Merge branch 'Release_2_8_1_Branch' into JAL-1372_referenceseq

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 44ecf76..eb45fa4 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -998,8 +998,8 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return hiddenRepSequences != null
-            && hiddenRepSequences.containsKey(seq);
+    return alignment.getSeqrep()==seq || (hiddenRepSequences != null
+            && hiddenRepSequences.containsKey(seq));
   }
 
   public SequenceGroup getRepresentedSequences(SequenceI seq)
@@ -1548,6 +1548,34 @@ public abstract class AlignmentViewport implements AlignViewportI
     }
     oldrfs.clear();
   }
+  /**
+   * show the reference sequence in the alignment view
+   */
+  private boolean displayReferenceSeq=false;
+  /**
+   * colour according to the reference sequence defined on the alignment
+   */
+  private boolean colourByReferenceSeq=false;
+
+  public boolean isDisplayReferenceSeq()
+  {
+    return alignment.hasSeqrep() && displayReferenceSeq;
+  }
+
+  public void setDisplayReferenceSeq(boolean displayReferenceSeq)
+  {
+    this.displayReferenceSeq = displayReferenceSeq;
+  }
+
+  public boolean isColourByReferenceSeq()
+  {
+    return alignment.hasSeqrep() && colourByReferenceSeq;
+  }
+
+  public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+  {
+    this.colourByReferenceSeq = colourByReferenceSeq;
+  }
 
   @Override
   public Color getSequenceColour(SequenceI seq)