JAL-3551 concatenate colour by sequence commands for all except PyMOL

[jalview.git] / src / jalview / ext / rbvi / chimera / ChimeraCommands.java

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index c355abe..c9dbc1d 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,6 +20,14 @@
  */
 package jalview.ext.rbvi.chimera;
 
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
@@ -36,14 +44,6 @@ import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.ColorUtils;
 
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
 /**
  * Routines for generating Chimera commands for Jalview/Chimera binding
  * 
@@ -641,4 +641,31 @@ public class ChimeraCommands extends StructureCommandsBase
     return new StructureCommand("open " + file);
   }
 
+  /**
+   * Overrides the default method to concatenate colour commands into one
+   */
+  @Override
+  public List<StructureCommandI> colourBySequence(
+          Map<Object, AtomSpecModel> colourMap)
+  {
+    List<StructureCommandI> commands = new ArrayList<>();
+    StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+    boolean first = true;
+    for (Object key : colourMap.keySet())
+    {
+      Color colour = (Color) key;
+      final AtomSpecModel colourData = colourMap.get(colour);
+      StructureCommandI command = getColourCommand(colourData, colour);
+      if (!first)
+      {
+        sb.append(getCommandSeparator());
+      }
+      first = false;
+      sb.append(command.getCommand());
+    }
+
+    commands.add(new StructureCommand(sb.toString()));
+    return commands;
+  }
+
 }