JAL-2416 order score models by order of addition rather than name

[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 a529502..8f6b2f1 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -35,6 +35,7 @@ import java.util.ArrayList;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.SortedMap;
 import java.util.TreeMap;
 
 /**
@@ -58,7 +59,7 @@ public class ChimeraCommands
           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
   {
-    Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
+    Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
             ssm, files, sequence, sr, fr, alignment);
 
     List<String> colourCommands = buildColourCommands(colourMap);
@@ -86,7 +87,7 @@ public class ChimeraCommands
    * @return
    */
   protected static List<String> buildColourCommands(
-          Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap)
+          Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap)
   {
     /*
      * This version concatenates all commands into a single String (semi-colon
@@ -161,12 +162,12 @@ public class ChimeraCommands
    * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
    * </pre>
    */
-  protected static Map<Color, Map<Integer, Map<String, List<int[]>>>> buildColoursMap(
+  protected static Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> buildColoursMap(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
   {
-    Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
+    Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, SortedMap<Integer, Map<String, List<int[]>>>>();
     Color lastColour = null;
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
@@ -232,7 +233,7 @@ public class ChimeraCommands
               addColourRange(colourMap, lastColour, pdbfnum, startPos,
                       lastPos, lastChain);
             }
-            break;
+            // break;
           }
         }
       }
@@ -251,13 +252,13 @@ public class ChimeraCommands
    * @param chain
    */
   protected static void addColourRange(
-          Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap,
+          Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap,
           Color colour, int model, int startPos, int endPos, String chain)
   {
     /*
      * Get/initialize map of data for the colour
      */
-    Map<Integer, Map<String, List<int[]>>> colourData = colourMap
+    SortedMap<Integer, Map<String, List<int[]>>> colourData = colourMap
             .get(colour);
     if (colourData == null)
     {