X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=af87e445ba5138f746196c8a5268a27c1e024839;hb=9da6fa6166a6cb1ca3725bea4d58029b8605fa5b;hp=cee271ae24ef397ae327a2d19de3eadf533f5eca;hpb=3bc2fbe640abb0d8941aead117c9624dd16773a3;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index cee271a..af87e44 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -20,18 +20,6 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import java.awt.Color;
-import java.net.BindException;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -49,6 +37,18 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.net.BindException;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+
 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 {
   // Chimera clause to exclude alternate locations in atom selection
@@ -86,11 +86,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   private boolean loadingFinished = true;
 
-  /*
-   * state flag used to check if the Chimera viewer's paint method can be called
-   */
-  private boolean finishedInit = false;
-
   public String fileLoadingError;
 
   /*
@@ -113,7 +108,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   String[] modelFileNames = null;
 
-  String lastMousedOverAtomSpec;
+  String lastHighlightCommand;
 
   private List<String> lastReply;
 
@@ -613,6 +608,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public void sendChimeraCommand(final String command, boolean logResponse)
   {
+    if (viewer == null)
+    {
+      // ? thread running after viewer shut down
+      return;
+    }
     viewerCommandHistory(false);
     if (lastCommand == null || !lastCommand.equals(command))
     {
@@ -818,8 +818,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * Construct and send a command to highlight zero, one or more atoms.
    * 
    * <pre>
-   * Done by generating a command like (to 'highlight' position 44)
-   *   show #0:44.C
+   * Done by generating a command like (to 'highlight' positions 44 and 46)
+   *   show #0:44,46.C
    * </pre>
    */
   @Override
@@ -829,8 +829,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     {
       return;
     }
-    StringBuilder atomSpecs = new StringBuilder();
+    StringBuilder cmd = new StringBuilder(128);
     boolean first = true;
+    boolean found = false;
+
     for (AtomSpec atom : atoms)
     {
       int pdbResNum = atom.getPdbResNum();
@@ -839,39 +841,42 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
       if (cms != null && !cms.isEmpty())
       {
-        /*
-         * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
-         * concatenate multiple 'show' commands
-         */
-        atomSpecs.append(first ? "" : ";show ");
+        if (first)
+        {
+          cmd.append("show #").append(cms.get(0).getModelNumber())
+                  .append(":");
+        }
+        else
+        {
+          cmd.append(",");
+        }
         first = false;
-        atomSpecs.append("#" + cms.get(0).getModelNumber());
-        atomSpecs.append(":" + pdbResNum);
+        cmd.append(cms.get(0).getModelNumber()).append(":");
+        cmd.append(pdbResNum);
         if (!chain.equals(" "))
         {
-          atomSpecs.append("." + chain);
+          cmd.append(".").append(chain);
         }
+        found = true;
       }
     }
-    String atomSpec = atomSpecs.toString();
+    String command = cmd.toString();
 
     /*
      * Avoid repeated commands for the same residue
      */
-    if (atomSpec.equals(lastMousedOverAtomSpec))
+    if (command.equals(lastHighlightCommand))
     {
       return;
     }
 
-    StringBuilder command = new StringBuilder(32);
     viewerCommandHistory(false);
-    if (atomSpec.length() > 0)
+    if (found)
     {
-      command.append("show ").append(atomSpec);
       viewer.sendChimeraCommand(command.toString(), false);
     }
     viewerCommandHistory(true);
-    this.lastMousedOverAtomSpec = atomSpec;
+    this.lastHighlightCommand = command;
   }
 
   /**
@@ -994,6 +999,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public abstract void refreshGUI();
 
+  @Override
   public void setLoadingFromArchive(boolean loadingFromArchive)
   {
     this.loadingFromArchive = loadingFromArchive;
@@ -1004,6 +1010,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @return true if Chimeral is still restoring state or loading is still going
    *         on (see setFinsihedLoadingFromArchive)
    */
+  @Override
   public boolean isLoadingFromArchive()
   {
     return loadingFromArchive && !loadingFinished;
@@ -1015,6 +1022,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * 
    * @param finishedLoading
    */
+  @Override
   public void setFinishedLoadingFromArchive(boolean finishedLoading)
   {
     loadingFinished = finishedLoading;
@@ -1079,16 +1087,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     return true;
   }
 
-  public boolean isFinishedInit()
-  {
-    return finishedInit;
-  }
-
-  public void setFinishedInit(boolean finishedInit)
-  {
-    this.finishedInit = finishedInit;
-  }
-
   /**
    * Returns a list of chains mapped in this viewer. Note this list is not
    * currently scoped per structure.
@@ -1125,4 +1123,30 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   {
     sendChimeraCommand("focus", false);
   }
+
+  /**
+   * Send a 'show' command for all atoms in the currently selected columns
+   * 
+   * @param vp
+   */
+  public void highlightSelection(AlignmentViewPanel vp)
+  {
+    List<Integer> cols = vp.getAlignViewport().getColumnSelection()
+            .getSelected();
+    AlignmentI alignment = vp.getAlignment();
+    StructureSelectionManager sm = getSsm();
+    for (SequenceI seq : alignment.getSequences())
+    {
+      /*
+       * convert selected columns into sequence positions
+       */
+      int[] positions = new int[cols.size()];
+      int i = 0;
+      for (Integer col : cols)
+      {
+        positions[i++] = seq.findPosition(col);
+      }
+      sm.highlightStructure(this, seq, positions);
+    }
+  }
 }