JAL-4392 Merging consensus secondary structure

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 0cfd03d..b7747f5 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -85,8 +85,12 @@ public interface AlignViewportI extends ViewStyleI
   boolean isValidCharWidth();
 
   boolean isShowConsensusHistogram();
+  
+  boolean isShowSSConsensusHistogram();
 
   boolean isShowSequenceLogo();
+  
+  boolean isShowSequenceSSLogo();
 
   boolean isNormaliseSequenceLogo();
 
@@ -129,6 +133,9 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   AlignmentAnnotation getAlignmentConsensusAnnotation();
+  
+  AlignmentAnnotation getAlignmentSecondaryStructureConsensusAnnotation();
+
 
   /**
    * get the container for alignment gap annotation
@@ -175,6 +182,9 @@ public interface AlignViewportI extends ViewStyleI
    * @param hconsensus
    */
   void setSequenceConsensusHash(ProfilesI hconsensus);
+  
+  void setSequenceSSConsensusHash(ProfilesI hSSConsensus);
+  
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -567,4 +577,7 @@ public interface AlignViewportI extends ViewStyleI
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
 
   ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
+
+  ProfilesI getSequenceSSConsensusHash();
+
 }