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

[jalview.git] / src / jalview / structure / StructureCommandsBase.java

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 44764db..e688b64 100644 (file)
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,22 +1,14 @@
 package jalview.structure;
 
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
-
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.LinkedHashMap;
 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
@@ -39,7 +31,8 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   }
 
   @Override
-  public String[] setAttributesForFeatures(StructureSelectionManager ssm,
+  public List<StructureCommandI> setAttributesForFeatures(
+          StructureSelectionManager ssm,
           String[] files, SequenceI[][] sequence, AlignmentViewPanel avp)
   {
     // default does nothing, override where this is implemented
@@ -74,8 +67,8 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param chain
    */
   public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
-          Object value,
-          int model, int startPos, int endPos, String chain)
+          Object value, String model, int startPos, int endPos,
+          String chain)
   {
     /*
      * Get/initialize map of data for the colour
@@ -94,35 +87,35 @@ 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
    */
   @Override
-  public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
+  public List<StructureCommandI> colourBySequence(
+          Map<Object, AtomSpecModel> colourMap)
   {
-    /*
-     * This version concatenates all commands into a single String (semi-colon
-     * delimited). If length limit issues arise, refactor to return one color
-     * command per colour.
-     */
-    List<String> commands = new ArrayList<>();
-    StringBuilder sb = new StringBuilder(256);
-    boolean firstColour = true;
+    List<StructureCommandI> commands = new ArrayList<>();
+    StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+    boolean first = true;
     for (Object key : colourMap.keySet())
     {
       Color colour = (Color) key;
-      if (!firstColour)
+      final AtomSpecModel colourData = colourMap.get(colour);
+      StructureCommandI command = getColourCommand(colourData, colour);
+      if (!first)
       {
-        sb.append(getCommandSeparator()).append(" ");
+        sb.append(getCommandSeparator());
       }
-      firstColour = false;
-      final AtomSpecModel colourData = colourMap.get(colour);
-      sb.append(getColourCommand(colourData, colour));
+      first = false;
+      sb.append(command.getCommand());
     }
-    commands.add(sb.toString());
 
-    return commands.toArray(new String[commands.size()]);
+    commands.add(new StructureCommand(sb.toString()));
+    return commands;
   }
 
   /**
@@ -133,7 +126,8 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param colour
    * @return
    */
-  protected String getColourCommand(AtomSpecModel atomSpecModel, Color colour)
+  protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
+          Color colour)
   {
     String atomSpec = getAtomSpec(atomSpecModel, false);
     return getColourCommand(atomSpec, colour);
@@ -147,21 +141,25 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param colour
    * @return
    */
-  protected abstract String getColourCommand(String atomSpec, Color colour);
+  protected abstract StructureCommandI getColourCommand(String atomSpec,
+          Color colour);
 
   @Override
-  public String colourByResidues(Map<String, Color> colours)
+  public List<StructureCommandI> colourByResidues(
+          Map<String, Color> colours)
   {
-    StringBuilder cmd = new StringBuilder(12 * colours.size());
-  
+    List<StructureCommandI> commands = new ArrayList<>();
     for (Entry<String, Color> entry : colours.entrySet())
     {
-      String residue = entry.getKey();
-      String atomSpec = getResidueSpec(residue);
-      cmd.append(getColourCommand(atomSpec, entry.getValue()));
-      cmd.append(getCommandSeparator());
+      commands.add(colourResidue(entry.getKey(), entry.getValue()));
     }
-    return cmd.toString();
+    return commands;
+  }
+
+  private StructureCommandI colourResidue(String resName, Color col)
+  {
+    String atomSpec = getResidueSpec(resName);
+    return getColourCommand(atomSpec, col);
   }
 
   /**