*/
package jalview.gui;
-import java.util.regex.*;
import java.util.*;
import java.awt.*;
import javax.swing.*;
import javax.swing.event.*;
+
import java.awt.event.*;
import java.io.*;
import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.structure.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
-import jalview.ws.ebi.EBIFetchClient;
-
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
public class AppJmol extends GStructureViewer implements Runnable,
- SequenceStructureBinding
+ SequenceStructureBinding, ViewSetProvider
{
AppJmolBinding jmb;
this(new String[]
{ file }, new String[]
{ id }, new SequenceI[][]
- { seq }, ap, loadStatus, bounds, viewid);
+ { seq }, ap, true, true, false, loadStatus, bounds, viewid);
}
+ ViewSelectionMenu seqColourBy;
+
/**
*
* @param files
* @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 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, 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);
- this.ap = ap;
+ addAlignmentPanel(ap);
+ if (useToAlign)
+ {
+ 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",
// bounds.width,bounds.height);
}
+ 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()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the jmol display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+ final ItemListener handler;
+ JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ _alignwith, handler = new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ alignStructs.setEnabled(_alignwith.size() > 0);
+ alignStructs.setToolTipText("Align structures using "
+ + _alignwith.size() + " linked alignment views");
+ }
+ });
+ handler.itemStateChanged(null);
+ 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;
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
+ String alreadyMapped = jmb.ssm.alreadyMappedToFile(
pdbentry.getId());
if (alreadyMapped != null)
if (option == JOptionPane.YES_OPTION)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
+ jmb.ssm.setMapping(seq, chains, alreadyMapped,
AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
{
if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
{
topJmol.jmb.addSequence(pe, seq);
+ topJmol.addAlignmentPanel(ap);
+ topJmol.buildJmolActionMenu();
break;
}
}
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
+ topJmol.useAlignmentPanelForSuperposition(ap);
topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
return;
}
}
// /////////////////////////////////
- jmb = new AppJmolBinding(this, new PDBEntry[]
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
{ pdbentry }, new SequenceI[][]
{ seq }, null, null);
- this.ap = ap;
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
if (pdbentry.getFile() != null)
{
}
/**
+ * list of sequenceSet ids associated with the view
+ */
+ ArrayList<String> _aps = new ArrayList();
+
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ AlignmentPanel[] t, list = new AlignmentPanel[0];
+ for (String setid : _aps)
+ {
+ AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
+ if (panels != null)
+ {
+ t = new AlignmentPanel[list.length + panels.length];
+ System.arraycopy(list, 0, t, 0, list.length);
+ System.arraycopy(panels, 0, t, list.length, panels.length);
+ list = t;
+ }
+ }
+
+ return list;
+ }
+
+ /**
+ * list of alignment panels to use for superposition
+ */
+ Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
+ /**
+ * list of alignment panels that are used for colouring structures by aligned
+ * sequences
+ */
+ Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
+ /**
+ * set the primary alignmentPanel reference and add another alignPanel to the
+ * list of ones to use for colouring and aligning
+ *
+ * @param nap
+ */
+ public void addAlignmentPanel(AlignmentPanel nap)
+ {
+ if (ap == null)
+ {
+ ap = nap;
+ }
+ if (!_aps.contains(nap.av.getSequenceSetId()))
+ {
+ _aps.add(nap.av.getSequenceSetId());
+ }
+ }
+
+ /**
+ * remove any references held to the given alignment panel
+ *
+ * @param nap
+ */
+ public void removeAlignmentPanel(AlignmentPanel nap)
+ {
+ try
+ {
+ _alignwith.remove(nap);
+ _colourwith.remove(nap);
+ if (ap == nap)
+ {
+ ap = null;
+ for (AlignmentPanel aps : getAllAlignmentPanels())
+ {
+ if (aps != nap)
+ {
+ ap = aps;
+ break;
+ }
+ }
+ }
+ } catch (Exception ex)
+ {
+ }
+ if (ap != null)
+ {
+ buildJmolActionMenu();
+ }
+ }
+
+ public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_alignwith.contains(nap))
+ {
+ _alignwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ if (_alignwith.contains(nap))
+ {
+ _alignwith.remove(nap);
+ }
+ }
+
+ 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);
+ if (!_colourwith.contains(nap))
+ {
+ _colourwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ if (_colourwith.contains(nap))
+ {
+ _colourwith.remove(nap);
+ }
+ }
+
+ /**
* pdb retrieval thread.
*/
private Thread worker = null;
if (frames[i] instanceof AppJmol)
{
AppJmol topJmol = ((AppJmol) frames[i]);
- if (topJmol.ap == ap2)
+ if (topJmol.isLinkedWith(ap2))
{
otherJmols.addElement(topJmol);
}
jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
null);
jmb.newJmolPopup(true, "Jmol", true);
+ if (command==null)
+ {
+ command="";
+ }
jmb.evalStateCommand(command);
jmb.setFinishedInit(true);
}
void closeViewer()
{
jmb.closeViewer();
-
+ ap = null;
+ _aps.clear();
+ _alignwith.clear();
+ _colourwith.clear();
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
jmb = null;
}
}
// refresh the sequence colours for the new structure(s)
- jmb.updateColours(ap);
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
// do superposition if asked to
if (alignAddedStructures)
{
{
public void run()
{
- jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+ alignStructs_withAllAlignPanels();
+ // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
}
});
alignAddedStructures = false;
{
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());
- // Set the colour using the current view for the associated alignframe
- jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures,
- ap.alignFrame.viewport.alignment);
+ if (_colourwith == null)
+ {
+ _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);
+ }
+ }
}
public void chainColour_actionPerformed(ActionEvent actionEvent)
return;
}
setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
this.setTitle(jmb.getViewerTitle());
if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
{
jmolActionMenu.setVisible(true);
}
+ if (!jmb.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
+ }
+ }
+
+ protected void buildJmolActionMenu()
+ {
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ for (Component c : jmolActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ jmolActionMenu.remove((JMenuItem) c);
+ }
+ }
+ final ItemListener handler;
}
/*
@Override
protected void alignStructs_actionPerformed(ActionEvent actionEvent)
{
+ alignStructs_withAllAlignPanels();
+ }
+ private void alignStructs_withAllAlignPanels()
+ {
+ if (ap == null)
+ {
+ return;
+ }
+ ;
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(ap);
+ }
+ ;
try
{
- jmb.superposeStructures(ap.av.getAlignment(), -1,
- ap.av.getColumnSelection());
+ AlignmentI[] als = new Alignment[_alignwith.size()];
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ int[] alm = new int[_alignwith.size()];
+ int a = 0;
+
+ for (AlignmentPanel ap : _alignwith)
+ {
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
+ }
+ jmb.superposeStructures(als, alm, alc);
} catch (Exception e)
{
- Cache.log.info("Couldn't align structures in alignframe "
- + ap.alignFrame.getTitle(), e);
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
+ {
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
}
+
}
public void setJalviewColourScheme(ColourSchemeI ucs)
}
+ /**
+ *
+ * @param alignment
+ * @return first alignment panel displaying given alignment, or the default
+ * alignment panel
+ */
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ {
+ for (AlignmentPanel ap : getAllAlignmentPanels())
+ {
+ if (ap.av.getAlignment() == alignment)
+ {
+ return ap;
+ }
+ }
+ return ap;
+ }
+
+ /**
+ *
+ * @param ap2
+ * @return true if this Jmol instance is linked with the given alignPanel
+ */
+ public boolean isLinkedWith(AlignmentPanel ap2)
+ {
+ return _aps.contains(ap2.av.getSequenceSetId());
+ }
+
+ public boolean isUsedforaligment(AlignmentPanel ap2)
+ {
+
+ return (_alignwith != null) && _alignwith.contains(ap2);
+ }
+
+ public boolean isUsedforcolourby(AlignmentPanel ap2)
+ {
+ 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