JAL-777/JAL-641 debugging
authorjprocter <Jim Procter>
Fri, 18 Feb 2011 17:33:41 +0000 (17:33 +0000)
committerjprocter <Jim Procter>
Fri, 18 Feb 2011 17:33:41 +0000 (17:33 +0000)
src/jalview/gui/AppJmol.java
src/jalview/gui/AppJmolBinding.java

index 19178f2..723b5f4 100644 (file)
@@ -19,9 +19,11 @@ package jalview.gui;
 
 import java.util.regex.*;
 import java.util.*;
+import java.util.List;
 import java.awt.*;
 import javax.swing.*;
 import javax.swing.event.*;
+
 import java.awt.event.*;
 import java.io.*;
 
@@ -30,6 +32,7 @@ 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.*;
@@ -42,8 +45,11 @@ import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
 import org.openscience.jmol.app.jmolpanel.AppConsole;
 
+import com.sun.org.apache.xml.internal.security.Init;
+import com.sun.xml.internal.bind.v2.runtime.unmarshaller.XsiNilLoader.Array;
+
 public class AppJmol extends GStructureViewer implements Runnable,
-        SequenceStructureBinding
+        SequenceStructureBinding, ViewSetProvider
 
 {
   AppJmolBinding jmb;
@@ -86,21 +92,25 @@ public class AppJmol extends GStructureViewer implements Runnable,
     this(new String[]
     { file }, new String[]
     { id }, new SequenceI[][]
-    { seq }, ap, loadStatus, bounds, viewid);
+    { seq }, ap, true,true, 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 loadStatus
    * @param bounds
    * @param viewid
    */
   public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
-          AlignmentPanel ap, String loadStatus, Rectangle bounds,
+          AlignmentPanel ap, boolean usetoColour,boolean useToAlign, String loadStatus, Rectangle bounds,
           String viewid)
   {
     PDBEntry[] pdbentrys = new PDBEntry[files.length];
@@ -116,10 +126,19 @@ public class AppJmol extends GStructureViewer implements Runnable,
     jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
 
     jmb.setLoadingFromArchive(true);
-    this.ap = ap;
+    addAlignmentPanel(ap);
+    if (useToAlign)
+    {
+      useAlignmentPanelForSuperposition(ap);
+    }
+    if (usetoColour)
+    {
+      useAlignmentPanelForColourbyseq(ap);
+    }
     this.setBounds(bounds);
     jmb.setColourBySequence(false);
     seqColour.setSelected(false);
+    initMenus();
     viewId = viewid;
     // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
     // bounds.width,bounds.height);
@@ -134,7 +153,66 @@ public class AppJmol extends GStructureViewer implements Runnable,
     initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
 
   }
+  private void initMenus() {
+    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,
@@ -182,6 +260,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
               if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
               {
                 topJmol.jmb.addSequence(pe, seq);
+                topJmol.addAlignmentPanel(ap);
+                topJmol.buildJmolActionMenu();
                 break;
               }
             }
@@ -209,6 +289,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
                 JOptionPane.YES_NO_OPTION);
         if (option == JOptionPane.YES_OPTION)
         {
+          topJmol.useAlignmentPanelForSuperposition(ap);
           topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
           return;
         }
@@ -219,9 +300,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
     jmb = new AppJmolBinding(this, new PDBEntry[]
     { pdbentry }, new SequenceI[][]
     { seq }, null, null);
-    this.ap = ap;
+    addAlignmentPanel(ap);
     setSize(400, 400); // probably should be a configurable/dynamic default here
-
+    initMenus();
+    
     if (pdbentry.getFile() != null)
     {
       initJmol("load \"" + pdbentry.getFile() + "\"");
@@ -244,6 +326,124 @@ public class AppJmol extends GStructureViewer implements Runnable,
   }
 
   /**
+   * 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
+   */
+  ArrayList<AlignmentPanel> _alignwith = new ArrayList();
+
+  /**
+   * list of alignment panels that are used for colouring structures by aligned
+   * sequences
+   */
+  ArrayList<AlignmentPanel> _colourwith = new ArrayList();
+
+  /**
+   * 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)
+  {
+    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;
@@ -316,7 +516,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
       if (frames[i] instanceof AppJmol)
       {
         AppJmol topJmol = ((AppJmol) frames[i]);
-        if (topJmol.ap == ap2)
+        if (topJmol.isLinkedWith(ap2))
         {
           otherJmols.addElement(topJmol);
         }
@@ -417,7 +617,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
   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;
@@ -572,7 +775,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
           }
         }
         // 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)
         {
@@ -580,7 +786,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
           {
             public void run()
             {
-              jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+              alignStructs_withAllAlignPanels();
+              // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
             }
           });
           alignAddedStructures = false;
@@ -705,9 +912,14 @@ public class AppJmol extends GStructureViewer implements Runnable,
   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
-    jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures,
-            ap.alignFrame.viewport.alignment);
+    for (AlignmentPanel ap : _colourwith)
+    {
+      jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+    }
   }
 
   public void chainColour_actionPerformed(ActionEvent actionEvent)
@@ -894,13 +1106,29 @@ public class AppJmol extends GStructureViewer implements Runnable,
       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 ArrayList<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;
   }
 
   /*
@@ -913,17 +1141,39 @@ public class AppJmol extends GStructureViewer implements Runnable,
   @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)
@@ -932,4 +1182,43 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
   }
 
+  /**
+   * 
+   * @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);
+  }
+
 }
index ed56ebb..c8d9ae3 100644 (file)
@@ -26,7 +26,9 @@ import java.util.BitSet;
 
 import javax.swing.JPanel;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
@@ -53,26 +55,27 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   FeatureRenderer fr = null;
 
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer()
+  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    if (appJmolWindow.ap.av.showSequenceFeatures)
+    AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
+    if (ap.av.showSequenceFeatures)
     {
       if (fr == null)
       {
-        fr = new FeatureRenderer(appJmolWindow.ap);
+        fr = new FeatureRenderer((AlignmentPanel)alignment);
       }
 
-      fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
-              .getFeatureRenderer());
+      fr.transferSettings(((AlignmentPanel)alignment).
+              seqPanel.seqCanvas.getFeatureRenderer());
     }
 
     return fr;
   }
 
   @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer()
+  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(appJmolWindow.ap.av);
+    return new SequenceRenderer(((AlignmentPanel)alignment).av);
   }
 
   public void sendConsoleEcho(String strEcho)
@@ -122,11 +125,13 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
+    AlignmentPanel ap = (AlignmentPanel) source,topap;
+    // ignore events from unrelated or non-user interactive frames
+    if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || appJmolWindow.isUsedforcolourby(ap))
       return;
-
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    if (!isLoadingFromArchive()) {
+      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    }
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -212,4 +217,13 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     }
 
   }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    if (svl instanceof SeqPanel) {
+      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+      
+    };
+  }
 }