Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2d2d10e..b4586ca 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,7 +20,6 @@
  */
 package jalview.ext.jmol;
 
-import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
@@ -76,8 +75,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   Hashtable<String, String> chainFile;
 
-  public String fileLoadingError;
-
   /*
    * the default or current model displayed if the model cannot be identified
    * from the selection message
@@ -241,6 +238,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param _hiddenCols
    *          an array of corresponding hidden columns for each alignment
    */
+  @Override
   public void superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
@@ -487,35 +485,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * colour any structures associated with sequences in the given alignment
-   * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
-   * if colourBySequence is enabled.
+   * Sends a set of colour commands to the structure viewer
+   * 
+   * @param colourBySequenceCommands
    */
-  public void colourBySequence(AlignmentViewPanel alignmentv)
+  @Override
+  protected void colourBySequence(
+          StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    boolean showFeatures = alignmentv.getAlignViewport()
-            .isShowSequenceFeatures();
-    if (!colourBySequence || !isLoadingFinished())
-    {
-      return;
-    }
-    if (getSsm() == null)
-    {
-      return;
-    }
-    String[] files = getPdbFile();
-
-    SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
-    FeatureRenderer fr = null;
-    if (showFeatures)
-    {
-      fr = getFeatureRenderer(alignmentv);
-    }
-    AlignmentI alignment = alignmentv.getAlignment();
-
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
-            files, sr, fr, alignment))
+    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
     {
       for (String cbyseq : cpdbbyseq.commands)
       {
@@ -531,6 +509,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param alignment
    * @return
    */
+  @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
@@ -598,17 +577,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * returns the current featureRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment);
-
-  /**
    * instruct the Jalview binding to update the pdbentries vector if necessary
    * prior to matching the jmol view's contents to the list of structure files
    * Jalview knows about.
@@ -717,16 +685,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return null;
   }
 
-  /**
-   * returns the current sequenceRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment);
+  
 
   // ///////////////////////////////
   // JmolStatusListener
@@ -1286,6 +1245,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   }
 
+  @Override
   public void setJalviewColourScheme(ColourSchemeI cs)
   {
     colourBySequence = false;
@@ -1300,10 +1260,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     command.append("select *;color white;");
     List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
             false);
-    for (String res : residueSet)
+    for (String resName : residueSet)
     {
-      Color col = cs.findColour(res.charAt(0));
-      command.append("select " + res + ";color[" + col.getRed() + ","
+      char res = resName.length() == 3 ? ResidueProperties
+              .getSingleCharacterCode(resName) : resName.charAt(0);
+      Color col = cs.findColour(res);
+      command.append("select " + resName + ";color[" + col.getRed() + ","
               + col.getGreen() + "," + col.getBlue() + "];");
     }
 
@@ -1400,6 +1362,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 
+  @Override
   public void setBackgroundColour(java.awt.Color col)
   {
     jmolHistory(false);