JAL-966 JAL-1738 JAL-345 interfaces for SearchResults and SearchResults.Match

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 80319be..2f733ed 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -36,7 +36,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenSequences;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
@@ -612,7 +612,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     boolean recalc = false;
     if (cs != null)
     {
-      cs.setConservationApplied(recalc = getConservationSelected());
+      recalc = getConservationSelected();
       if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
               || cs instanceof Blosum62ColourScheme)
       {
@@ -629,6 +629,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         cs.setConsensus(hconsensus);
         cs.setConservation(hconservation);
       }
+      cs.setConservationApplied(getConservationSelected());
       cs.alignmentChanged(alignment, hiddenRepSequences);
     }
     if (getColourAppliesToAllGroups())
@@ -1573,7 +1574,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public boolean isHiddenRepSequence(SequenceI seq)
   {
     return (hiddenRepSequences != null && hiddenRepSequences
-                    .containsKey(seq));
+            .containsKey(seq));
   }
 
   /**
@@ -2714,7 +2715,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    *          the SearchResults to add to
    * @return the offset (below top of visible region) of the matched sequence
    */
-  protected int findComplementScrollTarget(SearchResults sr)
+  protected int findComplementScrollTarget(SearchResultsI sr)
   {
     final AlignViewportI complement = getCodingComplement();
     if (complement == null || !complement.isFollowHighlight())
@@ -2796,8 +2797,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void expandColSelection(SequenceGroup sg, boolean wholewidth)
   {
     int sgs, sge;
-    if (sg != null
-            && (sgs = sg.getStartRes()) >= 0
+    if (sg != null && (sgs = sg.getStartRes()) >= 0
             && sg.getStartRes() <= (sge = sg.getEndRes())
             && !this.hasSelectedColumns())
     {