X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;fp=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=bfb2766953e177f3826f9d374f313751319e0ce5;hb=ce89ec35928a6cb2f05a655c44c39a0249beb2d6;hp=9d01eab7474ec0bd7b1ee1450b2c21c10c066f7a;hpb=2831036c3ecfc50d9e068b0331de6523c60e3631;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 9d01eab..bfb2766 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -8,12 +8,12 @@ import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.ArrayList;
-
 /**
  * Routines for generating Jmol commands for Jalview/Jmol binding
  * another cruisecontrol test.
@@ -26,20 +26,24 @@ public class JmolCommands
 
   /**
    * Jmol utility which constructs the commands to colour chains by the given alignment
+   * @returns Object[] { Object[] { <model being coloured>, 
    * 
    */
-  public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)
+  public static StructureMappingcommandSet[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)
   {
-    ArrayList<String> str = new ArrayList<String>();
-    StringBuffer command = new StringBuffer();
-  
+    
+    ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+    
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+      StringBuffer command = new StringBuffer();
+      StructureMappingcommandSet smc;
+      ArrayList<String> str = new ArrayList<String>();
   
       if (mapping == null || mapping.length < 1)
         continue;
-  
+      
       int lastPos = -1;
       for (int s = 0; s < sequence[pdbfnum].length; s++)
       {
@@ -100,13 +104,16 @@ public class JmolCommands
           }
         }
       }
+      {
+          // add final chunk
+          str.add(command.toString());
+          command.setLength(0);
+        }
+        // Finally, add the command set ready to be returned.
+        cset.add(new StructureMappingcommandSet(JmolCommands.class,files[pdbfnum], str.toArray(new String[str.size()])));
+
     }
-    {
-      // add final chunk
-      str.add(command.toString());
-      command.setLength(0);
-    }
-    return str.toArray(new String[str.size()]);
+    return cset.toArray(new StructureMappingcommandSet[cset.size()]);
   }
 
   public static StringBuffer condenseCommand(StringBuffer command, int pos)