Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index c01be4e..57258ef 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -22,7 +22,6 @@ package jalview.viewmodel;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -37,6 +36,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.ProfileI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
@@ -701,7 +701,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   /**
    * results of alignment consensus analysis for visible portion of view
    */
-  protected Profile[] hconsensus = null;
+  protected ProfileI[] hconsensus = null;
 
   /**
    * results of cDNA complement consensus visible portion of view
@@ -735,7 +735,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public void setSequenceConsensusHash(Profile[] hconsensus)
+  public void setSequenceConsensusHash(ProfileI[] hconsensus)
   {
     this.hconsensus = hconsensus;
   }
@@ -747,7 +747,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public Profile[] getSequenceConsensusHash()
+  public ProfileI[] getSequenceConsensusHash()
   {
     return hconsensus;
   }
@@ -1867,7 +1867,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       cs.setConsensus(hconsensus);
       if (cs.conservationApplied())
       {
-        cs.setConservation(Conservation.calculateConservation("All", 3,
+        cs.setConservation(Conservation.calculateConservation("All",
                 alignment.getSequences(), 0, alignment.getWidth(), false,
                 getConsPercGaps(), false));
       }