/*
- * 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.*;
this(new String[]
{ file }, new String[]
{ id }, new SequenceI[][]
- { seq }, ap, true,true, loadStatus, bounds, viewid);
+ { seq }, ap, true, true, false, loadStatus, bounds, viewid);
}
ViewSelectionMenu seqColourBy;
* @param ids
* @param seqs
* @param ap
- * @param usetoColour - add the alignment panel to the list used for colouring these structures
- * @param useToAlign - add the alignment panel to the list used for aligning these structures
+ * @param usetoColour
+ * - add the alignment panel to the list used for colouring these
+ * structures
+ * @param useToAlign
+ * - add the alignment panel to the list used for aligning these
+ * structures
+ * @param leaveColouringToJmol
+ * - do not update the colours from any other source. Jmol is handling them
* @param loadStatus
* @param bounds
* @param viewid
*/
public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
- AlignmentPanel ap, boolean usetoColour,boolean useToAlign, String loadStatus, Rectangle bounds,
- String viewid)
+ AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol,
+ String loadStatus, Rectangle bounds, String viewid)
{
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
}
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
- jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
{
useAlignmentPanelForSuperposition(ap);
}
+ if (leaveColouringToJmol || !usetoColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ jmolColour.setSelected(true);
+ }
if (usetoColour)
{
useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ jmolColour.setSelected(false);
}
this.setBounds(bounds);
- jmb.setColourBySequence(false);
- seqColour.setSelected(false);
initMenus();
viewId = viewid;
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
}
- private void initMenus() {
+
+ private void initMenus()
+ {
+ seqColour.setSelected(jmb.isColourBySequence());
+ jmolColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith==null)
+ {
+ _colourwith=new Vector<AlignmentPanel>();
+ }
+ if (_alignwith==null)
+ {
+ _alignwith=new Vector<AlignmentPanel>();
+ }
+
seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
new ItemListener()
{
viewMenu.add(seqColourBy);
final ItemListener handler;
JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
- _alignwith, handler=new ItemListener()
+ _alignwith, handler = new ItemListener()
{
@Override
jmolActionMenu.add(alpanels);
jmolActionMenu.addMenuListener(new MenuListener()
{
-
+
@Override
public void menuSelected(MenuEvent e)
{
handler.itemStateChanged(null);
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
// TODO Auto-generated method stub
-
+
}
-
+
@Override
public void menuCanceled(MenuEvent e)
{
// TODO Auto-generated method stub
-
+
}
});
-
}
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;
// ////////////////////////////////
// Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
+ String alreadyMapped = ap.getStructureSelectionManager().alreadyMappedToFile(
pdbentry.getId());
if (alreadyMapped != null)
if (option == JOptionPane.YES_OPTION)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
+ // 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, 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);
- setSize(400, 400); // probably should be a configurable/dynamic default here
- initMenus();
-
- if (pdbentry.getFile() != null)
+ useAlignmentPanelForColourbyseq(ap);
+ if (pdbentrys.length>1)
{
- initJmol("load \"" + pdbentry.getFile() + "\"");
+ alignAddedStructures=true;
+ useAlignmentPanelForSuperposition(ap);
}
- else
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ 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();
/**
* list of alignment panels to use for superposition
*/
- ArrayList<AlignmentPanel> _alignwith = new ArrayList();
+ Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
- ArrayList<AlignmentPanel> _colourwith = new ArrayList();
+ Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
/**
* set the primary alignmentPanel reference and add another alignPanel to the
}
}
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
+ {
+ useAlignmentPanelForColourbyseq(nap);
+ jmb.setColourBySequence(enableColourBySeq);
+ seqColour.setSelected(enableColourBySeq);
+ jmolColour.setSelected(!enableColourBySeq);
+ }
public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
{
addAlignmentPanel(nap);
jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
null);
jmb.newJmolPopup(true, "Jmol", true);
+ if (command==null)
+ {
+ command="";
+ }
jmb.evalStateCommand(command);
jmb.setFinishedInit(true);
}
"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;
{
for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
{
- cap.appendText(StructureSelectionManager
- .getStructureSelectionManager().printMapping(
+ cap.appendText(jmb.printMapping(
jmb.pdbentry[pdbe].getFile()));
cap.appendText("\n");
}
im.writeImage();
}
}
-
+ public void jmolColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (jmolColour.isSelected()) {
+ // disable automatic sequence colouring.
+ jmb.setColourBySequence(false);
+ }
+ }
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith==null) { _colourwith=new ArrayList<AlignmentPanel>();};
- if (_colourwith.size()==0){ _colourwith.add(ap); };
-
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
+ if (_colourwith == null)
{
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (jmb.isColourBySequence())
+ {
+ if (!jmb.isLoadingFromArchive())
+ {
+ if (_colourwith.size()==0 && ap!=null) {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(ap.alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ }
}
}
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);
{
jmolActionMenu.setVisible(true);
}
- if (!jmb.isLoadingFromArchive()) {
+ if (!jmb.isLoadingFromArchive())
+ {
seqColour_actionPerformed(null);
}
}
protected void buildJmolActionMenu()
{
- if (_alignwith==null) { _alignwith=new ArrayList<AlignmentPanel>();}
- if (_alignwith.size()==0 && ap!=null) { _alignwith.add(ap);};
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
for (Component c : jmolActionMenu.getMenuComponents())
{
if (c != alignStructs)
private void alignStructs_withAllAlignPanels()
{
- if (ap==null) { return; };
- if (_alignwith.size()==0) { _alignwith.add(ap);};
+ if (ap == null)
+ {
+ return;
+ }
+ ;
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(ap);
+ }
+ ;
try
{
AlignmentI[] als = new Alignment[_alignwith.size()];
return (_colourwith != null) && _colourwith.contains(ap2);
}
+ /**
+ *
+ * @return TRUE if the view is NOT being coloured by sequence associations.
+ */
+ public boolean isColouredByJmol()
+ {
+ return !jmb.isColourBySequence();
+ }
+
+
}
git://source.jalview.org / jalview.git / blobdiff