JAL-1681 show cDNA consensus on protein alignment - first version

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 037f19e..374e0be 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -75,6 +75,13 @@ public interface AlignViewportI extends ViewStyleI
 
   Hashtable[] getSequenceConsensusHash();
 
+  /**
+   * Get consensus data table for the cDNA complement of this alignment (if any)
+   * 
+   * @return
+   */
+  Hashtable[] getComplementConsensusHash();
+
   Hashtable[] getRnaStructureConsensusHash();
 
   boolean isIgnoreGapsConsensus();
@@ -93,6 +100,13 @@ public interface AlignViewportI extends ViewStyleI
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
+   * get the container for cDNA complement consensus annotation
+   * 
+   * @return
+   */
+  AlignmentAnnotation getComplementConsensusAnnotation();
+
+  /**
    * Test to see if viewport is still open and active
    * 
    * @return true indicates that all references to viewport should be dropped
@@ -120,6 +134,13 @@ public interface AlignViewportI extends ViewStyleI
   void setSequenceConsensusHash(Hashtable[] hconsensus);
 
   /**
+   * Set the cDNA complement consensus for the viewport
+   * 
+   * @param hconsensus
+   */
+  void setComplementConsensusHash(Hashtable[] hconsensus);
+
+  /**
    * 
    * @return the alignment annotatino row for the structure consensus
    *         calculation