
+
+ // need to wait around until script has finished
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length))
+ {
+ try
{
- try
- {
- Thread.sleep(35);
- } catch (Exception e)
- {
- }
- }
- // refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(35);
+ } catch (Exception e)
{
- jmb.updateColours(ap);
}
- // do superposition if asked to
- if (alignAddedStructures)
+ }
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ public void run()
{
- public void run()
- {
- alignStructs_withAllAlignPanels();
- // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
- }
- });
- alignAddedStructures = false;
- }
- addingStructures = false;
+ alignStructs_withAllAlignPanels();
+ // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+ }
+ });
+ alignAddedStructures = false;
}
+ addingStructures = false;
+
}
_started = false;
worker = null;
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
-
+
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
git://source.jalview.org / jalview.git / blobdiff