JAL-1370 allow show unconserved to reflect differences from the current reference...

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index d444630..b048e91 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -201,7 +201,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
 
     char s = ' ';
-
+    boolean srep = av.isDisplayReferenceSeq();
     for (int i = start; i <= end; i++)
     {
       graphics.setColor(Color.black);
@@ -226,9 +226,7 @@ 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,
                   '.');
         }
       }
@@ -253,7 +251,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+          s = getDisplayChar(srep, i, s,
                   '.');
 
         }
@@ -286,10 +284,12 @@ 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)
     {

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index a4325fe..2875f8d 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -287,6 +287,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else
     {
+      boolean srep = av.isDisplayReferenceSeq();
       boolean getboxColour = false;
       for (int i = start; i <= end; i++)
       {
@@ -332,7 +333,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (currentSequenceGroup.getShowNonconserved()) // todo optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+            s = getDisplayChar(srep, i, s,
                     '.');
 
           }
@@ -375,7 +376,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           }
           if (av.getShowUnconserved())
           {
-            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+            s = getDisplayChar(srep, i, s,
                     '.');
 
           }
@@ -390,10 +391,12 @@ 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)
     {