JAL-1957 enabled multi-chain mapping and highlight for Chimera viewer

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index cee271a..cae2457 100644 (file)
--- 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;
 
   /*
@@ -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))
     {
@@ -831,6 +831,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
     StringBuilder atomSpecs = new StringBuilder();
     boolean first = true;
+
     for (AtomSpec atom : atoms)
     {
       int pdbResNum = atom.getPdbResNum();
@@ -843,9 +844,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
          * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
          * concatenate multiple 'show' commands
          */
-        atomSpecs.append(first ? "" : ";show ");
+        atomSpecs.append(first ? "" : ",");
         first = false;
-        atomSpecs.append("#" + cms.get(0).getModelNumber());
+        atomSpecs.append(cms.get(0).getModelNumber());
         atomSpecs.append(":" + pdbResNum);
         if (!chain.equals(" "))
         {
@@ -867,7 +868,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     viewerCommandHistory(false);
     if (atomSpec.length() > 0)
     {
-      command.append("show ").append(atomSpec);
+      command.append("show #").append(atomSpec);
       viewer.sendChimeraCommand(command.toString(), false);
     }
     viewerCommandHistory(true);
@@ -994,6 +995,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public abstract void refreshGUI();
 
+  @Override
   public void setLoadingFromArchive(boolean loadingFromArchive)
   {
     this.loadingFromArchive = loadingFromArchive;
@@ -1004,6 +1006,7 @@ 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 +1018,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * 
    * @param finishedLoading
    */
+  @Override
   public void setFinishedLoadingFromArchive(boolean finishedLoading)
   {
     loadingFinished = finishedLoading;
@@ -1079,16 +1083,6 @@ 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.