JAL-98 null reference to globalColourScheme as it has ref to consensus

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index bd55668..1afe586 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.Profile;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -44,7 +45,6 @@ import jalview.datamodel.SequenceI;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.structure.CommandListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
@@ -58,6 +58,7 @@ import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
 import java.awt.Color;
+import java.beans.PropertyChangeSupport;
 import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.BitSet;
@@ -699,7 +700,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   /**
    * results of alignment consensus analysis for visible portion of view
    */
-  protected Hashtable[] hconsensus = null;
+  protected Profile[] hconsensus = null;
 
   /**
    * results of cDNA complement consensus visible portion of view
@@ -733,7 +734,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public void setSequenceConsensusHash(Hashtable[] hconsensus)
+  public void setSequenceConsensusHash(Profile[] hconsensus)
   {
     this.hconsensus = hconsensus;
   }
@@ -745,7 +746,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public Hashtable[] getSequenceConsensusHash()
+  public Profile[] getSequenceConsensusHash()
   {
     return hconsensus;
   }
@@ -807,7 +808,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConservation(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (alignment.isNucleotide() || conservation == null
+    if (alignment.isNucleotide()
+            || (conservation == null && quality == null)
             || !autoCalculateConsensus)
     {
       return;
@@ -913,6 +915,37 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return false;
   }
 
+  public void setAlignment(AlignmentI align)
+  {
+    this.alignment = align;
+  }
+
+  /**
+   * Clean up references when this viewport is closed
+   */
+  @Override
+  public void dispose()
+  {
+    /*
+     * defensively null out references to large objects in case
+     * this object is not garbage collected (as if!)
+     */
+    consensus = null;
+    complementConsensus = null;
+    strucConsensus = null;
+    conservation = null;
+    quality = null;
+    groupConsensus = null;
+    groupConservation = null;
+    hconsensus = null;
+    hcomplementConsensus = null;
+    // colour scheme may hold reference to consensus
+    globalColourScheme = null;
+    // TODO remove listeners from changeSupport?
+    changeSupport = null;
+    setAlignment(null);
+  }
+
   @Override
   public boolean isClosed()
   {
@@ -1107,6 +1140,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
+  public boolean hasSelectedColumns()
+  {
+    ColumnSelection columnSelection = getColumnSelection();
+    return columnSelection != null && columnSelection.hasSelectedColumns();
+  }
+
+  @Override
   public boolean hasHiddenColumns()
   {
     return colSel != null && colSel.hasHiddenColumns();
@@ -1233,10 +1273,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ignoreGapsInConsensusCalculation;
   }
 
-  // / property change stuff
-
+  // property change stuff
   // JBPNote Prolly only need this in the applet version.
-  private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
           this);
 
   protected boolean showConservation = true;
@@ -1537,7 +1576,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public boolean isHiddenRepSequence(SequenceI seq)
   {
     return (hiddenRepSequences != null && hiddenRepSequences
-                    .containsKey(seq));
+            .containsKey(seq));
   }
 
   /**
@@ -1827,9 +1866,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
       cs.setConsensus(hconsensus);
       if (cs.conservationApplied())
       {
-        cs.setConservation(Conservation.calculateConservation("All",
-                ResidueProperties.propHash, 3, alignment.getSequences(), 0,
-                alignment.getWidth(), false, getConsPercGaps(), false));
+        cs.setConservation(Conservation.calculateConservation("All", 3,
+                alignment.getSequences(), 0, alignment.getWidth(), false,
+                getConsPercGaps(), false));
       }
     }
 
@@ -2730,7 +2769,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       }
       seqMappings = MappingUtils
               .findMappingsForSequenceAndOthers(sequence, mappings,
-                      getCodingComplement().getAlignment());
+                      getCodingComplement().getAlignment().getSequences());
       if (!seqMappings.isEmpty())
       {
         break;
@@ -2760,11 +2799,9 @@ 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())
-            && (colSel == null || colSel.getSelected() == null || colSel
-                    .getSelected().size() == 0))
+            && !this.hasSelectedColumns())
     {
       if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
       {