X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=b05c168c50f1649db40a440e68116dabdd09c8c5;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=b009948d0e7869dc7355b821d3bf8e7e21ccb6f5;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index b009948..b05c168 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -23,6 +23,7 @@ package jalview.ext.rbvi.chimera;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -92,8 +93,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   private boolean loadingFinished = true;
 
-  public String fileLoadingError;
-
   /*
    * Map of ChimeraModel objects keyed by PDB full local file name
    */
@@ -116,6 +115,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   private long loadNotifiesHandled = 0;
 
+  private Thread chimeraMonitor;
+
   /**
    * Open a PDB structure file in Chimera and set up mappings from Jalview.
    * 
@@ -199,8 +200,38 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
   {
     super(ssm, pdbentry, sequenceIs, protocol);
-    viewer = new ChimeraManager(
-            new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+    viewer = new ChimeraManager(new StructureManager(true));
+  }
+
+  /**
+   * Starts a thread that waits for the Chimera process to finish, so that we
+   * can then close the associated resources. This avoids leaving orphaned
+   * Chimera viewer panels in Jalview if the user closes Chimera.
+   */
+  protected void startChimeraProcessMonitor()
+  {
+    final Process p = viewer.getChimeraProcess();
+    chimeraMonitor = new Thread(new Runnable()
+    {
+
+      @Override
+      public void run()
+      {
+        try
+        {
+          p.waitFor();
+          JalviewStructureDisplayI display = getViewer();
+          if (display != null)
+          {
+            display.closeViewer(false);
+          }
+        } catch (InterruptedException e)
+        {
+          // exit thread if Chimera Viewer is closed in Jalview
+        }
+      }
+    });
+    chimeraMonitor.start();
   }
 
   /**
@@ -221,18 +252,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Construct a title string for the viewer window based on the data Jalview
-   * knows about
-   * 
-   * @param verbose
-   * @return
-   */
-  public String getViewerTitle(boolean verbose)
-  {
-    return getViewerTitle("Chimera", verbose);
-  }
-
-  /**
    * Tells Chimera to display only the specified chains
    * 
    * @param toshow
@@ -288,9 +307,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     lastCommand = null;
     viewer = null;
 
+    if (chimeraMonitor != null)
+    {
+      chimeraMonitor.interrupt();
+    }
     releaseUIResources();
   }
 
+  @Override
   public void colourByChain()
   {
     colourBySequence = false;
@@ -306,6 +330,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * <li>all others - white</li>
    * </ul>
    */
+  @Override
   public void colourByCharge()
   {
     colourBySequence = false;
@@ -327,6 +352,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param _hiddenCols
    *          an array of corresponding hidden columns for each alignment
    */
+  @Override
   public void superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
@@ -568,23 +594,29 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   /**
    * Launch Chimera, unless an instance linked to this object is already
-   * running. Returns true if chimera is successfully launched, or already
+   * running. Returns true if Chimera is successfully launched, or already
    * running, else false.
    * 
    * @return
    */
   public boolean launchChimera()
   {
-    if (!viewer.isChimeraLaunched())
-    {
-      return viewer.launchChimera(StructureManager.getChimeraPaths());
-    }
     if (viewer.isChimeraLaunched())
     {
       return true;
     }
-    log("Failed to launch Chimera!");
-    return false;
+
+    boolean launched = viewer.launchChimera(StructureManager
+            .getChimeraPaths());
+    if (launched)
+    {
+      startChimeraProcessMonitor();
+    }
+    else
+    {
+      log("Failed to launch Chimera!");
+    }
+    return launched;
   }
 
   /**
@@ -637,34 +669,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           String progressMsg);
 
   /**
-   * colour any structures associated with sequences in the given alignment
-   * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
-   * if colourBySequence is enabled.
+   * Sends a set of colour commands to the structure viewer
+   * 
+   * @param colourBySequenceCommands
    */
-  public void colourBySequence(boolean showFeatures,
-          jalview.api.AlignmentViewPanel alignmentv)
+  @Override
+  protected void colourBySequence(
+          StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    if (!colourBySequence || !loadingFinished)
-    {
-      return;
-    }
-    if (getSsm() == null)
-    {
-      return;
-    }
-    String[] files = getPdbFile();
-
-    SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
-    FeatureRenderer fr = null;
-    if (showFeatures)
-    {
-      fr = getFeatureRenderer(alignmentv);
-    }
-    AlignmentI alignment = alignmentv.getAlignment();
-
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
-            files, sr, fr, alignment))
+    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
     {
       for (String command : cpdbbyseq.commands)
       {
@@ -680,6 +693,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param alignment
    * @return
    */
+  @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
@@ -715,40 +729,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   // //////////////////////////
 
   /**
-   * returns the current featureRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment);
-
-  /**
    * instruct the Jalview binding to update the pdbentries vector if necessary
    * prior to matching the viewer's contents to the list of structure files
    * Jalview knows about.
    */
   public abstract void refreshPdbEntries();
 
-  private int getModelNum(String modelFileName)
-  {
-    String[] mfn = getPdbFile();
-    if (mfn == null)
-    {
-      return -1;
-    }
-    for (int i = 0; i < mfn.length; i++)
-    {
-      if (mfn[i].equalsIgnoreCase(modelFileName))
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-
   /**
    * map between index of model filename returned from getPdbFile and the first
    * index of models from this file in the viewer. Note - this is not trimmed -
@@ -771,17 +757,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * returns the current sequenceRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment);
-
-  /**
    * Construct and send a command to highlight zero, one or more atoms. We do
    * this by sending an "rlabel" command to show the residue label at that
    * position.
@@ -933,6 +908,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     return loadNotifiesHandled;
   }
 
+  @Override
   public void setJalviewColourScheme(ColourSchemeI cs)
   {
     colourBySequence = false;
@@ -949,12 +925,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
     List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
             false);
-    for (String res : residueSet)
+    for (String resName : residueSet)
     {
-      Color col = cs.findColour(res.charAt(0));
+      char res = resName.length() == 3 ? ResidueProperties
+              .getSingleCharacterCode(resName) : resName.charAt(0);
+      Color col = cs.findColour(res, 0, null, null, 0f);
       command.append("color " + col.getRed() / normalise + ","
               + col.getGreen() / normalise + "," + col.getBlue()
-              / normalise + " ::" + res + ";");
+              / normalise + " ::" + resName + ";");
     }
 
     sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
@@ -1005,6 +983,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    *      .html
    * @param col
    */
+  @Override
   public void setBackgroundColour(Color col)
   {
     viewerCommandHistory(false);
@@ -1057,13 +1036,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Returns a list of chains mapped in this viewer. Note this list is not
-   * currently scoped per structure.
-   * 
-   * @return
-   */
-
-  /**
    * Send a 'focus' command to Chimera to recentre the visible display
    */
   public void focusView()