JAL-3404 explicit getModelForPdbFile lookup

[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 44bcbe4..3498f23 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -40,6 +40,7 @@ import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
+import jalview.util.StructureCommands;
 
 import java.awt.Color;
 import java.io.File;
@@ -76,8 +77,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private static final String ALPHACARBON = "CA";
 
-  private List<String> chainNames = new ArrayList<>();
-
   private Hashtable<String, String> chainFile = new Hashtable<>();
 
   /*
@@ -648,37 +647,26 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           String progressMsg);
 
   /**
-   * Sends a set of colour commands to the structure viewer
+   * Constructs a set of colour commands and sends them to the structure viewer
    * 
-   * @param colourBySequenceCommands
+   * @param viewPanel
    */
   @Override
-  protected void colourBySequence(
-          StructureMappingcommandSet[] colourBySequenceCommands)
+  protected void colourBySequence(AlignmentViewPanel viewPanel)
   {
-    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+    Map<Object, AtomSpecModel> colourMap = StructureCommands
+            .buildColoursMap(this, viewPanel);
+
+    String[] commands = ChimeraCommands
+            .getColourBySequenceCommand(colourMap, this);
+
+    for (String command : commands)
     {
-      for (String command : cpdbbyseq.commands)
-      {
-        sendAsynchronousCommand(command, COLOURING_CHIMERA);
-      }
+      sendAsynchronousCommand(command, COLOURING_CHIMERA);
     }
   }
 
   /**
-   * @param files
-   * @param viewPanel
-   * @return
-   */
-  @Override
-  protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, AlignmentViewPanel viewPanel)
-  {
-    return ChimeraCommands.getColourBySequenceCommand(files, viewPanel,
-            this);
-  }
-
-  /**
    * @param command
    */
   protected void executeWhenReady(String command)
@@ -1021,20 +1009,9 @@ 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
-   */
-  @Override
-  public List<String> getChainNames()
-  {
-    return chainNames;
-  }
-
-  /**
    * Send a 'focus' command to Chimera to recentre the visible display
    */
+  @Override
   public void focusView()
   {
     sendChimeraCommand("focus", false);
@@ -1298,7 +1275,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     cmd.append("ribbon ").append(atomSpec);
     if (!isShowAlignmentOnly())
     {
-      cmd.append("chain @CA|P; ribbon");
+      cmd.append("; chain @CA|P");
     }
     if (refocus)
     {
@@ -1306,4 +1283,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
     sendChimeraCommand(cmd.toString(), false);
   }
+
+  @Override
+  public int getModelForPdbFile(String fileName, int fileIndex)
+  {
+    if (chimeraMaps.containsKey(fileName))
+    {
+      List<ChimeraModel> models = chimeraMaps.get(fileName);
+      if (!models.isEmpty())
+      {
+        return models.get(0).getModelNumber();
+      }
+    }
+    return -1;
+  }
 }