X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolCommands.java;h=e4f9f5f8d27911efec4a26791c70e98e05898071;hb=27f24d1f14b8e8704d72797286f7a6e5f60b2119;hp=115efa15f7408d0f4ed070020e36824537acf608;hpb=aa643d0f2f5f506df2771e216af1618549d32050;p=jalview.git

diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java
index 115efa1..e4f9f5f 100644
--- a/src/jalview/ext/pymol/PymolCommands.java
+++ b/src/jalview/ext/pymol/PymolCommands.java
@@ -3,6 +3,7 @@ package jalview.ext.pymol;
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
@@ -209,4 +210,27 @@ public class PymolCommands extends StructureCommandsBase
     return new StructureCommand("load", file);
   }
 
+  /**
+   * Overrides the default implementation (which generates concatenated
+   * commands) to generate one per colour (because the XML-RPC interface to
+   * PyMOL only accepts one command at a time)
+   * 
+   * @param colourMap
+   * @return
+   */
+  @Override
+  public List<StructureCommandI> colourBySequence(
+          Map<Object, AtomSpecModel> colourMap)
+  {
+    List<StructureCommandI> commands = new ArrayList<>();
+    for (Object key : colourMap.keySet())
+    {
+      Color colour = (Color) key;
+      final AtomSpecModel colourData = colourMap.get(colour);
+      commands.add(getColourCommand(colourData, colour));
+    }
+  
+    return commands;
+  }
+
 }