X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=74466a1873da158efe69e02d17ec252d091e2dd5;hb=63a18b71aa3ed6503b6fbb8ec3543b5d66ed3f70;hp=44fef0eb74bd8f39cab4ed73067ee5640dd75b44;hpb=20cbd628749ac9c90b8596c386a24c5778f42c49;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 44fef0e..74466a1 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -160,6 +160,29 @@ 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);
 
   void setSequenceColour(SequenceI seq, Color col);