Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a66855e..bca3c85 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -22,6 +22,7 @@ package jalview.viewmodel;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -33,7 +34,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
@@ -948,13 +948,15 @@ public abstract class AlignmentViewport
     groupConsensus = null;
     groupConservation = null;
     hconsensus = null;
+    hconservation = null;
     hcomplementConsensus = null;
     gapcounts = null;
-    // colour scheme may hold reference to consensus
-    residueShading = null;
-    // TODO remove listeners from changeSupport?
+    calculator = null;
+    residueShading = null; // may hold a reference to Consensus
     changeSupport = null;
     ranges = null;
+    currentTree = null;
+    selectionGroup = null;
     setAlignment(null);
   }
 
@@ -1336,7 +1338,10 @@ public abstract class AlignmentViewport
   public void removePropertyChangeListener(
           java.beans.PropertyChangeListener listener)
   {
-    changeSupport.removePropertyChangeListener(listener);
+    if (changeSupport != null)
+    {
+      changeSupport.removePropertyChangeListener(listener);
+    }
   }
 
   /**
@@ -1675,13 +1680,6 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public CigarArray getViewAsCigars(boolean selectedRegionOnly)
-  {
-    return new CigarArray(alignment, alignment.getHiddenColumns(),
-            (selectedRegionOnly ? selectionGroup : null));
-  }
-
-  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -2783,7 +2781,7 @@ public abstract class AlignmentViewport
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
     for (int seqNo = ranges
-            .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+            .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2879,6 +2877,8 @@ public abstract class AlignmentViewport
    */
   private SearchResultsI searchResults = null;
 
+  protected TreeModel currentTree = null;
+
   @Override
   public boolean hasSearchResults()
   {
@@ -2937,4 +2937,16 @@ public abstract class AlignmentViewport
             + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
     return sq;
   }
+
+  @Override
+  public void setCurrentTree(TreeModel tree)
+  {
+    currentTree = tree;
+  }
+
+  @Override
+  public TreeModel getCurrentTree()
+  {
+    return currentTree;
+  }
 }