X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=930d6fec513500032652d4ff4492fd6a3d289e9d;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=148f252870edbbf3eb9cdce60d2ae1170483d4f6;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 148f252..930d6fe 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,13 +20,7 @@
  */
 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.ColorI;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
@@ -37,6 +31,12 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
+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
  * 
@@ -58,7 +58,7 @@ public class ChimeraCommands
           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
   {
-    Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
+    Map<ColorI, Map<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
             ssm, files, sequence, sr, fr, alignment);
 
     List<String> colourCommands = buildColourCommands(colourMap);
@@ -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>
    * 
@@ -87,7 +86,7 @@ public class ChimeraCommands
    * @return
    */
   protected static List<String> buildColourCommands(
-          Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap)
+          Map<ColorI, Map<Integer, Map<String, List<int[]>>>> colourMap)
   {
     /*
      * This version concatenates all commands into a single String (semi-colon
@@ -97,7 +96,7 @@ public class ChimeraCommands
     List<String> commands = new ArrayList<String>();
     StringBuilder sb = new StringBuilder(256);
     boolean firstColour = true;
-    for (Color colour : colourMap.keySet())
+    for (ColorI colour : colourMap.keySet())
     {
       String colourCode = ColorUtils.toTkCode(colour);
       if (!firstColour)
@@ -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;
@@ -161,13 +161,13 @@ 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<ColorI, Map<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[]>>>>();
-    Color lastColour = null;
+    Map<ColorI, Map<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<ColorI, Map<Integer, Map<String, List<int[]>>>>();
+    ColorI lastColour = null;
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -202,7 +202,7 @@ public class ChimeraCommands
                 continue;
               }
 
-              Color colour = sr.getResidueColour(seq, r, fr);
+              ColorI colour = sr.getResidueColour(seq, r, fr);
               final String chain = mapping[m].getChain();
 
               /*
@@ -232,7 +232,7 @@ public class ChimeraCommands
               addColourRange(colourMap, lastColour, pdbfnum, startPos,
                       lastPos, lastChain);
             }
-            break;
+            // break;
           }
         }
       }
@@ -251,8 +251,8 @@ public class ChimeraCommands
    * @param chain
    */
   protected static void addColourRange(
-          Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap,
-          Color colour, int model, int startPos, int endPos, String chain)
+          Map<ColorI, Map<Integer, Map<String, List<int[]>>>> colourMap,
+          ColorI colour, int model, int startPos, int endPos, String chain)
   {
     /*
      * Get/initialize map of data for the colour
@@ -287,8 +287,7 @@ public class ChimeraCommands
     /*
      * Add the start/end positions
      */
-    chainData.add(new int[]
-    { startPos, endPos });
+    chainData.add(new int[] { startPos, endPos });
   }
 
 }