Merge branch 'features/JAL-2295setChimeraAttributes' into

[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 07c0015..c4aa2e7 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -60,13 +60,13 @@ public class ChimeraCommands
    * @param alignment
    * @return
    */
-  public static StructureMappingcommandSet getColourBySequenceCommand(
+  public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
   {
-    Map<Object, AtomSpecModel> colourMap = buildColoursMap(
-            ssm, files, sequence, sr, fr, alignment);
+    Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
+            sequence, sr, fr, alignment);
 
     List<String> colourCommands = buildColourCommands(colourMap);
 
@@ -74,7 +74,7 @@ public class ChimeraCommands
             ChimeraCommands.class, null,
             colourCommands.toArray(new String[colourCommands.size()]));
 
-    return cs;
+    return new StructureMappingcommandSet[] { cs };
   }
 
   /**
@@ -113,8 +113,7 @@ public class ChimeraCommands
       }
       sb.append("color ").append(colourCode).append(" ");
       firstColour = false;
-      final AtomSpecModel colourData = colourMap
-              .get(colour);
+      final AtomSpecModel colourData = colourMap.get(colour);
       sb.append(colourData.getAtomSpec());
     }
     commands.add(sb.toString());
@@ -240,7 +239,7 @@ public class ChimeraCommands
               {
                 if (startPos != -1)
                 {
-                  addRange(colourMap, lastColour, pdbfnum, startPos,
+                  addColourRange(colourMap, lastColour, pdbfnum, startPos,
                           lastPos, lastChain);
                 }
                 startPos = pos;
@@ -252,8 +251,8 @@ public class ChimeraCommands
             // final colour range
             if (lastColour != null)
             {
-              addRange(colourMap, lastColour, pdbfnum, startPos,
-                      lastPos, lastChain);
+              addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
+                      lastChain);
             }
             // break;
           }
@@ -273,7 +272,7 @@ public class ChimeraCommands
    * @param endPos
    * @param chain
    */
-  protected static void addRange(Map<Object, AtomSpecModel> map,
+  protected static void addColourRange(Map<Object, AtomSpecModel> map,
           Object key, int model, int startPos, int endPos, String chain)
   {
     /*
@@ -341,7 +340,7 @@ public class ChimeraCommands
     {
       return theMap;
     }
-    
+
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -432,7 +431,7 @@ public class ChimeraCommands
         }
         for (int[] range : mappedRanges)
         {
-          addRange(featureValues, value, modelNumber, range[0], range[1],
+          addColourRange(featureValues, value, modelNumber, range[0], range[1],
                   mapping.getChain());
         }
       }