X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=f232e92fbe4501b805b9fa404f4d39045739a460;hb=9201765247470c08d366abef2713c1c736adf2cb;hp=b68008a0495a467e946fcd83b38e05ba11fb0052;hpb=98db6c30a9d5539276236a7885bf22a161aa9df9;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
old mode 100755
new mode 100644
index b68008a..11321eb
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,1867 +1,1149 @@
- /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
  */
-public class AlignViewport
+public class AlignViewport extends AlignmentViewport implements
+        SelectionSource
 {
-    int startRes;
-    int endRes;
-    int startSeq;
-    int endSeq;
-    boolean showJVSuffix = true;
-    boolean showText = true;
-    boolean showColourText = false;
-    boolean showBoxes = true;
-    boolean wrapAlignment = false;
-    boolean renderGaps = true;
-    boolean showSequenceFeatures = false;
-    boolean showAnnotation = true;
-    boolean colourAppliesToAllGroups = true;
-    ColourSchemeI globalColourScheme = null;
-    boolean conservationColourSelected = false;
-    boolean abovePIDThreshold = false;
-    SequenceGroup selectionGroup;
-    int charHeight;
-    int charWidth;
-    boolean validCharWidth;
-    int wrappedWidth;
-    Font font;
-    boolean seqNameItalics;
-    AlignmentI alignment;
-    ColumnSelection colSel = new ColumnSelection();
-    int threshold;
-    int increment;
-    NJTree currentTree = null;
-    boolean scaleAboveWrapped = false;
-    boolean scaleLeftWrapped = true;
-    boolean scaleRightWrapped = true;
-    boolean hasHiddenColumns = false;
-    boolean hasHiddenRows = false;
-    boolean showHiddenMarkers = true;
-
-    boolean cursorMode = false;
-
-    // The following vector holds the features which are
-    // currently visible, in the correct order or rendering
-    Hashtable featuresDisplayed = null;
-
-
-    /** DOCUMENT ME!! */
-    public Hashtable [] hconsensus;
-    AlignmentAnnotation consensus;
-    AlignmentAnnotation conservation;
-    AlignmentAnnotation quality;
-    boolean autoCalculateConsensus = true;
-
-    /** DOCUMENT ME!! */
-    public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
-    // JBPNote Prolly only need this in the applet version.
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
-      PropertyChangeSupport(this);
-
-    boolean ignoreGapsInConsensusCalculation = false;
-
-    boolean isDataset = false;
-
-    boolean antiAlias = false;
-
-    boolean padGaps = false;
-
-    Rectangle explodedPosition;
-
-    String viewName;
-
-    String sequenceSetID;
-
-    boolean gatherViewsHere = false;
-
-    Stack historyList = new Stack();
-    Stack redoList = new Stack();
-
-    Hashtable sequenceColours;
-
-    int thresholdTextColour = 0;
-    Color textColour = Color.black;
-    Color textColour2 = Color.white;
-
-    boolean rightAlignIds = false;
-
-    Hashtable hiddenRepSequences;
-
-
-    /**
-     * Creates a new AlignViewport object.
-     *
-     * @param al DOCUMENT ME!
-     */
-    public AlignViewport(AlignmentI al)
-    {
-        setAlignment(al);
-        init();
-    }
-    /**
-     * Create a new AlignViewport with hidden regions
-     * @param al AlignmentI
-     * @param hiddenColumns ColumnSelection
-     */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
-  {
-      setAlignment(al);
-    if (hiddenColumns != null)
-    {
-        this.colSel = hiddenColumns;
-        if (hiddenColumns.getHiddenColumns() != null)
-      {
-          hasHiddenColumns = true;
-      }
-    }
-      init();
-    }
-
-    void init()
-    {
-        this.startRes = 0;
-        this.endRes = alignment.getWidth() - 1;
-        this.startSeq = 0;
-        this.endSeq = alignment.getHeight() - 1;
-
-      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
-
-      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-      showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
-
-      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-
-      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
-      padGaps = Cache.getDefault("PAD_GAPS", true);
-
-       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
-       String fontSize = Cache.getDefault("FONT_SIZE", "10");
-
-       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
-
-       int style = 0;
-
-       if (fontStyle.equals("bold"))
-       {
-         style = 1;
-       }
-       else if (fontStyle.equals("italic"))
-       {
-         style = 2;
-       }
+  Font font;
 
-       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+  NJTree currentTree = null;
 
-       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
+  boolean cursorMode = false;
 
+  boolean antiAlias = false;
 
-        // We must set conservation and consensus before setting colour,
-        // as Blosum and Clustal require this to be done
-        if(hconsensus==null && !isDataset)
-        {
-          if(!alignment.isNucleotide())
-          {
-            conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than " +
-                ConsPercGaps + "% gaps",
-                new Annotation[1], 0f,
-                11f,
-                AlignmentAnnotation.BAR_GRAPH);
-            conservation.hasText = true;
-            conservation.autoCalculated=true;
-
-
-            if (Cache.getDefault("SHOW_CONSERVATION", true))
-            {
-              alignment.addAnnotation(conservation);
-            }
-
-            if (Cache.getDefault("SHOW_QUALITY", true))
-            {
-              quality = new AlignmentAnnotation("Quality",
-                                                "Alignment Quality based on Blosum62 scores",
-                                                new Annotation[1],
-                                                0f,
-                                                11f,
-                                                AlignmentAnnotation.BAR_GRAPH);
-              quality.hasText = true;
-              quality.autoCalculated=true;
-
-              alignment.addAnnotation(quality);
-            }
-          }
-
-          consensus = new AlignmentAnnotation("Consensus", "PID",
-                                               new Annotation[1], 0f, 100f,
-                                               AlignmentAnnotation.BAR_GRAPH);
-          consensus.hasText = true;
-          consensus.autoCalculated=true;
-
-           if (Cache.getDefault("SHOW_IDENTITY", true))
-           {
-             alignment.addAnnotation(consensus);
-           }
-        }
-
-        if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
-        {
-          globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+  private Rectangle explodedGeometry;
 
-            if (globalColourScheme instanceof UserColourScheme)
-            {
-                globalColourScheme = UserDefinedColours.loadDefaultColours();
-        ( (UserColourScheme) globalColourScheme).setThreshold(0,
-            getIgnoreGapsConsensus());
-            }
+  String viewName;
 
-            if (globalColourScheme != null)
-            {
-                globalColourScheme.setConsensus(hconsensus);
-            }
-        }
+  /*
+   * Flag set true on the view that should 'gather' multiple views of the same
+   * sequence set id when a project is reloaded. Set false on all views when
+   * they are 'exploded' into separate windows. Set true on the current view
+   * when 'Gather' is performed, and also on the first tab when the first new
+   * view is created.
+   */
+  private boolean gatherViewsHere = false;
 
-        wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
-    }
+  private AnnotationColumnChooser annotationColumnSelectionState;
 
+  /**
+   * Creates a new AlignViewport object.
+   * 
+   * @param al
+   *          alignment to view
+   */
+  public AlignViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    init();
+  }
 
+  /**
+   * Create a new AlignViewport object with a specific sequence set ID
+   * 
+   * @param al
+   * @param seqsetid
+   *          (may be null - but potential for ambiguous constructor exception)
+   */
+  public AlignViewport(AlignmentI al, String seqsetid)
+  {
+    this(al, seqsetid, null);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowSequenceFeatures(boolean b)
+  public AlignViewport(AlignmentI al, String seqsetid, String viewid)
+  {
+    sequenceSetID = seqsetid;
+    viewId = viewid;
+    // TODO remove these once 2.4.VAMSAS release finished
+    if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
     {
-        showSequenceFeatures = b;
+      Cache.log.debug("Setting viewport's sequence set id : "
+              + sequenceSetID);
     }
-
-    public boolean getShowSequenceFeatures()
+    if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
     {
-      return showSequenceFeatures;
-    }
-
-  class ConservationThread
-      extends Thread
-    {
-      AlignmentPanel ap;
-      public ConservationThread(AlignmentPanel ap)
-      {
-        this.ap = ap;
-      }
-
-      public void run()
-      {
-        try
-        {
-          updatingConservation = true;
-
-          while (UPDATING_CONSERVATION)
-          {
-            try
-            {
-              if (ap != null)
-              {
-              ap.paintAlignment(true);
-              }
-              Thread.sleep(200);
-            }
-            catch (Exception ex)
-            {
-              ex.printStackTrace();
-            }
-          }
-
-          UPDATING_CONSERVATION = true;
-
-
-          int alWidth = alignment.getWidth();
-          if(alWidth<0)
-        {
-            return;
-        }
-
-          Conservation cons = new jalview.analysis.Conservation("All",
-              jalview.schemes.ResidueProperties.propHash, 3,
-              alignment.getSequences(), 0, alWidth -1);
-
-          cons.calculate();
-          cons.verdict(false, ConsPercGaps);
-
-          if (quality!=null)
-          {
-            cons.findQuality();
-          }
-
-          char [] sequence = cons.getConsSequence().getSequence();
-          float minR;
-          float minG;
-          float minB;
-          float maxR;
-          float maxG;
-          float maxB;
-          minR = 0.3f;
-          minG = 0.0f;
-          minB = 0f;
-          maxR = 1.0f - minR;
-          maxG = 0.9f - minG;
-          maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
-
-          float min = 0f;
-          float max = 11f;
-          float qmin = 0f;
-          float qmax = 0f;
-
-          char c;
-
-          conservation.annotations = new Annotation[alWidth];
-
-          if (quality!=null)
-          {
-            quality.graphMax = cons.qualityRange[1].floatValue();
-            quality.annotations = new Annotation[alWidth];
-            qmin = cons.qualityRange[0].floatValue();
-            qmax = cons.qualityRange[1].floatValue();
-          }
-
-          for (int i = 0; i < alWidth; i++)
-          {
-            float value = 0;
-
-            c = sequence[i];
-
-            if (Character.isDigit(c))
-          {
-              value = (int) (c - '0');
-          }
-            else if (c == '*')
-          {
-              value = 11;
-          }
-            else if (c == '+')
-          {
-              value = 10;
-          }
-
-            float vprop = value - min;
-            vprop /= max;
-            conservation.annotations[i] =
-                new Annotation(String.valueOf(c),
-                               String.valueOf(value), ' ', value,
-                               new Color(minR + (maxR * vprop),
-                                         minG + (maxG * vprop),
-                                         minB + (maxB * vprop)));
-
-            // Quality calc
-            if (quality!=null)
-            {
-              value = ( (Double) cons.quality.get(i)).floatValue();
-              vprop = value - qmin;
-              vprop /= qmax;
-            quality.annotations[i] = new Annotation(" ", String.valueOf(value),
-                ' ',
-                                               value,
-                                               new Color(minR + (maxR * vprop),
-                  minG + (maxG * vprop),
-                  minB + (maxB * vprop)));
-            }
-          }
-        }
-        catch (OutOfMemoryError error)
-        {
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-
-
-            public void run()
-            {
-              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Out of memory calculating conservation!!"
-                  +
-                  "\nSee help files for increasing Java Virtual Machine memory."
-                  , "Out of memory",
-                  javax.swing.JOptionPane.WARNING_MESSAGE);
-            }
-          });
-
-          conservation = null;
-          quality = null;
-
-          System.out.println("Conservation calculation: " + error);
-          System.gc();
-
-        }
-
-        UPDATING_CONSERVATION = false;
-        updatingConservation = false;
-
-        if(ap!=null)
-        {
-        ap.paintAlignment(true);
-        }
-
-      }
-    }
-
-
-    ConservationThread conservationThread;
-
-    ConsensusThread consensusThread;
-
-    boolean consUpdateNeeded = false;
-
-    static boolean UPDATING_CONSENSUS = false;
-
-    static boolean UPDATING_CONSERVATION = false;
-
-    boolean updatingConsensus = false;
-
-    boolean updatingConservation = false;
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConservation(final AlignmentPanel ap)
-    {
-      if (alignment.isNucleotide() || conservation==null)
-    {
-        return;
-    }
-
-      conservationThread = new ConservationThread(ap);
-      conservationThread.start();
+      Cache.log.debug("Setting viewport's view id : " + viewId);
     }
+    setAlignment(al);
+    init();
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConsensus(final AlignmentPanel ap)
+  /**
+   * Create a new AlignViewport with hidden regions
+   * 
+   * @param al
+   *          AlignmentI
+   * @param hiddenColumns
+   *          ColumnSelection
+   */
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+  {
+    setAlignment(al);
+    if (hiddenColumns != null)
     {
-      consensusThread = new ConsensusThread(ap);
-      consensusThread.start();
+      colSel = hiddenColumns;
     }
+    init();
+  }
 
-  class ConsensusThread
-      extends Thread
-    {
-      AlignmentPanel ap;
-      public ConsensusThread(AlignmentPanel ap)
-      {
-        this.ap = ap;
-      }
-      public void run()
-      {
-        updatingConsensus = true;
-        while (UPDATING_CONSENSUS)
-        {
-          try
-          {
-            if (ap != null)
-            {
-            ap.paintAlignment(true);
-            }
-
-            Thread.sleep(200);
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
-          }
-        }
-
-
-        UPDATING_CONSENSUS = true;
-
-        try
-        {
-          int aWidth = alignment.getWidth();
-          if(aWidth<0)
-        {
-            return;
-        }
-
-          consensus.annotations = null;
-          consensus.annotations = new Annotation[aWidth];
-
-
-          hconsensus = new Hashtable[aWidth];
-          AAFrequency.calculate(alignment.getSequencesArray(),
-                                0,
-                                alignment.getWidth(),
-                                hconsensus);
-
-          for (int i = 0; i < aWidth; i++)
-          {
-            float value = 0;
-            if (ignoreGapsInConsensusCalculation)
-          {
-              value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
-                  floatValue();
-          }
-            else
-          {
-              value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
-                  floatValue();
-          }
-
-            String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-            String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
-
-            if (maxRes.length() > 1)
-            {
-              mouseOver = "[" + maxRes + "] ";
-              maxRes = "+";
-            }
-
-            mouseOver += ( (int) value + "%");
-          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
-              value);
-          }
-
-
-          if (globalColourScheme != null)
-        {
-            globalColourScheme.setConsensus(hconsensus);
-        }
-
-        }
-        catch (OutOfMemoryError error)
-        {
-          alignment.deleteAnnotation(consensus);
-
-          consensus = null;
-          hconsensus = null;
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            public void run()
-            {
-              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Out of memory calculating consensus!!"
-                  +
-                  "\nSee help files for increasing Java Virtual Machine memory."
-                  , "Out of memory",
-                  javax.swing.JOptionPane.WARNING_MESSAGE);
-            }
-          });
-
-          System.out.println("Consensus calculation: " + error);
-          System.gc();
-        }
-        UPDATING_CONSENSUS = false;
-        updatingConsensus = false;
+  /**
+   * New viewport with hidden columns and an existing sequence set id
+   * 
+   * @param al
+   * @param hiddenColumns
+   * @param seqsetid
+   *          (may be null)
+   */
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+          String seqsetid)
+  {
+    this(al, hiddenColumns, seqsetid, null);
+  }
 
-        if (ap != null)
-        {
-        ap.paintAlignment(true);
-        }
-      }
-    }
-    /**
-     * get the consensus sequence as displayed under the PID consensus annotation row.
-     * @return consensus sequence as a new sequence object
-     */
-  public SequenceI getConsensusSeq()
+  /**
+   * New viewport with hidden columns and an existing sequence set id and viewid
+   * 
+   * @param al
+   * @param hiddenColumns
+   * @param seqsetid
+   *          (may be null)
+   * @param viewid
+   *          (may be null)
+   */
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+          String seqsetid, String viewid)
   {
-      if (consensus==null)
+    sequenceSetID = seqsetid;
+    viewId = viewid;
+    // TODO remove these once 2.4.VAMSAS release finished
+    if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
     {
-        updateConsensus(null);
+      Cache.log.debug("Setting viewport's sequence set id : "
+              + sequenceSetID);
     }
-      if (consensus==null)
+    if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
     {
-        return null;
+      Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-      StringBuffer seqs=new StringBuffer();
-    for (int i = 0; i < consensus.annotations.length; i++)
+    setAlignment(al);
+    if (hiddenColumns != null)
     {
-      if (consensus.annotations[i] != null)
-      {
-          if (consensus.annotations[i].description.charAt(0) == '[')
-        {
-            seqs.append(consensus.annotations[i].description.charAt(1));
-        }
-          else
-        {
-            seqs.append(consensus.annotations[i].displayCharacter);
-        }
-      }
+      colSel = hiddenColumns;
     }
+    init();
+  }
 
-      SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus " +
-                      ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
-                       ""));
-      return sq;
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceGroup getSelectionGroup()
-    {
-        return selectionGroup;
-    }
+  /**
+   * Apply any settings saved in user preferences
+   */
+  private void applyViewProperties()
+  {
+    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
+    viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
+    setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+    setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+    setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
+    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+    setPadGaps(Cache.getDefault("PAD_GAPS", true));
+    setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+    setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+    viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+    viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+    viewStyle.setShowUnconserved(Cache
+            .getDefault("SHOW_UNCONSERVED", false));
+    sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+    followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+    sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+            Preferences.SORT_ANNOTATIONS,
+            SequenceAnnotationOrder.NONE.name()));
+    showAutocalculatedAbove = Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE, false);
+    viewStyle.setScaleProteinAsCdna(Cache.getDefault(
+            Preferences.SCALE_PROTEIN_TO_CDNA, true));
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void setSelectionGroup(SequenceGroup sg)
-    {
-        selectionGroup = sg;
-    }
+  void init()
+  {
+    ranges = new ViewportRanges(this.alignment);
+    applyViewProperties();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getConservationSelected()
-    {
-        return conservationColourSelected;
-    }
+    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+    String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setConservationSelected(boolean b)
-    {
-        conservationColourSelected = b;
-    }
+    int style = 0;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getAbovePIDThreshold()
+    if (fontStyle.equals("bold"))
     {
-        return abovePIDThreshold;
+      style = 1;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setAbovePIDThreshold(boolean b)
+    else if (fontStyle.equals("italic"))
     {
-        abovePIDThreshold = b;
+      style = 2;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
-    {
-        return startRes;
-    }
+    setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
-    {
-        return endRes;
-    }
+    alignment
+            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartSeq()
+    // We must set conservation and consensus before setting colour,
+    // as Blosum and Clustal require this to be done
+    if (hconsensus == null && !isDataset)
     {
-        return startSeq;
+      if (!alignment.isNucleotide())
+      {
+        showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+        showQuality = Cache.getDefault("SHOW_QUALITY", true);
+        showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+                false);
+      }
+      showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
+              true);
+      showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+      normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+              false);
+      showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
+      showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     */
-    public void setGlobalColourScheme(ColourSchemeI cs)
+    initAutoAnnotation();
+    String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+            : Preferences.DEFAULT_COLOUR_PROT;
+    String schemeName = Cache.getProperty(colourProperty);
+    if (schemeName == null)
     {
-        globalColourScheme = cs;
+      // only DEFAULT_COLOUR available in Jalview before 2.9
+      schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+              ResidueColourScheme.NONE);
     }
+    ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+            alignment, schemeName);
+    residueShading = new ResidueShader(colourScheme);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColourSchemeI getGlobalColourScheme()
+    if (colourScheme instanceof UserColourScheme)
     {
-        return globalColourScheme;
+      residueShading = new ResidueShader(
+              UserDefinedColours.loadDefaultColours());
+      residueShading.setThreshold(0, isIgnoreGapsConsensus());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setStartRes(int res)
+    if (residueShading != null)
     {
-        this.startRes = res;
+      residueShading.setConsensus(hconsensus);
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setStartSeq(int seq)
+  /**
+   * 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)
     {
-        this.startSeq = seq;
+      updateConsensus(null);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setEndRes(int res)
+    if (consensus == null)
     {
-        if (res > (alignment.getWidth() - 1))
-        {
-            // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-            res = alignment.getWidth() - 1;
-        }
-
-        if (res < 0)
-        {
-            res = 0;
-        }
-
-        this.endRes = res;
+      return null;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setEndSeq(int seq)
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
     {
-        if (seq > alignment.getHeight())
+      if (consensus.annotations[i] != null)
+      {
+        if (consensus.annotations[i].description.charAt(0) == '[')
         {
-            seq = alignment.getHeight();
+          seqs.append(consensus.annotations[i].description.charAt(1));
         }
-
-        if (seq < 0)
+        else
         {
-            seq = 0;
+          seqs.append(consensus.annotations[i].displayCharacter);
         }
-
-        this.endSeq = seq;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndSeq()
-    {
-        return endSeq;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param f DOCUMENT ME!
-     */
-    public void setFont(Font f)
-    {
-        font = f;
-
-        Container c = new Container();
-
-        java.awt.FontMetrics fm = c.getFontMetrics(font);
-        setCharHeight(fm.getHeight());
-        setCharWidth(fm.charWidth('M'));
-        validCharWidth = true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Font getFont()
-    {
-        return font;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setCharWidth(int w)
-    {
-        this.charWidth = w;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharWidth()
-    {
-        return charWidth;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param h DOCUMENT ME!
-     */
-    public void setCharHeight(int h)
-    {
-        this.charHeight = h;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharHeight()
-    {
-        return charHeight;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setWrappedWidth(int w)
-    {
-        this.wrappedWidth = w;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWrappedWidth()
-    {
-        return wrappedWidth;
+      }
     }
 
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentI getAlignment()
-    {
-        return alignment;
-    }
+  boolean validCharWidth;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param align DOCUMENT ME!
-     */
-    public void setAlignment(AlignmentI align)
-    {
-        this.alignment = align;
-    }
+  /**
+   * update view settings with the given font. You may need to call
+   * alignPanel.fontChanged to update the layout geometry
+   * 
+   * @param setGrid
+   *          when true, charWidth/height is set according to font mentrics
+   */
+  public void setFont(Font f, boolean setGrid)
+  {
+    font = f;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setWrapAlignment(boolean state)
-    {
-        wrapAlignment = state;
-    }
+    Container c = new Container();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowText(boolean state)
+    java.awt.FontMetrics fm = c.getFontMetrics(font);
+    int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
+            .getCharHeight();
+    if (setGrid)
     {
-        showText = state;
+      setCharHeight(fm.getHeight());
+      setCharWidth(ww);
     }
+    viewStyle.setFontName(font.getName());
+    viewStyle.setFontStyle(font.getStyle());
+    viewStyle.setFontSize(font.getSize());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setRenderGaps(boolean state)
-    {
-        renderGaps = state;
-    }
+    validCharWidth = true;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
-    {
-        return showColourText;
-    }
+  @Override
+  public void setViewStyle(ViewStyleI settingsForView)
+  {
+    super.setViewStyle(settingsForView);
+    setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
+            viewStyle.getFontSize()), false);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
-    {
-        showColourText = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Font getFont()
+  {
+    return font;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowBoxes(boolean state)
-    {
-        showBoxes = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param align
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void setAlignment(AlignmentI align)
+  {
+    replaceMappings(align);
+    super.setAlignment(align);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getWrapAlignment()
-    {
-        return wrapAlignment;
-    }
+  /**
+   * Replace any codon mappings for this viewport with those for the given
+   * viewport
+   * 
+   * @param align
+   */
+  public void replaceMappings(AlignmentI align)
+  {
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+    /*
+     * Deregister current mappings (if any)
      */
-    public boolean getShowText()
-    {
-        return showText;
-    }
+    deregisterMappings();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+    /*
+     * Register new mappings (if any)
      */
-    public boolean getShowBoxes()
+    if (align != null)
     {
-        return showBoxes;
+      StructureSelectionManager ssm = StructureSelectionManager
+              .getStructureSelectionManager(Desktop.instance);
+      ssm.registerMappings(align.getCodonFrames());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+    /*
+     * replace mappings on our alignment
      */
-    public char getGapCharacter()
+    if (alignment != null && align != null)
     {
-        return getAlignment().getGapCharacter();
+      alignment.setCodonFrames(align.getCodonFrames());
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gap DOCUMENT ME!
-     */
-    public void setGapCharacter(char gap)
+  protected void deregisterMappings()
+  {
+    AlignmentI al = getAlignment();
+    if (al != null)
     {
-        if (getAlignment() != null)
+      List<AlignedCodonFrame> mappings = al.getCodonFrames();
+      if (mappings != null)
+      {
+        StructureSelectionManager ssm = StructureSelectionManager
+                .getStructureSelectionManager(Desktop.instance);
+        for (AlignedCodonFrame acf : mappings)
         {
-            getAlignment().setGapCharacter(gap);
+          if (noReferencesTo(acf))
+          {
+            ssm.deregisterMapping(acf);
+          }
         }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param thresh DOCUMENT ME!
-     */
-    public void setThreshold(int thresh)
-    {
-        threshold = thresh;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getThreshold()
-    {
-        return threshold;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param inc DOCUMENT ME!
-     */
-    public void setIncrement(int inc)
-    {
-        increment = inc;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getIncrement()
-    {
-        return increment;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColumnSelection getColumnSelection()
-    {
-        return colSel;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tree DOCUMENT ME!
-     */
-    public void setCurrentTree(NJTree tree)
-    {
-        currentTree = tree;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public NJTree getCurrentTree()
-    {
-        return currentTree;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setColourAppliesToAllGroups(boolean b)
-    {
-        colourAppliesToAllGroups = b;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourAppliesToAllGroups()
-    {
-        return colourAppliesToAllGroups;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowJVSuffix()
-    {
-        return showJVSuffix;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowJVSuffix(boolean b)
-    {
-        showJVSuffix = b;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowAnnotation()
-    {
-        return showAnnotation;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowAnnotation(boolean b)
-    {
-        showAnnotation = b;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleAboveWrapped()
-    {
-        return scaleAboveWrapped;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleLeftWrapped()
-    {
-        return scaleLeftWrapped;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleRightWrapped()
-    {
-        return scaleRightWrapped;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleAboveWrapped(boolean b)
-    {
-        scaleAboveWrapped = b;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleLeftWrapped(boolean b)
-    {
-        scaleLeftWrapped = b;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleRightWrapped(boolean b)
-    {
-        scaleRightWrapped = b;
-    }
-
-    /**
-     * Property change listener for changes in alignment
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void addPropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
-    {
-        changeSupport.addPropertyChangeListener(listener);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void removePropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
-    {
-        changeSupport.removePropertyChangeListener(listener);
-    }
-
-    /**
-     * Property change listener for changes in alignment
-     *
-     * @param prop DOCUMENT ME!
-     * @param oldvalue DOCUMENT ME!
-     * @param newvalue DOCUMENT ME!
-     */
-    public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
-    {
-        changeSupport.firePropertyChange(prop, oldvalue, newvalue);
-    }
-
-    public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
-    {
-      ignoreGapsInConsensusCalculation = b;
-      updateConsensus(ap);
-      if(globalColourScheme!=null)
-      {
-      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-                                      ignoreGapsInConsensusCalculation);
       }
     }
+  }
 
-    public boolean getIgnoreGapsConsensus()
-    {
-     return ignoreGapsInConsensusCalculation;
-    }
-
-    public void setDataset(boolean b)
-    {
-      isDataset = b;
-    }
-
-    public boolean isDataset()
-    {
-      return isDataset;
-    }
-
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  public char getGapCharacter()
+  {
+    return getAlignment().getGapCharacter();
+  }
 
-    public void hideSelectedColumns()
-    {
-      if (colSel.size() < 1)
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param gap
+   *          DOCUMENT ME!
+   */
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
     {
-        return;
+      getAlignment().setGapCharacter(gap);
     }
+  }
 
-      colSel.hideSelectedColumns();
-      setSelectionGroup(null);
-
-      hasHiddenColumns = true;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param tree
+   *          DOCUMENT ME!
+   */
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
+  }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public NJTree getCurrentTree()
+  {
+    return currentTree;
+  }
 
-    public void hideColumns(int start, int end)
-    {
-      if(start==end)
+  /**
+   * returns the visible column regions of the alignment
+   * 
+   * @param selectedRegionOnly
+   *          true to just return the contigs intersecting with the selected
+   *          area
+   * @return
+   */
+  public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+  {
+    int[] viscontigs = null;
+    int start = 0, end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
     {
-        colSel.hideColumns(start);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
     }
-      else
+    else
     {
-        colSel.hideColumns(start, end);
-    }
-
-      hasHiddenColumns = true;
+      end = alignment.getWidth();
     }
+    viscontigs = colSel.getVisibleContigs(start, end);
+    return viscontigs;
+  }
 
-    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
-    {
-      int sSize = sg.getSize();
-      if(sSize < 2)
+  /**
+   * get hash of undo and redo list for the alignment
+   * 
+   * @return long[] { historyList.hashCode, redoList.hashCode };
+   */
+  public long[] getUndoRedoHash()
+  {
+    // TODO: JAL-1126
+    if (historyList == null || redoList == null)
     {
-        return;
+      return new long[] { -1, -1 };
     }
+    return new long[] { historyList.hashCode(), this.redoList.hashCode() };
+  }
 
-      if(hiddenRepSequences==null)
+  /**
+   * test if a particular set of hashcodes are different to the hashcodes for
+   * the undo and redo list.
+   * 
+   * @param undoredo
+   *          the stored set of hashcodes as returned by getUndoRedoHash
+   * @return true if the hashcodes differ (ie the alignment has been edited) or
+   *         the stored hashcode array differs in size
+   */
+  public boolean isUndoRedoHashModified(long[] undoredo)
+  {
+    if (undoredo == null)
     {
-        hiddenRepSequences = new Hashtable();
+      return true;
     }
-
-       hiddenRepSequences.put(repSequence, sg);
-
-      //Hide all sequences except the repSequence
-      SequenceI [] seqs = new SequenceI[sSize-1];
-      int index = 0;
-      for(int i=0; i<sSize; i++)
+    long[] cstate = getUndoRedoHash();
+    if (cstate.length != undoredo.length)
     {
-        if(sg.getSequenceAt(i)!=repSequence)
-        {
-          if(index==sSize-1)
-        {
-            return;
-        }
-
-          seqs[index++] = sg.getSequenceAt(i);
-        }
-    }
-
-      hideSequence(seqs);
-
+      return true;
     }
 
-    public void hideAllSelectedSeqs()
-    {
-    if (selectionGroup == null || selectionGroup.getSize()<1)
+    for (int i = 0; i < cstate.length; i++)
     {
-        return;
+      if (cstate[i] != undoredo[i])
+      {
+        return true;
+      }
     }
+    return false;
+  }
 
-      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+  public boolean followSelection = true;
 
-      hideSequence(seqs);
+  /**
+   * @return true if view selection should always follow the selections
+   *         broadcast by other selection sources
+   */
+  public boolean getFollowSelection()
+  {
+    return followSelection;
+  }
 
-      setSelectionGroup(null);
-    }
+  /**
+   * Send the current selection to be broadcast to any selection listeners.
+   */
+  @Override
+  public void sendSelection()
+  {
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance).sendSelection(
+                    new SequenceGroup(getSelectionGroup()),
+                    new ColumnSelection(getColumnSelection()), this);
+  }
 
-    public void hideSequence(SequenceI [] seq)
+  /**
+   * return the alignPanel containing the given viewport. Use this to get the
+   * components currently handling the given viewport.
+   * 
+   * @param av
+   * @return null or an alignPanel guaranteed to have non-null alignFrame
+   *         reference
+   */
+  public AlignmentPanel getAlignPanel()
+  {
+    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+            .getSequenceSetId());
+    for (int p = 0; aps != null && p < aps.length; p++)
     {
-      if(seq!=null)
+      if (aps[p].av == this)
       {
-        for (int i = 0; i < seq.length; i++)
-        {
-          alignment.getHiddenSequences().hideSequence(seq[i]);
-        }
-        hasHiddenRows = true;
-        firePropertyChange("alignment", null, alignment.getSequences());
+        return aps[p];
       }
     }
+    return null;
+  }
+
+  public boolean getSortByTree()
+  {
+    return sortByTree;
+  }
+
+  public void setSortByTree(boolean sort)
+  {
+    sortByTree = sort;
+  }
 
-    public void showSequence(int index)
+  /**
+   * Returns the (Desktop) instance of the StructureSelectionManager
+   */
+  @Override
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+  }
+
+  /**
+   * 
+   * @param pdbEntries
+   * @return an array of SequenceI arrays, one for each PDBEntry, listing which
+   *         sequences in the alignment hold a reference to it
+   */
+  public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+  {
+    List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+    for (PDBEntry pdb : pdbEntries)
     {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index
-          , hiddenRepSequences);
-      if(tmp.size()>0)
+      List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
+      for (SequenceI sq : alignment.getSequences())
       {
-        if(selectionGroup==null)
+        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
+                .getAllPDBEntries();
+        if (pdbRefEntries == null)
         {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
+          continue;
         }
-
-        for (int t = 0; t < tmp.size(); t++)
+        for (PDBEntry pdbRefEntry : pdbRefEntries)
         {
-          selectionGroup.addSequence(
-              (SequenceI) tmp.elementAt(t), false
-              );
+          if (pdbRefEntry.getId().equals(pdb.getId()))
+          {
+            if (pdbRefEntry.getChainCode() != null
+                    && pdb.getChainCode() != null)
+            {
+              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+                      pdb.getChainCode())
+                      && !choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
+            }
+            else
+            {
+              if (!choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
+            }
+
+          }
         }
-        firePropertyChange("alignment", null, alignment.getSequences());
       }
+      seqvectors
+              .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
+    }
+    return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+  }
+
+  @Override
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
+  /**
+   * 
+   * @return true if alignment characters should be displayed
+   */
+  @Override
+  public boolean isValidCharWidth()
+  {
+    return validCharWidth;
+  }
+
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+
+  public AutoCalcSetting getCalcIdSettingsFor(String calcId)
+  {
+    return calcIdParams.get(calcId);
+  }
 
-      if(alignment.getHiddenSequences().getSize()<1)
+  public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+          boolean needsUpdate)
+  {
+    calcIdParams.put(calcId, settings);
+    // TODO: create a restart list to trigger any calculations that need to be
+    // restarted after load
+    // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+    if (needsUpdate)
     {
-        hasHiddenRows = false;
+      Cache.log.debug("trigger update for " + calcId);
     }
   }
 
-    public void showColumn(int col)
+  /**
+   * Method called when another alignment's edit (or possibly other) command is
+   * broadcast to here.
+   *
+   * To allow for sequence mappings (e.g. protein to cDNA), we have to first
+   * 'unwind' the command on the source sequences (in simulation, not in fact),
+   * and then for each edit in turn:
+   * <ul>
+   * <li>compute the equivalent edit on the mapped sequences</li>
+   * <li>apply the mapped edit</li>
+   * <li>'apply' the source edit to the working copy of the source sequences</li>
+   * </ul>
+   * 
+   * @param command
+   * @param undo
+   * @param ssm
+   */
+  @Override
+  public void mirrorCommand(CommandI command, boolean undo,
+          StructureSelectionManager ssm, VamsasSource source)
+  {
+    /*
+     * Do nothing unless we are a 'complement' of the source. May replace this
+     * with direct calls not via SSM.
+     */
+    if (source instanceof AlignViewportI
+            && ((AlignViewportI) source).getCodingComplement() == this)
     {
-      colSel.revealHiddenColumns(col);
-      if(colSel.getHiddenColumns()==null)
+      // ok to continue;
+    }
+    else
     {
-        hasHiddenColumns = false;
+      return;
     }
-  }
 
-    public void showAllHiddenColumns()
+    CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+            getGapCharacter());
+    if (mappedCommand != null)
     {
-      colSel.revealAllHiddenColumns();
-      hasHiddenColumns = false;
+      AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
+      mappedCommand.doCommand(views);
+      getAlignPanel().alignmentChanged();
     }
+  }
+
+  /**
+   * Add the sequences from the given alignment to this viewport. Optionally,
+   * may give the user the option to open a new frame, or split panel, with cDNA
+   * and protein linked.
+   * 
+   * @param toAdd
+   * @param title
+   */
+  public void addAlignment(AlignmentI toAdd, String title)
+  {
+    // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
+
+    // JBPComment: title is a largely redundant parameter at the moment
+    // JBPComment: this really should be an 'insert/pre/append' controller
+    // JBPComment: but the DNA/Protein check makes it a bit more complex
+
+    // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+    // this comment:
+    // TODO: create undo object for this JAL-1101
+
+    /*
+     * Ensure datasets are created for the new alignment as
+     * mappings operate on dataset sequences
+     */
+    toAdd.setDataset(null);
+
+    /*
+     * Check if any added sequence could be the object of a mapping or
+     * cross-reference; if so, make the mapping explicit 
+     */
+    getAlignment().realiseMappings(toAdd.getSequences());
 
-    public void showAllHiddenSeqs()
+    /*
+     * If any cDNA/protein mappings exist or can be made between the alignments, 
+     * offer to open a split frame with linked alignments
+     */
+    if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
     {
-      if(alignment.getHiddenSequences().getSize()>0)
+      if (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
-        if(selectionGroup==null)
+        if (openLinkedAlignment(toAdd, title))
         {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
+          return;
         }
-        Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
-        for(int t=0; t<tmp.size(); t++)
-        {
-          selectionGroup.addSequence(
-              (SequenceI)tmp.elementAt(t), false
-              );
-        }
-        firePropertyChange("alignment", null, alignment.getSequences());
-        hasHiddenRows = false;
-        hiddenRepSequences = null;
       }
     }
 
+    /*
+     * No mappings, or offer declined - add sequences to this alignment
+     */
+    // TODO: JAL-407 regardless of above - identical sequences (based on ID and
+    // provenance) should share the same dataset sequence
 
-
-    public void invertColumnSelection()
+    AlignmentI al = getAlignment();
+    String gap = String.valueOf(al.getGapCharacter());
+    for (int i = 0; i < toAdd.getHeight(); i++)
     {
-      for(int i=0; i<alignment.getWidth(); i++)
+      SequenceI seq = toAdd.getSequenceAt(i);
+      /*
+       * experimental!
+       * - 'align' any mapped sequences as per existing 
+       *    e.g. cdna to genome, domain hit to protein sequence
+       * very experimental! (need a separate menu option for this)
+       * - only add mapped sequences ('select targets from a dataset')
+       */
+      if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
       {
-        if(colSel.contains(i))
-      {
-          colSel.removeElement(i);
-      }
-        else
-        {
-          if (!hasHiddenColumns || colSel.isVisible(i))
-          {
-            colSel.addElement(i);
-          }
-        }
+        al.addSequence(seq);
       }
     }
 
-    public int adjustForHiddenSeqs(int alignmentIndex)
-    {
-      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
-    }
+    setEndSeq(getAlignment().getHeight());
+    firePropertyChange("alignment", null, getAlignment().getSequences());
+  }
 
-    /**
-     * This method returns an array of new SequenceI objects 
-     * derived from the whole alignment or just the current
-     * selection with start and end points adjusted
-     * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
-     * @return String[]
-     */
-    public SequenceI[] getSelectionAsNewSequence()
-    {
-      SequenceI[] sequences;
+  /**
+   * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+   * alignment, either as a standalone alignment or in a split frame. Returns
+   * true if the new alignment was opened, false if not, because the user
+   * declined the offer.
+   * 
+   * @param al
+   * @param title
+   */
+  protected boolean openLinkedAlignment(AlignmentI al, String title)
+  {
+    String[] options = new String[] {
+        MessageManager.getString("action.no"),
+        MessageManager.getString("label.split_window"),
+        MessageManager.getString("label.new_window"), };
+    final String question = JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.open_split_window?"));
+    int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+            MessageManager.getString("label.open_split_window"),
+            JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+            options, options[0]);
 
-      if (selectionGroup == null)
-    {
-        sequences = alignment.getSequencesArray();
-        AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); 
-        for (int i=0; i<sequences.length; i++)
-        {
-          sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation
-        }
-    }
-      else
+    if (response != 1 && response != 2)
     {
-        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+      return false;
     }
+    final boolean openSplitPane = (response == 1);
+    final boolean openInNewWindow = (response == 2);
 
-      return sequences;
-    }
-    /**
-     * get the currently selected sequence objects or all the sequences in the alignment.
-     * @return array of references to sequence objects
+    /*
+     * Identify protein and dna alignments. Make a copy of this one if opening
+     * in a new split pane.
      */
-    public SequenceI[] getSequenceSelection()
-    {
-      SequenceI[] sequences;
-      if (selectionGroup==null)
-      {
-        sequences = alignment.getSequencesArray();
-      }
-      else
-      {
-        sequences = selectionGroup.getSequencesInOrder(alignment);
-      }
-      return sequences;
-    }
-    /**
-     * This method returns the visible alignment as text, as
-     * seen on the GUI, ie if columns are hidden they will not
-     * be returned in the result.
-     * Use this for calculating trees, PCA, redundancy etc on views
-     * which contain hidden columns.
-     * @return String[]
+    AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+            : getAlignment();
+    AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+    final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+    /*
+     * Map sequences. At least one should get mapped as we have already passed
+     * the test for 'mappability'. Any mappings made will be added to the
+     * protein alignment. Note creating dataset sequences on the new alignment
+     * is a pre-requisite for building mappings.
      */
-  public jalview.datamodel.CigarArray getViewAsCigars(boolean
-      selectedRegionOnly)
-    {
-      CigarArray selection=null;
-      SequenceI [] seqs= null;
-      int i, iSize;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
-      {
-        iSize = selectionGroup.getSize();
-        seqs = selectionGroup.getSequencesInOrder(alignment);
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
-      }
-      else
-      {
-        iSize = alignment.getHeight();
-        seqs = alignment.getSequencesArray();
-        end = alignment.getWidth()-1;
-      }
-      SeqCigar[] selseqs = new SeqCigar[iSize];
-      for(i=0; i<iSize; i++)
-      {
-        selseqs[i] = new SeqCigar(seqs[i], start, end);
-      }
-      selection=new CigarArray(selseqs);
-      // now construct the CigarArray operations
-    if (hasHiddenColumns)
-    {
-        Vector regions = colSel.getHiddenColumns();
-        int [] region;
-        int hideStart, hideEnd;
-        int last=start;
-        for (int j = 0; last<end & j < regions.size(); j++)
-        {
-          region = (int[]) regions.elementAt(j);
-          hideStart = region[0];
-          hideEnd = region[1];
-          // edit hidden regions to selection range
-        if (hideStart < last)
-        {
-            if (hideEnd > last)
-            {
-              hideStart = last;
-          }
-          else
-          {
-              continue;
-          }
-        }
+    al.setDataset(null);
+    AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
 
-          if (hideStart>end)
-        {
-            break;
-        }
+    /*
+     * Create the AlignFrame for the added alignment. If it is protein, mappings
+     * are registered with StructureSelectionManager as a side-effect.
+     */
+    AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+    newAlignFrame.setTitle(title);
+    newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+            "label.successfully_loaded_file", new Object[] { title }));
 
-          if (hideEnd>end)
-        {
-            hideEnd=end;
-        }
+    // TODO if we want this (e.g. to enable reload of the alignment from file),
+    // we will need to add parameters to the stack.
+    // if (!protocol.equals(DataSourceType.PASTE))
+    // {
+    // alignFrame.setFileName(file, format);
+    // }
 
-          if (hideStart>hideEnd)
-        {
-            break;
-        }
-          /**
-           * form operations...
-           */
-          if (last<hideStart)
-        {
-            selection.addOperation(CigarArray.M, hideStart-last);
-        }
-          selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
-          last = hideEnd+1;
-        }
-        // Final match if necessary.
-        if (last<end)
-      {
-          selection.addOperation(CigarArray.M, end-last+1);
-      }
-    }
-    else
+    if (openInNewWindow)
     {
-        selection.addOperation(CigarArray.M, end-start+1);
-      }
-      return selection;
+      Desktop.addInternalFrame(newAlignFrame, title,
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
     }
-    /**
-     * return a compact representation of the current alignment selection to
-     * pass to an analysis function
-     * @param selectedOnly boolean true to just return the selected view
-     * @return AlignmentView
-     */
-  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
-  {
-      // JBPNote:
-      // this is here because the AlignmentView constructor modifies the CigarArray
-      // object. Refactoring of Cigar and alignment view representation should
-      // be done to remove redundancy.
-      CigarArray aligview = getViewAsCigars(selectedOnly);
-    if (aligview != null)
+
+    try
     {
-        return new AlignmentView(aligview,
-                               (selectedOnly && selectionGroup != null) ?
-                               selectionGroup.getStartRes() : 0);
-      }
-      return null;
-    }
-    /**
-     * This method returns the visible alignment as text, as
-     * seen on the GUI, ie if columns are hidden they will not
-     * be returned in the result.
-     * Use this for calculating trees, PCA, redundancy etc on views
-     * which contain hidden columns.
-     * @return String[]
-     */
-    public String [] getViewAsString(boolean selectedRegionOnly)
+      newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+              "SHOW_FULLSCREEN", false));
+    } catch (java.beans.PropertyVetoException ex)
     {
-      String [] selection = null;
-      SequenceI [] seqs= null;
-      int i, iSize;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
-      {
-        iSize = selectionGroup.getSize();
-        seqs = selectionGroup.getSequencesInOrder(alignment);
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes()+1;
-      }
-      else
-      {
-        iSize = alignment.getHeight();
-        seqs = alignment.getSequencesArray();
-        end = alignment.getWidth();
-      }
+    }
 
-      selection = new String[iSize];
-    if (hasHiddenColumns)
+    if (openSplitPane)
     {
-        selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+      al.alignAs(thisAlignment);
+      protein = openSplitFrame(newAlignFrame, thisAlignment);
     }
-    else
-    {
-        for(i=0; i<iSize; i++)
-        {
-          selection[i] = seqs[i].getSequenceAsString(start, end);
-        }
 
-      }
-      return selection;
-    }
+    return true;
+  }
 
-  public int [][] getVisibleRegionBoundaries(int min, int max)
+  /**
+   * Helper method to open a new SplitFrame holding linked dna and protein
+   * alignments.
+   * 
+   * @param newAlignFrame
+   *          containing a new alignment to be shown
+   * @param complement
+   *          cdna/protein complement alignment to show in the other split half
+   * @return the protein alignment in the split frame
+   */
+  protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+          AlignmentI complement)
   {
-    Vector regions = new Vector();
-    int start = min;
-    int end = max;
-
-    do
-    {
-      if (hasHiddenColumns)
-      {
-        if (start == 0)
-        {
-          start = colSel.adjustForHiddenColumns(start);
-        }
+    /*
+     * Make a new frame with a copy of the alignment we are adding to. If this
+     * is protein, the mappings to cDNA will be registered with
+     * StructureSelectionManager as a side-effect.
+     */
+    AlignFrame copyMe = new AlignFrame(complement,
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+    copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+
+    AlignmentI al = newAlignFrame.viewport.getAlignment();
+    final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+            : newAlignFrame;
+    final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
+    cdnaFrame.setVisible(true);
+    proteinFrame.setVisible(true);
+    String linkedTitle = MessageManager
+            .getString("label.linked_view_title");
+
+    /*
+     * Open in split pane. DNA sequence above, protein below.
+     */
+    JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+    Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+    return proteinFrame.viewport.getAlignment();
+  }
 
-        end = colSel.getHiddenBoundaryRight(start);
-        if (start == end)
-        {
-          end = max;
-        }
-        if (end > max)
-        {
-          end = max;
-        }
-      }
+  public AnnotationColumnChooser getAnnotationColumnSelectionState()
+  {
+    return annotationColumnSelectionState;
+  }
 
-      regions.addElement(new int[]
-                         {start, end});
+  public void setAnnotationColumnSelectionState(
+          AnnotationColumnChooser currentAnnotationColumnSelectionState)
+  {
+    this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+  }
 
-      if (hasHiddenColumns)
-      {
-        start = colSel.adjustForHiddenColumns(end);
-        start = colSel.getHiddenBoundaryLeft(start) + 1;
-      }
+  @Override
+  public void setIdWidth(int i)
+  {
+    super.setIdWidth(i);
+    AlignmentPanel ap = getAlignPanel();
+    if (ap != null)
+    {
+      // modify GUI elements to reflect geometry change
+      Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
+              .getPreferredSize();
+      idw.width = i;
+      getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
     }
-    while (end < max);
-
-    int[][] startEnd = new int[regions.size()][2];
+  }
 
-    regions.copyInto(startEnd);
+  public Rectangle getExplodedGeometry()
+  {
+    return explodedGeometry;
+  }
 
-    return startEnd;
+  public void setExplodedGeometry(Rectangle explodedPosition)
+  {
+    this.explodedGeometry = explodedPosition;
+  }
 
+  public boolean isGatherViewsHere()
+  {
+    return gatherViewsHere;
   }
 
-    public boolean getShowHiddenMarkers()
-    {
-      return showHiddenMarkers;
-    }
+  public void setGatherViewsHere(boolean gatherViewsHere)
+  {
+    this.gatherViewsHere = gatherViewsHere;
+  }
 
-    public void setShowHiddenMarkers(boolean show)
+  /**
+   * If this viewport has a (Protein/cDNA) complement, then scroll the
+   * complementary alignment to match this one.
+   */
+  public void scrollComplementaryAlignment()
+  {
+    /*
+     * Populate a SearchResults object with the mapped location to scroll to. If
+     * there is no complement, or it is not following highlights, or no mapping
+     * is found, the result will be empty.
+     */
+    SearchResultsI sr = new SearchResults();
+    int verticalOffset = findComplementScrollTarget(sr);
+    if (!sr.isEmpty())
     {
-      showHiddenMarkers = show;
+      // TODO would like next line without cast but needs more refactoring...
+      final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+              .getAlignPanel();
+      complementPanel.setDontScrollComplement(true);
+      complementPanel.scrollToCentre(sr, verticalOffset);
     }
+  }
 
-    public String getSequenceSetId()
-    {
-      if(sequenceSetID==null)
+  /**
+   * Answers true if no alignment holds a reference to the given mapping
+   * 
+   * @param acf
+   * @return
+   */
+  protected boolean noReferencesTo(AlignedCodonFrame acf)
+  {
+    AlignFrame[] frames = Desktop.getAlignFrames();
+    if (frames == null)
     {
-        sequenceSetID =  alignment.hashCode()+"";
-    }
-
-      return sequenceSetID;
+      return true;
     }
-
-    public void alignmentChanged(AlignmentPanel ap)
+    for (AlignFrame af : frames)
     {
-        if (padGaps)
-    {
-          alignment.padGaps();
-    }
-
-        if (hconsensus != null && autoCalculateConsensus)
-        {
-          updateConsensus(ap);
-          updateConservation(ap);
-        }
-
-        //Reset endRes of groups if beyond alignment width
-        int alWidth = alignment.getWidth();
-        Vector groups = alignment.getGroups();
-        if(groups!=null)
+      if (!af.isClosed())
+      {
+        for (AlignmentViewPanel ap : af.getAlignPanels())
         {
-          for(int i=0; i<groups.size(); i++)
+          AlignmentI al = ap.getAlignment();
+          if (al != null && al.getCodonFrames().contains(acf))
           {
-            SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-            if(sg.getEndRes()>alWidth)
-        {
-              sg.setEndRes(alWidth-1);
+            return false;
           }
         }
+      }
     }
+    return true;
+  }
 
-        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
+  /**
+   * Applies the supplied feature settings descriptor to currently known
+   * features. This supports an 'initial configuration' of feature colouring
+   * based on a preset or user favourite. This may then be modified in the usual
+   * way using the Feature Settings dialogue.
+   * 
+   * @param featureSettings
+   */
+  @Override
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    if (featureSettings == null)
     {
-          selectionGroup.setEndRes(alWidth-1);
-    }
-
-        resetAllColourSchemes();
-
-       // alignment.adjustSequenceAnnotations();
+      return;
     }
 
+    FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
+            .getFeatureRenderer();
+    fr.findAllFeatures(true);
+    List<String> renderOrder = fr.getRenderOrder();
+    FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
+    displayed.clear();
+    // TODO this clears displayed.featuresRegistered - do we care?
 
-    void resetAllColourSchemes()
+    /*
+     * set feature colour if specified by feature settings
+     * set visibility of all features
+     */
+    for (String type : renderOrder)
     {
-      ColourSchemeI cs = globalColourScheme;
-      if(cs!=null)
+      FeatureColourI preferredColour = featureSettings
+              .getFeatureColour(type);
+      if (preferredColour != null)
       {
-        if (cs instanceof ClustalxColourScheme)
-        {
-          ( (ClustalxColourScheme) cs).
-              resetClustalX(alignment.getSequences(),
-                            alignment.getWidth());
-        }
-
-        cs.setConsensus(hconsensus);
-        if (cs.conservationApplied())
-        {
-          Alignment al = (Alignment) alignment;
-          Conservation c = new Conservation("All",
-                                            ResidueProperties.propHash, 3,
-                                            al.getSequences(), 0,
-                                            al.getWidth() - 1);
-          c.calculate();
-          c.verdict(false, ConsPercGaps);
-
-          cs.setConservation(c);
-        }
+        fr.setColour(type, preferredColour);
       }
-
-      int s, sSize = alignment.getGroups().size();
-      for(s=0; s<sSize; s++)
+      if (featureSettings.isFeatureDisplayed(type))
       {
-        SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
-        if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
-        {
-          ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(hiddenRepSequences), sg.getWidth());
-        }
-        sg.recalcConservation();
+        displayed.setVisible(type);
       }
     }
 
-
-    public Color getSequenceColour(SequenceI seq)
-    {
-      if(sequenceColours==null || !sequenceColours.containsKey(seq))
-    {
-        return Color.white;
-    }
-      else
-    {
-        return (Color)sequenceColours.get(seq);
-    }
-  }
-
-    public void setSequenceColour(SequenceI seq, Color col)
-    {
-      if(sequenceColours==null)
+    /*
+     * set visibility of feature groups
+     */
+    for (String group : fr.getFeatureGroups())
     {
-        sequenceColours = new Hashtable();
+      fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
     }
 
-      if(col == null)
+    /*
+     * order the features
+     */
+    if (featureSettings.optimiseOrder())
     {
-        sequenceColours.remove(seq);
+      // TODO not supported (yet?)
     }
-      else
+    else
     {
-        sequenceColours.put(seq, col);
-    }
+      fr.orderFeatures(featureSettings);
     }
-    /**
-     * returns the visible column regions of the alignment
-     * @param selectedRegionOnly true to just return the contigs intersecting with the selected area
-     * @return
-     */
-    public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) {
-      int[] viscontigs=null;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
-      {
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes()+1;
-      }
-      else
-      {
-        end = alignment.getWidth();
-      }
-      viscontigs = colSel.getVisibleContigs(start, end);
-      return viscontigs;
-    }
-
+    fr.setTransparency(featureSettings.getTransparency());
+  }
 
 }