JAL-2430 colour columns hidden in alignment gray on structure

[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 bb9df8a..e665982 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,9 +20,11 @@
  */
 package jalview.ext.rbvi.chimera;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureMapping;
@@ -57,16 +59,16 @@ public class ChimeraCommands
    * @param sequence
    * @param sr
    * @param fr
-   * @param alignment
+   * @param viewport
    * @return
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          AlignViewportI viewport)
   {
     Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
-            sequence, sr, fr, alignment);
+            sequence, sr, fr, viewport);
 
     List<String> colourCommands = buildColourCommands(colourMap);
 
@@ -173,9 +175,8 @@ public class ChimeraCommands
 
   /**
    * <pre>
-   * Build a data structure which maps contiguous subsequences for each colour. 
-   * This generates a data structure from which we can easily generate the 
-   * Chimera command for colour by sequence.
+   * Build a data structure which records contiguous subsequences for each colour. 
+   * From this we can easily generate the Chimera command for colour by sequence.
    * Color
    *     Model number
    *         Chain
@@ -186,10 +187,13 @@ public class ChimeraCommands
   protected static Map<Object, AtomSpecModel> buildColoursMap(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          AlignViewportI viewport)
   {
+    ColumnSelection cs = viewport.getColumnSelection();
+    AlignmentI al = viewport.getAlignment();
     Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
     Color lastColour = null;
+
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -207,9 +211,9 @@ public class ChimeraCommands
         {
           final SequenceI seq = sequence[pdbfnum][s];
           if (mapping[m].getSequence() == seq
-                  && (sp = alignment.findIndex(seq)) > -1)
+                  && (sp = al.findIndex(seq)) > -1)
           {
-            SequenceI asp = alignment.getSequenceAt(sp);
+            SequenceI asp = al.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
             {
               // no mapping to gaps in sequence
@@ -225,6 +229,16 @@ public class ChimeraCommands
               }
 
               Color colour = sr.getResidueColour(seq, r, fr);
+
+              /*
+               * darker colour for hidden regions
+               */
+              if (!cs.isVisible(r))
+              {
+                // colour = ColorUtils.darkerThan(colour);
+                colour = Color.GRAY;
+              }
+
               final String chain = mapping[m].getChain();
 
               /*
@@ -477,7 +491,7 @@ public class ChimeraCommands
          */
         StringBuilder sb = new StringBuilder(128);
         String featureValue = value.toString();
-        featureValue.replaceAll("'", "&#39;");
+        featureValue = featureValue.replaceAll("\\'", "&#39;");
         sb.append("setattr r ").append(attributeName).append(" '")
                 .append(featureValue).append("' ");
         sb.append(values.get(value).getAtomSpec());