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

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

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 148f252..a551ca2 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,13 +20,6 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
@@ -37,6 +30,13 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
 /**
  * Routines for generating Chimera commands for Jalview/Chimera binding
  * 
@@ -67,8 +67,7 @@ public class ChimeraCommands
             ChimeraCommands.class, null,
             colourCommands.toArray(new String[0]));
 
-    return new StructureMappingcommandSet[]
-    { cs };
+    return new StructureMappingcommandSet[] { cs };
   }
 
   /**
@@ -79,7 +78,7 @@ public class ChimeraCommands
    * <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
    * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
    * 
-   * @see http
+   * @see http 
    *      ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
    *      .html </pre>
    * 
@@ -107,7 +106,8 @@ public class ChimeraCommands
       sb.append("color ").append(colourCode).append(" ");
       firstColour = false;
       boolean firstModelForColour = true;
-      final Map<Integer, Map<String, List<int[]>>> colourData = colourMap.get(colour);
+      final Map<Integer, Map<String, List<int[]>>> colourData = colourMap
+              .get(colour);
       for (Integer model : colourData.keySet())
       {
         boolean firstPositionForModel = true;
@@ -232,7 +232,7 @@ public class ChimeraCommands
               addColourRange(colourMap, lastColour, pdbfnum, startPos,
                       lastPos, lastChain);
             }
-            break;
+            // break;
           }
         }
       }
@@ -287,8 +287,7 @@ public class ChimeraCommands
     /*
      * Add the start/end positions
      */
-    chainData.add(new int[]
-    { startPos, endPos });
+    chainData.add(new int[] { startPos, endPos });
   }
 
 }