Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index f1f2d30..906cb59 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -20,8 +20,6 @@
  */
 package jalview.structures.models;
 
-import java.util.Locale;
-
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
@@ -31,6 +29,7 @@ import java.util.BitSet;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import javax.swing.SwingUtilities;
@@ -41,7 +40,7 @@ import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.MappedFeatures;
@@ -61,6 +60,7 @@ import jalview.structure.AtomSpec;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureCommandsI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
@@ -69,9 +69,9 @@ import jalview.util.MessageManager;
 
 /**
  * 
- * A base class to hold common function for 3D structure model binding.
- * Initial version created by refactoring JMol and Chimera binding models, but
- * other structure viewers could in principle be accommodated in future.
+ * A base class to hold common function for 3D structure model binding. Initial
+ * version created by refactoring JMol and Chimera binding models, but other
+ * structure viewers could in principle be accommodated in future.
  * 
  * @author gmcarstairs
  *
@@ -91,6 +91,9 @@ public abstract class AAStructureBindingModel
 
     public String chain = "";
 
+    /**
+     * is the mapped sequence not protein ?
+     */
     public boolean isRna;
 
     /*
@@ -167,6 +170,9 @@ public abstract class AAStructureBindingModel
 
   protected boolean colourBySequence = true;
 
+  /**
+   * true if all sequences appear to be nucleotide
+   */
   private boolean nucleotide;
 
   private boolean finishedInit = false;
@@ -584,7 +590,6 @@ public abstract class AAStructureBindingModel
       }
     }
   }
-  
 
   @Override
   public abstract void highlightAtoms(List<AtomSpec> atoms);
@@ -716,7 +721,7 @@ public abstract class AAStructureBindingModel
               structures[pdbfnum].chain = chain;
             }
             structures[pdbfnum].pdbId = mapping.getPdbId();
-            structures[pdbfnum].isRna = theSequence.getRNA() != null;
+            structures[pdbfnum].isRna = !theSequence.isProtein();
 
             /*
              * move on to next pdb file (ignore sequences for other chains
@@ -919,6 +924,9 @@ public abstract class AAStructureBindingModel
       // todo better way to ensure synchronous than setting getReply true!!
       executeCommands(commandGenerator.showBackbone(), true, null);
 
+      AtomSpecType backbone = structures[refStructure].isRna
+              ? AtomSpecType.PHOSPHATE
+              : AtomSpecType.ALPHA;
       /*
        * superpose each (other) structure to the reference in turn
        */
@@ -928,12 +936,13 @@ public abstract class AAStructureBindingModel
         {
           AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
           List<StructureCommandI> commands = commandGenerator
-                  .superposeStructures(refAtoms, atomSpec);
+                  .superposeStructures(refAtoms, atomSpec, backbone);
           List<String> replies = executeCommands(commands, true, null);
           for (String reply : replies)
           {
             // return this error (Chimera only) to the user
-            if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
+            if (reply.toLowerCase(Locale.ROOT)
+                    .contains("unequal numbers of atoms"))
             {
               error += "; " + reply;
             }
@@ -1270,6 +1279,12 @@ public abstract class AAStructureBindingModel
   @Override
   public void updateColours(Object source)
   {
+    if (getViewer() == null)
+    {
+      // can happen if a viewer was not instantiated or cleaned up and is still
+      // registered - mostly during tests
+      return;
+    }
     AlignmentViewPanel ap = (AlignmentViewPanel) source;
     // ignore events from panels not used to colour this view
     if (!getViewer().isUsedForColourBy(ap))
@@ -1497,7 +1512,7 @@ public abstract class AAStructureBindingModel
       saveSession(f);
     } catch (IOException e)
     {
-      Cache.log.error(String.format("Error saving %s session: %s", prefix,
+      Console.error(String.format("Error saving %s session: %s", prefix,
               e.toString()));
     }