Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

[jalview.git] / src / jalview / appletgui / SequenceRenderer.java

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 31e2b9f..05a6d68 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.api.FeatureRenderer;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -86,6 +87,31 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     return resBoxColour;
   }
 
+  /**
+   * Get the residue colour at the given sequence position - as determined by
+   * the sequence group colour (if any), else the colour scheme, possibly
+   * overridden by a feature colour.
+   * 
+   * @param seq
+   * @param position
+   * @param fr
+   * @return
+   */
+  @Override
+  public Color getResidueColour(final SequenceI seq, int position,
+          FeatureRenderer fr)
+  {
+    // TODO replace 8 or so code duplications with calls to this method
+    // (refactored as needed)
+    Color col = getResidueBoxColour(seq, position);
+
+    if (fr != null)
+    {
+      col = fr.findFeatureColour(col, seq, position);
+    }
+    return col;
+  }
+
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
     if (cs != null)
@@ -204,7 +230,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
 
     char s = ' ';
-
+    boolean srep = av.isDisplayReferenceSeq();
     for (int i = start; i <= end; i++)
     {
       graphics.setColor(Color.black);
@@ -229,9 +255,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (currentSequenceGroup.getShowNonconserved())
         {
-          // cheat - use this if we have a consensus for each group: s =
-          // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+          s = getDisplayChar(srep, i, s,
                   '.');
         }
       }
@@ -256,7 +280,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+          s = getDisplayChar(srep, i, s,
                   '.');
 
         }
@@ -289,10 +313,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
   }
 
-  private char getDisplayChar(AlignmentAnnotation consensus, int position,
+  private char getDisplayChar(final boolean usesrep, int position,
           char s, char c)
   {
-    char conschar = consensus.annotations[position].displayCharacter
+    // TODO - use currentSequenceGroup rather than alignemnt 
+    // currentSequenceGroup.getConsensus()
+    char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
             .charAt(0);
     if (conschar != '-' && s == conschar)
     {