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

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 797c25b..9c05a37 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -98,7 +98,7 @@ public class JmolCommands extends StructureCommandsBase
                     c.getBlue());
   }
 
-
+  @Deprecated
   public String[] colourBySequence(StructureSelectionManager ssm,
           String[] files,
           SequenceI[][] sequence, SequenceRenderer sr,

diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java
index 115efa1..e4f9f5f 100644 (file)
--- 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;
+  }
+
 }

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;
+  }
+
 }

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 8c6ea4e..e688b64 100644 (file)
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,14 +1,14 @@
 package jalview.structure;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.SequenceI;
-
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.SequenceI;
+
 /**
  * A base class holding methods useful to all classes that implement commands
  * for structure viewers
@@ -87,6 +87,9 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * Traverse the map of colours/models/chains/positions to construct a list of
    * 'color' commands (one per distinct colour used). The format of each command
    * is specific to the structure viewer.
+   * <p>
+   * The default implementation returns a single command containing one command
+   * per colour, concatenated.
    * 
    * @param colourMap
    * @return
@@ -95,18 +98,23 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   public List<StructureCommandI> colourBySequence(
           Map<Object, AtomSpecModel> colourMap)
   {
-    /*
-     * default implementation creates one command per colour;
-     * override to concatenate colour commands if wanted
-     */
     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);
-      commands.add(getColourCommand(colourData, 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;
   }