JAL-3551 working proof of concept of Jalview driving PyMOL

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

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 44764db..8c6ea4e 100644 (file)
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,18 +1,10 @@
 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;
@@ -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
@@ -99,30 +92,22 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @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.
+     * default implementation creates one command per colour;
+     * override to concatenate colour commands if wanted
      */
-    List<String> commands = new ArrayList<>();
-    StringBuilder sb = new StringBuilder(256);
-    boolean firstColour = true;
+    List<StructureCommandI> commands = new ArrayList<>();
     for (Object key : colourMap.keySet())
     {
       Color colour = (Color) key;
-      if (!firstColour)
-      {
-        sb.append(getCommandSeparator()).append(" ");
-      }
-      firstColour = false;
       final AtomSpecModel colourData = colourMap.get(colour);
-      sb.append(getColourCommand(colourData, colour));
+      commands.add(getColourCommand(colourData, colour));
     }
-    commands.add(sb.toString());
 
-    return commands.toArray(new String[commands.size()]);
+    return commands;
   }
 
   /**
@@ -133,7 +118,8 @@ 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 +133,25 @@ 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);
   }
 
   /**