X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=b38979b06227c8d7d34a902b3b3e2a69c89b5a8e;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=0e6cac3fb5d7a02a32e29c05339fc1c2723a59b9;hpb=3d56aaf4e194de0e0e814ac027de3233ed5457e7;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 0e6cac3..b38979b 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -1,3 +1,20 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
 /**
  * 
  */
@@ -8,14 +25,16 @@ 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.
+ * 
  * @author JimP
  *
  */
@@ -24,20 +43,24 @@ 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++)
       {
@@ -98,13 +121,16 @@ 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)