Merge branch 'Release_2_8_1_Branch' into JAL-1372_referenceseq

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 44fef0e..74466a1 100644 (file)
--- 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);