From 02a105b77e97c60c8529cce96cdad1aade5d99a2 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 30 Aug 2013 11:58:27 +0100
Subject: [PATCH] JAL-1370 JAL-1371 flags for display and colour of view
 with/without reference sequence

---
 src/jalview/api/AlignViewportI.java          |   23 +++++++++++++++++++++
 src/jalview/viewmodel/AlignmentViewport.java |   28 ++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index f42293d..54019c6 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -154,5 +154,28 @@ public interface AlignViewportI
    */
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
+  
+  /**
+   * @return true if a reference sequence is set and should be displayed
+   */
+  public boolean isDisplayReferenceSeq();
+
+  /**
+   * @return set the flag for displaying reference sequences when they are
+   *         available
+   */
+  public void setDisplayReferenceSeq(boolean displayReferenceSeq);
+
+  /**
+   * @return true if colourschemes should render according to reference sequence
+   *         rather than consensus if available
+   */
+  public boolean isColourByReferenceSeq();
+
+  /**
+   * @return true set flag for deciding if colourschemes should render according
+   *         to reference sequence rather than consensus if available
+   */
+  public void setColourByReferenceSeq(boolean colourByReferenceSeq);
 
 }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d65486d..05f69b1 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1534,5 +1534,33 @@ 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;
+  }
 
 }
-- 
1.7.10.2