update author list in license for (JAL-826)

[jalview.git] / src / jalview / ext / jmol / JmolCommands.java

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 0e6cac3..b38979b 100644 (file)
--- 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/>.
+ *******************************************************************************/
 /**\r
  * \r
  */\r
@@ -8,14 +25,16 @@ import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;\r
 import jalview.datamodel.SequenceI;\r
 import jalview.structure.StructureMapping;\r
+import jalview.structure.StructureMappingcommandSet;\r
 import jalview.structure.StructureSelectionManager;\r
 import jalview.util.Comparison;\r
 \r
 import java.awt.Color;\r
 import java.util.ArrayList;\r
-\r
 /**\r
  * Routines for generating Jmol commands for Jalview/Jmol binding\r
+ * another cruisecontrol test.\r
+ * \r
  * @author JimP\r
  *\r
  */\r
@@ -24,20 +43,24 @@ public class JmolCommands
 \r
   /**\r
    * Jmol utility which constructs the commands to colour chains by the given alignment\r
+   * @returns Object[] { Object[] { <model being coloured>, \r
    * \r
    */\r
-  public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
+  public static StructureMappingcommandSet[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
   {\r
-    ArrayList<String> str = new ArrayList<String>();\r
-    StringBuffer command = new StringBuffer();\r
-  \r
+    \r
+    ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();\r
+    \r
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
     {\r
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
+      StringBuffer command = new StringBuffer();\r
+      StructureMappingcommandSet smc;\r
+      ArrayList<String> str = new ArrayList<String>();\r
   \r
       if (mapping == null || mapping.length < 1)\r
         continue;\r
-  \r
+      \r
       int lastPos = -1;\r
       for (int s = 0; s < sequence[pdbfnum].length; s++)\r
       {\r
@@ -98,13 +121,16 @@ public class JmolCommands
           }\r
         }\r
       }\r
+      {\r
+          // add final chunk\r
+          str.add(command.toString());\r
+          command.setLength(0);\r
+        }\r
+        // Finally, add the command set ready to be returned.\r
+        cset.add(new StructureMappingcommandSet(JmolCommands.class,files[pdbfnum], str.toArray(new String[str.size()])));\r
+\r
     }\r
-    {\r
-      // add final chunk\r
-      str.add(command.toString());\r
-      command.setLength(0);\r
-    }\r
-    return str.toArray(new String[str.size()]);\r
+    return cset.toArray(new StructureMappingcommandSet[cset.size()]);\r
   }\r
 \r
   public static StringBuffer condenseCommand(StringBuffer command, int pos)\r