X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=7849c2d1ea69cf2d66429f688f1c3f5f16f89de7;hb=fbfbbe26bee37143d5279fe4d254a5a89c96b021;hp=39621c53215034ee3dae89d936ea99b5cf777cf2;hpb=4d890895e6aabfc36d45d3b53781ee2cf5cfafdc;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 39621c5..7849c2d 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -22,7 +22,9 @@ package jalview.viewmodel;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeaturesDisplayedI;
@@ -30,11 +32,12 @@ import jalview.api.ViewStyleI;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.ProfilesI;
@@ -67,6 +70,7 @@ import java.util.BitSet;
 import java.util.Deque;
 import java.util.HashMap;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -77,10 +81,10 @@ import java.util.Map;
  * @author jimp
  * 
  */
-public abstract class AlignmentViewport implements AlignViewportI,
-        CommandListener, VamsasSource
+public abstract class AlignmentViewport
+        implements AlignViewportI, CommandListener, VamsasSource
 {
-  final protected ViewportRanges ranges;
+  protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -92,9 +96,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   FeaturesDisplayedI featuresDisplayed = null;
 
-  protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> historyList = new ArrayDeque<>();
 
-  protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> redoList = new ArrayDeque<>();
 
   /**
    * alignment displayed in the viewport. Please use get/setter
@@ -405,6 +409,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setWrapAlignment(boolean state)
   {
     viewStyle.setWrapAlignment(state);
+    ranges.setWrappedMode(state);
   }
 
   /**
@@ -567,8 +572,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setSeqNameItalics(default1);
   }
 
-
-
   @Override
   public AlignmentI getAlignment()
   {
@@ -609,7 +612,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
-  protected ResidueShaderI residueShading;
+  protected ResidueShaderI residueShading = new ResidueShader();
 
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
@@ -642,6 +645,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         residueShading.setConservation(hconservation);
       }
+      /*
+       * reset conservation flag in case just set to false if
+       * Conservation was null (calculation still in progress)
+       */
+      residueShading.setConservationApplied(getConservationSelected());
       residueShading.alignmentChanged(alignment, hiddenRepSequences);
     }
 
@@ -657,11 +665,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
          * retain any colour thresholds per group while
          * changing choice of colour scheme (JAL-2386)
          */
-        sg.setColourScheme(cs);
+        sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg));
         if (cs != null)
         {
-          sg.getGroupColourScheme()
-                  .alignmentChanged(sg, hiddenRepSequences);
+          sg.getGroupColourScheme().alignmentChanged(sg,
+                  hiddenRepSequences);
         }
       }
     }
@@ -670,8 +678,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public ColourSchemeI getGlobalColourScheme()
   {
-    return residueShading == null ? null : residueShading
-            .getColourScheme();
+    return residueShading == null ? null : residueShading.getColourScheme();
   }
 
   @Override
@@ -704,13 +711,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   /**
    * results of cDNA complement consensus visible portion of view
    */
-  protected Hashtable[] hcomplementConsensus = null;
+  protected Hashtable<String, Object>[] hcomplementConsensus = null;
 
   /**
    * results of secondary structure base pair consensus for visible portion of
    * view
    */
-  protected Hashtable[] hStrucConsensus = null;
+  protected Hashtable<String, Object>[] hStrucConsensus = null;
 
   protected Conservation hconservation = null;
 
@@ -739,7 +746,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public void setComplementConsensusHash(Hashtable[] hconsensus)
+  public void setComplementConsensusHash(
+          Hashtable<String, Object>[] hconsensus)
   {
     this.hcomplementConsensus = hconsensus;
   }
@@ -751,19 +759,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public Hashtable[] getComplementConsensusHash()
+  public Hashtable<String, Object>[] getComplementConsensusHash()
   {
     return hcomplementConsensus;
   }
 
   @Override
-  public Hashtable[] getRnaStructureConsensusHash()
+  public Hashtable<String, Object>[] getRnaStructureConsensusHash()
   {
     return hStrucConsensus;
   }
 
   @Override
-  public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+  public void setRnaStructureConsensusHash(
+          Hashtable<String, Object>[] hStrucConsensus)
   {
     this.hStrucConsensus = hStrucConsensus;
 
@@ -819,11 +828,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator
-            .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
+    if (calculator.getRegisteredWorkersOfClass(
+            jalview.workers.ConservationThread.class) == null)
     {
-      calculator.registerWorker(new jalview.workers.ConservationThread(
-              this, ap));
+      calculator.registerWorker(
+              new jalview.workers.ConservationThread(this, ap));
     }
   }
 
@@ -837,7 +846,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+    if (calculator
+            .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -868,8 +878,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       }
       if (doConsensus)
       {
-        if (calculator
-                .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+        if (calculator.getRegisteredWorkersOfClass(
+                ComplementConsensusThread.class) == null)
         {
           calculator
                   .registerWorker(new ComplementConsensusThread(this, ap));
@@ -893,7 +903,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
+    if (calculator.getRegisteredWorkersOfClass(
+            StrucConsensusThread.class) == null)
     {
       calculator.registerWorker(new StrucConsensusThread(this, ap));
     }
@@ -943,11 +954,16 @@ public abstract class AlignmentViewport implements AlignViewportI,
     groupConsensus = null;
     groupConservation = null;
     hconsensus = null;
+    hconservation = null;
     hcomplementConsensus = null;
-    // colour scheme may hold reference to consensus
-    residueShading = null;
-    // TODO remove listeners from changeSupport?
+    gapcounts = null;
+    calculator = null;
+    residueShading = null; // may hold a reference to Consensus
     changeSupport = null;
+    ranges = null;
+    currentTree = null;
+    selectionGroup = null;
+    colSel = null;
     setAlignment(null);
   }
 
@@ -1113,7 +1129,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setHiddenColumns(HiddenColumns hidden)
   {
     this.alignment.setHiddenColumns(hidden);
-    // this.colSel = colsel;
   }
 
   @Override
@@ -1160,7 +1175,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean hasHiddenColumns()
   {
-    return colSel != null
+    return alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns();
   }
 
@@ -1183,8 +1198,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (sequenceSetID != null)
     {
-      System.err
-              .println("Warning - overwriting a sequenceSetId for a viewport!");
+      System.err.println(
+              "Warning - overwriting a sequenceSetId for a viewport!");
     }
     sequenceSetID = new String(newid);
   }
@@ -1298,7 +1313,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showOccupancy = true;
 
-  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+  private Map<SequenceI, Color> sequenceColours = new HashMap<>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -1330,7 +1345,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void removePropertyChangeListener(
           java.beans.PropertyChangeListener listener)
   {
-    changeSupport.removePropertyChangeListener(listener);
+    if (changeSupport != null)
+    {
+      changeSupport.removePropertyChangeListener(listener);
+    }
   }
 
   /**
@@ -1391,6 +1409,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
   // common hide/show seq stuff
   public void showAllHiddenSeqs()
   {
+    int startSeq = ranges.getStartSeq();
+    int endSeq = ranges.getEndSeq();
+
     if (alignment.getHiddenSequences().getSize() > 0)
     {
       if (selectionGroup == null)
@@ -1398,8 +1419,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionGroup = new SequenceGroup();
         selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
-      List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
-              hiddenRepSequences);
+      List<SequenceI> tmp = alignment.getHiddenSequences()
+              .showAll(hiddenRepSequences);
       for (SequenceI seq : tmp)
       {
         selectionGroup.addSequence(seq, false);
@@ -1408,6 +1429,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
       hiddenRepSequences = null;
 
+      ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
       firePropertyChange("alignment", null, alignment.getSequences());
       // used to set hasHiddenRows/hiddenRepSequences here, after the property
       // changed event
@@ -1417,8 +1440,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public void showSequence(int index)
   {
-    List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
-            index, hiddenRepSequences);
+    int startSeq = ranges.getStartSeq();
+    int endSeq = ranges.getEndSeq();
+
+    List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
+            hiddenRepSequences);
     if (tmp.size() > 0)
     {
       if (selectionGroup == null)
@@ -1432,6 +1458,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionGroup.addSequence(seq, false);
         setSequenceAnnotationsVisible(seq, true);
       }
+
+      ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
       firePropertyChange("alignment", null, alignment.getSequences());
       sendSelection();
     }
@@ -1453,6 +1482,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public void hideSequence(SequenceI[] seq)
   {
+    /*
+     * cache offset to first visible sequence
+     */
+    int startSeq = ranges.getStartSeq();
+
     if (seq != null)
     {
       for (int i = 0; i < seq.length; i++)
@@ -1460,6 +1494,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         alignment.getHiddenSequences().hideSequence(seq[i]);
         setSequenceAnnotationsVisible(seq[i], false);
       }
+      ranges.setStartSeq(startSeq);
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
@@ -1489,8 +1524,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
 
     int gsize = selectionGroup.getSize();
-    SequenceI[] hseqs = selectionGroup.getSequences().toArray(
-            new SequenceI[gsize]);
+    SequenceI[] hseqs = selectionGroup.getSequences()
+            .toArray(new SequenceI[gsize]);
 
     hideSequence(hseqs);
     setSelectionGroup(null);
@@ -1528,7 +1563,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+      hiddenRepSequences = new Hashtable<>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1580,8 +1615,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return (hiddenRepSequences != null && hiddenRepSequences
-            .containsKey(seq));
+    return (hiddenRepSequences != null
+            && hiddenRepSequences.containsKey(seq));
   }
 
   /**
@@ -1599,14 +1634,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(
-            alignmentIndex);
+    return alignment.getHiddenSequences()
+            .adjustForHiddenSeqs(alignmentIndex);
   }
 
   @Override
   public void invertColumnSelection()
   {
     colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+    isColSelChanged(true);
   }
 
   @Override
@@ -1652,13 +1688,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public CigarArray getViewAsCigars(boolean selectedRegionOnly)
-  {
-    return new CigarArray(alignment, alignment.getHiddenColumns(),
-            (selectedRegionOnly ? selectionGroup : null));
-  }
-
-  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -1670,10 +1699,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
           boolean selectedOnly, boolean markGroups)
   {
     return new AlignmentView(alignment, alignment.getHiddenColumns(),
-            selectionGroup, alignment.getHiddenColumns() != null
+            selectionGroup,
+            alignment.getHiddenColumns() != null
                     && alignment.getHiddenColumns().hasHiddenColumns(),
-            selectedOnly,
-            markGroups);
+            selectedOnly, markGroups);
   }
 
   @Override
@@ -1719,8 +1748,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
     if (alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns())
     {
-      selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
-              start, end, seqs);
+      for (i = 0; i < iSize; i++)
+      {
+        Iterator<int[]> blocks = alignment.getHiddenColumns()
+                .getVisContigsIterator(start, end + 1, false);
+        selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
+      }
     }
     else
     {
@@ -1736,7 +1769,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
-    ArrayList<int[]> regions = new ArrayList<int[]>();
+    ArrayList<int[]> regions = new ArrayList<>();
     int start = min;
     int end = max;
 
@@ -1747,10 +1780,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         if (start == 0)
         {
-          start = hidden.adjustForHiddenColumns(start);
+          start = hidden.visibleToAbsoluteColumn(start);
         }
 
-        end = hidden.getHiddenBoundaryRight(start);
+        end = hidden.getNextHiddenBoundary(false, start);
         if (start == end)
         {
           end = max;
@@ -1765,12 +1798,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
       if (hidden != null && hidden.hasHiddenColumns())
       {
-        start = hidden.adjustForHiddenColumns(end);
-        start = hidden.getHiddenBoundaryLeft(start) + 1;
+        start = hidden.visibleToAbsoluteColumn(end);
+        start = hidden.getNextHiddenBoundary(true, start) + 1;
       }
     } while (end < max);
 
-    int[][] startEnd = new int[regions.size()][2];
+    // int[][] startEnd = new int[regions.size()][2];
 
     return regions;
   }
@@ -1779,7 +1812,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
           boolean selectedOnly)
   {
-    ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
     AlignmentAnnotation[] aa;
     if ((aa = alignment.getAlignmentAnnotation()) != null)
     {
@@ -1788,13 +1821,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
         if (selectedOnly && selectionGroup != null)
         {
-          alignment.getHiddenColumns().makeVisibleAnnotation(
-                  selectionGroup.getStartRes(),
-                  selectionGroup.getEndRes(), clone);
+          clone.makeVisibleAnnotation(selectionGroup.getStartRes(),
+                  selectionGroup.getEndRes(), alignment.getHiddenColumns());
         }
         else
         {
-          alignment.getHiddenColumns().makeVisibleAnnotation(clone);
+          clone.makeVisibleAnnotation(alignment.getHiddenColumns());
         }
         ala.add(clone);
       }
@@ -1979,8 +2011,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       gapcounts = new AlignmentAnnotation("Occupancy",
               MessageManager.getString("label.occupancy_descr"),
-              new Annotation[1], 0f,
-              alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+              new Annotation[1], 0f, alignment.getHeight(),
+              AlignmentAnnotation.BAR_GRAPH);
       gapcounts.hasText = true;
       gapcounts.autoCalculated = true;
       gapcounts.scaleColLabel = true;
@@ -1998,8 +2030,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         conservation = new AlignmentAnnotation("Conservation",
                 MessageManager.formatMessage("label.conservation_descr",
-                        getConsPercGaps()), new Annotation[1],
-                0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+                        getConsPercGaps()),
+                new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
         alignment.addAnnotation(conservation);
@@ -2125,7 +2157,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
      * TODO reorder the annotation rows according to group/sequence ordering on
      * alignment
      */
-    boolean sortg = true;
+    // boolean sortg = true;
 
     // remove old automatic annotation
     // add any new annotation
@@ -2133,7 +2165,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     // intersect alignment annotation with alignment groups
 
     AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
-    List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> oldrfs = new ArrayList<>();
     if (aan != null)
     {
       for (int an = 0; an < aan.length; an++)
@@ -2235,7 +2267,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void clearSequenceColours()
   {
     sequenceColours.clear();
-  };
+  }
 
   @Override
   public AlignViewportI getCodingComplement()
@@ -2479,8 +2511,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle = new ViewStyle(settingsForView);
     if (residueShading != null)
     {
-      residueShading.setConservationApplied(settingsForView
-              .isConservationColourSelected());
+      residueShading.setConservationApplied(
+              settingsForView.isConservationColourSelected());
     }
   }
 
@@ -2648,7 +2680,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sortAnnotationsBy;
   }
 
-  public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+  public void setSortAnnotationsBy(
+          SequenceAnnotationOrder sortAnnotationsBy)
   {
     this.sortAnnotationsBy = sortAnnotationsBy;
   }
@@ -2675,6 +2708,42 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setScaleProteinAsCdna(b);
   }
 
+  @Override
+  public boolean isProteinFontAsCdna()
+  {
+    return viewStyle.isProteinFontAsCdna();
+  }
+
+  @Override
+  public void setProteinFontAsCdna(boolean b)
+  {
+    viewStyle.setProteinFontAsCdna(b);
+  }
+
+  @Override
+  public void setShowComplementFeatures(boolean b)
+  {
+    viewStyle.setShowComplementFeatures(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeatures()
+  {
+    return viewStyle.isShowComplementFeatures();
+  }
+
+  @Override
+  public void setShowComplementFeaturesOnTop(boolean b)
+  {
+    viewStyle.setShowComplementFeaturesOnTop(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeaturesOnTop()
+  {
+    return viewStyle.isShowComplementFeaturesOnTop();
+  }
+
   /**
    * @return true if view should scroll to show the highlighted region of a
    *         sequence
@@ -2714,8 +2783,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return 0;
     }
     boolean iAmProtein = !getAlignment().isNucleotide();
-    AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
-            .getAlignment();
+    AlignmentI proteinAlignment = iAmProtein ? getAlignment()
+            : complement.getAlignment();
     if (proteinAlignment == null)
     {
       return 0;
@@ -2746,7 +2815,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
-    for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+    for (int seqNo = ranges
+            .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2757,9 +2827,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         continue;
       }
-      seqMappings = MappingUtils
-              .findMappingsForSequenceAndOthers(sequence, mappings,
-                      getCodingComplement().getAlignment().getSequences());
+      seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
+              mappings,
+              getCodingComplement().getAlignment().getSequences());
       if (!seqMappings.isEmpty())
       {
         break;
@@ -2834,8 +2904,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionIsDefinedGroup = gps.contains(selectionGroup);
       }
     }
-    return selectionGroup.getContext() == alignment
-            || selectionIsDefinedGroup;
+    return selectionGroup.isDefined() || selectionIsDefinedGroup;
   }
 
   /**
@@ -2843,6 +2912,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private SearchResultsI searchResults = null;
 
+  protected TreeModel currentTree = null;
+
   @Override
   public boolean hasSearchResults()
   {
@@ -2860,4 +2931,176 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
+
+  @Override
+  public ContactListI getContactList(AlignmentAnnotation _aa, int column)
+  {
+    return alignment.getContactListFor(_aa, column);
+  }
+
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation
+   * row.
+   * 
+   * @return consensus sequence as a new sequence object
+   */
+  public SequenceI getConsensusSeq()
+  {
+    if (consensus == null)
+    {
+      updateConsensus(null);
+    }
+    if (consensus == null)
+    {
+      return null;
+    }
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
+    {
+      Annotation annotation = consensus.annotations[i];
+      if (annotation != null)
+      {
+        String description = annotation.description;
+        if (description != null && description.startsWith("["))
+        {
+          // consensus is a tie - just pick the first one
+          seqs.append(description.charAt(1));
+        }
+        else
+        {
+          seqs.append(annotation.displayCharacter);
+        }
+      }
+    }
+
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;
+  }
+
+  @Override
+  public void setCurrentTree(TreeModel tree)
+  {
+    currentTree = tree;
+  }
+
+  @Override
+  public TreeModel getCurrentTree()
+  {
+    return currentTree;
+  }
+
+  @Override
+  public AlignmentExportData getAlignExportData(
+          AlignExportSettingsI options)
+  {
+    AlignmentI alignmentToExport = null;
+    String[] omitHidden = null;
+    alignmentToExport = null;
+
+    if (hasHiddenColumns() && !options.isExportHiddenColumns())
+    {
+      omitHidden = getViewAsString(false,
+              options.isExportHiddenSequences());
+    }
+
+    int[] alignmentStartEnd = new int[2];
+    if (hasHiddenRows() && options.isExportHiddenSequences())
+    {
+      alignmentToExport = getAlignment().getHiddenSequences()
+              .getFullAlignment();
+    }
+    else
+    {
+      alignmentToExport = getAlignment();
+    }
+    alignmentStartEnd = getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
+    AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+            omitHidden, alignmentStartEnd);
+    return ed;
+  }
+
+  /**
+   * flag set to indicate if structure views might be out of sync with sequences
+   * in the alignment
+   */
+
+  private boolean needToUpdateStructureViews = false;
+
+  @Override
+  public boolean isUpdateStructures()
+  {
+    return needToUpdateStructureViews;
+  }
+
+  @Override
+  public void setUpdateStructures(boolean update)
+  {
+    needToUpdateStructureViews = update;
+  }
+
+  @Override
+  public boolean needToUpdateStructureViews()
+  {
+    boolean update = needToUpdateStructureViews;
+    needToUpdateStructureViews = false;
+    return update;
+  }
+
+  @Override
+  public void addSequenceGroup(SequenceGroup sequenceGroup)
+  {
+    alignment.addGroup(sequenceGroup);
+
+    Color col = sequenceGroup.idColour;
+    if (col != null)
+    {
+      col = col.brighter();
+
+      for (SequenceI sq : sequenceGroup.getSequences())
+      {
+        setSequenceColour(sq, col);
+      }
+    }
+
+    if (codingComplement != null)
+    {
+      SequenceGroup mappedGroup = MappingUtils
+              .mapSequenceGroup(sequenceGroup, this, codingComplement);
+      if (mappedGroup.getSequences().size() > 0)
+      {
+        codingComplement.getAlignment().addGroup(mappedGroup);
+
+        if (col != null)
+        {
+          for (SequenceI seq : mappedGroup.getSequences())
+          {
+            codingComplement.setSequenceColour(seq, col);
+          }
+        }
+      }
+      // propagate the structure view update flag according to our own setting
+      codingComplement.setUpdateStructures(needToUpdateStructureViews);
+    }
+  }
+
+  @Override
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+  {
+    int start = 0;
+    int end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
+    {
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
+    }
+    else
+    {
+      end = alignment.getWidth();
+    }
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
+  }
 }