Merge branch 'features/JAL-1738_JAL-345_selectionfromhighlight' into develop

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 6ecfe99..fecccb0 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;
@@ -37,7 +36,8 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenSequences;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
@@ -613,7 +613,7 @@ 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)
       {
@@ -630,6 +630,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         cs.setConsensus(hconsensus);
         cs.setConservation(hconservation);
       }
+      cs.setConservationApplied(getConservationSelected());
       cs.alignmentChanged(alignment, hiddenRepSequences);
     }
     if (getColourAppliesToAllGroups())
@@ -700,7 +701,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   /**
    * results of alignment consensus analysis for visible portion of view
    */
-  protected Profile[] hconsensus = null;
+  protected ProfilesI hconsensus = null;
 
   /**
    * results of cDNA complement consensus visible portion of view
@@ -734,7 +735,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public void setSequenceConsensusHash(Profile[] hconsensus)
+  public void setSequenceConsensusHash(ProfilesI hconsensus)
   {
     this.hconsensus = hconsensus;
   }
@@ -746,7 +747,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public Profile[] getSequenceConsensusHash()
+  public ProfilesI getSequenceConsensusHash()
   {
     return hconsensus;
   }
@@ -939,7 +940,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     groupConservation = null;
     hconsensus = null;
     hcomplementConsensus = null;
-    // TODO removed listeners from changeSupport?
+    // colour scheme may hold reference to consensus
+    globalColourScheme = null;
+    // TODO remove listeners from changeSupport?
     changeSupport = null;
     setAlignment(null);
   }
@@ -1574,7 +1577,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public boolean isHiddenRepSequence(SequenceI seq)
   {
     return (hiddenRepSequences != null && hiddenRepSequences
-                    .containsKey(seq));
+            .containsKey(seq));
   }
 
   /**
@@ -1864,7 +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));
       }
@@ -2715,7 +2718,7 @@ 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())
@@ -2797,8 +2800,7 @@ 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())
     {
@@ -2823,6 +2825,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean selectionIsDefinedGroup = false;
 
+
   @Override
   public boolean isSelectionDefinedGroup()
   {
@@ -2846,4 +2849,27 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return selectionGroup.getContext() == alignment
             || selectionIsDefinedGroup;
   }
+
+  /**
+   * null, or currently highlighted results on this view
+   */
+  private SearchResultsI searchResults = null;
+
+  @Override
+  public boolean hasSearchResults()
+  {
+    return searchResults != null;
+  }
+
+  @Override
+  public void setSearchResults(SearchResultsI results)
+  {
+    searchResults = results;
+  }
+
+  @Override
+  public SearchResultsI getSearchResults()
+  {
+    return searchResults;
+  }
 }