X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=c9a3a8019a8f920fbba29892ae27e495d7271991;hb=af259f508805faf2da90585ee9a67cd7853bf5aa;hp=1e65084fe4949a75fc2cbce764079c4cd76ec42a;hpb=299d350019dc2701cd2d9812e8ce1285146bc045;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1e65084..c9a3a80 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,19 +20,9 @@
  */
 package jalview.viewmodel;
 
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
 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;
@@ -44,8 +34,8 @@ 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;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -62,12 +52,25 @@ import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ComplementConsensusThread;
 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;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -75,10 +78,10 @@ import jalview.workers.StrucConsensusThread;
  * @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();
 
@@ -90,9 +93,9 @@ 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
@@ -403,6 +406,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setWrapAlignment(boolean state)
   {
     viewStyle.setWrapAlignment(state);
+    ranges.setWrappedMode(state);
   }
 
   /**
@@ -565,8 +569,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setSeqNameItalics(default1);
   }
 
-
-
   @Override
   public AlignmentI getAlignment()
   {
@@ -607,7 +609,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
-  protected ResidueShaderI residueShading;
+  protected ResidueShaderI residueShading = new ResidueShader();
 
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
@@ -640,6 +642,11 @@ 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);
     }
 
@@ -655,11 +662,12 @@ 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);
         }
       }
     }
@@ -668,8 +676,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public ColourSchemeI getGlobalColourScheme()
   {
-    return residueShading == null ? null : residueShading
-            .getColourScheme();
+    return residueShading == null ? null : residueShading.getColourScheme();
   }
 
   @Override
@@ -817,11 +824,11 @@ 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));
     }
   }
 
@@ -831,11 +838,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
+    if (consensus == null || !autoCalculateConsensus)
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+    if (calculator
+            .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -866,8 +874,8 @@ 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));
@@ -891,7 +899,8 @@ 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));
     }
@@ -941,11 +950,16 @@ 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);
   }
 
@@ -1108,9 +1122,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
-  public void setHiddenColumns(ColumnSelection colsel)
+  public void setHiddenColumns(HiddenColumns hidden)
   {
-    this.colSel = colsel;
+    this.alignment.setHiddenColumns(hidden);
   }
 
   @Override
@@ -1157,7 +1171,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean hasHiddenColumns()
   {
-    return colSel != null && colSel.hasHiddenColumns();
+    return alignment.getHiddenColumns() != null
+            && alignment.getHiddenColumns().hasHiddenColumns();
   }
 
   public void updateHiddenColumns()
@@ -1179,8 +1194,8 @@ 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);
   }
@@ -1292,7 +1307,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showConsensus = true;
 
-  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+  protected boolean showOccupancy = true;
+
+  private Map<SequenceI, Color> sequenceColours = new HashMap<>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -1324,7 +1341,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void removePropertyChangeListener(
           java.beans.PropertyChangeListener listener)
   {
-    changeSupport.removePropertyChangeListener(listener);
+    if (changeSupport != null)
+    {
+      changeSupport.removePropertyChangeListener(listener);
+    }
   }
 
   /**
@@ -1352,7 +1372,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return;
     }
 
-    colSel.hideSelectedColumns();
+    colSel.hideSelectedColumns(alignment);
     setSelectionGroup(null);
     isColSelChanged(true);
   }
@@ -1361,30 +1381,33 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (start == end)
     {
-      colSel.hideColumns(start);
+      colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
     }
     else
     {
-      colSel.hideColumns(start, end);
+      alignment.getHiddenColumns().hideColumns(start, end);
     }
     isColSelChanged(true);
   }
 
   public void showColumn(int col)
   {
-    colSel.revealHiddenColumns(col);
+    alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
     isColSelChanged(true);
   }
 
   public void showAllHiddenColumns()
   {
-    colSel.revealAllHiddenColumns();
+    alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
     isColSelChanged(true);
   }
 
   // common hide/show seq stuff
   public void showAllHiddenSeqs()
   {
+    int startSeq = ranges.getStartSeq();
+    int endSeq = ranges.getEndSeq();
+
     if (alignment.getHiddenSequences().getSize() > 0)
     {
       if (selectionGroup == null)
@@ -1392,8 +1415,8 @@ 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);
@@ -1402,6 +1425,8 @@ 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
@@ -1411,8 +1436,11 @@ 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)
@@ -1426,6 +1454,9 @@ 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();
     }
@@ -1447,6 +1478,11 @@ 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++)
@@ -1454,6 +1490,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         alignment.getHiddenSequences().hideSequence(seq[i]);
         setSequenceAnnotationsVisible(seq[i], false);
       }
+      ranges.setStartSeq(startSeq);
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
@@ -1483,8 +1520,8 @@ 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);
@@ -1522,7 +1559,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+      hiddenRepSequences = new Hashtable<>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1574,8 +1611,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return (hiddenRepSequences != null && hiddenRepSequences
-            .containsKey(seq));
+    return (hiddenRepSequences != null
+            && hiddenRepSequences.containsKey(seq));
   }
 
   /**
@@ -1593,14 +1630,15 @@ 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());
+    colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+    isColSelChanged(true);
   }
 
   @Override
@@ -1646,13 +1684,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public CigarArray getViewAsCigars(boolean selectedRegionOnly)
-  {
-    return new CigarArray(alignment, colSel,
-            (selectedRegionOnly ? selectionGroup : null));
-  }
-
-  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -1663,9 +1694,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
   {
-    return new AlignmentView(alignment, colSel, selectionGroup,
-            colSel != null && colSel.hasHiddenColumns(), selectedOnly,
-            markGroups);
+    return new AlignmentView(alignment, alignment.getHiddenColumns(),
+            selectionGroup,
+            alignment.getHiddenColumns() != null
+                    && alignment.getHiddenColumns().hasHiddenColumns(),
+            selectedOnly, markGroups);
   }
 
   @Override
@@ -1708,9 +1741,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
 
     selection = new String[iSize];
-    if (colSel != null && colSel.hasHiddenColumns())
+    if (alignment.getHiddenColumns() != null
+            && alignment.getHiddenColumns().hasHiddenColumns())
     {
-      selection = colSel.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
     {
@@ -1726,20 +1765,21 @@ 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;
 
     do
     {
-      if (colSel != null && colSel.hasHiddenColumns())
+      HiddenColumns hidden = alignment.getHiddenColumns();
+      if (hidden != null && hidden.hasHiddenColumns())
       {
         if (start == 0)
         {
-          start = colSel.adjustForHiddenColumns(start);
+          start = hidden.visibleToAbsoluteColumn(start);
         }
 
-        end = colSel.getHiddenBoundaryRight(start);
+        end = hidden.getNextHiddenBoundary(false, start);
         if (start == end)
         {
           end = max;
@@ -1752,10 +1792,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
       regions.add(new int[] { start, end });
 
-      if (colSel != null && colSel.hasHiddenColumns())
+      if (hidden != null && hidden.hasHiddenColumns())
       {
-        start = colSel.adjustForHiddenColumns(end);
-        start = colSel.getHiddenBoundaryLeft(start) + 1;
+        start = hidden.visibleToAbsoluteColumn(end);
+        start = hidden.getNextHiddenBoundary(true, start) + 1;
       }
     } while (end < max);
 
@@ -1768,7 +1808,7 @@ 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)
     {
@@ -1777,12 +1817,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
         if (selectedOnly && selectionGroup != null)
         {
-          colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
-                  selectionGroup.getEndRes(), clone);
+          clone.makeVisibleAnnotation(
+                  selectionGroup.getStartRes(), selectionGroup.getEndRes(),
+                  alignment.getHiddenColumns());
         }
         else
         {
-          colSel.makeVisibleAnnotation(clone);
+          clone.makeVisibleAnnotation(alignment.getHiddenColumns());
         }
         ala.add(clone);
       }
@@ -1898,24 +1939,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         initRNAStructure();
       }
-      consensus = new AlignmentAnnotation("Consensus", "PID",
+      consensus = new AlignmentAnnotation("Consensus",
+              MessageManager.getString("label.consensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
-      gapcounts = new AlignmentAnnotation("Occupancy",
-              "Number of aligned positions",
-              new Annotation[1], 0f, alignment.getHeight(),
-              AlignmentAnnotation.BAR_GRAPH);
-      initGapCounts(gapcounts);
+      initGapCounts();
 
       initComplementConsensus();
     }
   }
 
   /**
-   * If this is a protein alignment and there are mappings to cDNA, add the cDNA
-   * consensus annotation.
+   * If this is a protein alignment and there are mappings to cDNA, adds the
+   * cDNA consensus annotation and returns true, else returns false.
    */
-  public void initComplementConsensus()
+  public boolean initComplementConsensus()
   {
     if (!alignment.isNucleotide())
     {
@@ -1939,12 +1977,16 @@ public abstract class AlignmentViewport implements AlignViewportI,
         if (doConsensus)
         {
           complementConsensus = new AlignmentAnnotation("cDNA Consensus",
-                  "PID for cDNA", new Annotation[1], 0f, 100f,
+                  MessageManager
+                          .getString("label.complement_consensus_descr"),
+                  new Annotation[1], 0f, 100f,
                   AlignmentAnnotation.BAR_GRAPH);
           initConsensus(complementConsensus);
+          return true;
         }
       }
     }
+    return false;
   }
 
   private void initConsensus(AlignmentAnnotation aa)
@@ -1960,15 +2002,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   // these should be extracted from the view model - style and settings for
   // derived annotation
-  private void initGapCounts(AlignmentAnnotation counts)
+  private void initGapCounts()
   {
-    counts.hasText = false;
-    counts.autoCalculated = true;
-    counts.graph = AlignmentAnnotation.BAR_GRAPH;
-
-    if (showConsensus)
+    if (showOccupancy)
     {
-      alignment.addAnnotation(counts);
+      gapcounts = new AlignmentAnnotation("Occupancy",
+              MessageManager.getString("label.occupancy_descr"),
+              new Annotation[1], 0f, alignment.getHeight(),
+              AlignmentAnnotation.BAR_GRAPH);
+      gapcounts.hasText = true;
+      gapcounts.autoCalculated = true;
+      gapcounts.scaleColLabel = true;
+      gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+      alignment.addAnnotation(gapcounts);
     }
   }
 
@@ -1979,9 +2026,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
       if (conservation == null)
       {
         conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than "
-                        + getConsPercGaps() + "% gaps", new Annotation[1],
-                0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+                MessageManager.formatMessage("label.conservation_descr",
+                        getConsPercGaps()),
+                new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
         alignment.addAnnotation(conservation);
@@ -1996,7 +2043,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       if (quality == null)
       {
         quality = new AlignmentAnnotation("Quality",
-                "Alignment Quality based on Blosum62 scores",
+                MessageManager.getString("label.quality_descr"),
                 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         quality.hasText = true;
         quality.autoCalculated = true;
@@ -2009,7 +2056,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (alignment.hasRNAStructure() && strucConsensus == null)
     {
-      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+      strucConsensus = new AlignmentAnnotation("StrucConsensus",
+              MessageManager.getString("label.strucconsensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       strucConsensus.hasText = true;
       strucConsensus.autoCalculated = true;
@@ -2114,7 +2162,7 @@ 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++)
@@ -2460,8 +2508,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle = new ViewStyle(settingsForView);
     if (residueShading != null)
     {
-      residueShading.setConservationApplied(settingsForView
-              .isConservationColourSelected());
+      residueShading.setConservationApplied(
+              settingsForView.isConservationColourSelected());
     }
   }
 
@@ -2629,7 +2677,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sortAnnotationsBy;
   }
 
-  public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+  public void setSortAnnotationsBy(
+          SequenceAnnotationOrder sortAnnotationsBy)
   {
     this.sortAnnotationsBy = sortAnnotationsBy;
   }
@@ -2656,6 +2705,42 @@ 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
@@ -2695,8 +2780,8 @@ 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;
@@ -2727,7 +2812,8 @@ 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))
@@ -2738,9 +2824,9 @@ 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;
@@ -2815,8 +2901,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionIsDefinedGroup = gps.contains(selectionGroup);
       }
     }
-    return selectionGroup.getContext() == alignment
-            || selectionIsDefinedGroup;
+    return selectionGroup.isDefined() || selectionIsDefinedGroup;
   }
 
   /**
@@ -2824,6 +2909,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private SearchResultsI searchResults = null;
 
+  protected TreeModel currentTree = null;
+
   @Override
   public boolean hasSearchResults()
   {
@@ -2841,4 +2928,139 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
+
+  /**
+   * 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;
+  }
+
+  /**
+   * 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));
+  }
 }