JAL-1628 method to hide insertions to current sequence selection

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a2da591..98b8d64 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -649,9 +649,14 @@ public abstract class AlignmentViewport implements AlignViewportI
     return colSel;
   }
 
+  @Override
   public void setColumnSelection(ColumnSelection colSel)
   {
     this.colSel = colSel;
+    if (colSel != null)
+    {
+      updateHiddenColumns();
+    }
   }
 
   /**
@@ -675,7 +680,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   public void updateHiddenColumns()
   {
-    hasHiddenColumns = colSel.getHiddenColumns() != null;
+    hasHiddenColumns = colSel.hasHiddenColumns();
   }
 
   protected boolean hasHiddenRows = false;
@@ -1031,8 +1036,8 @@ 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)
@@ -1603,6 +1608,34 @@ 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)