From: jprocter <Jim Procter>
Date: Thu, 7 Sep 2006 11:39:36 +0000 (+0000)
Subject: added copy consensus sequence to consensus annotation popup menu
X-Git-Tag: Release_2_1_1~15
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d545553b53ac1bd1e29eb72250cdb29745f7292f;p=jalview.git

added copy consensus sequence to consensus annotation popup menu
---

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 0013bc0..eb832f2 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,1035 +1,1060 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * 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.
- *
- * 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
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class AlignViewport
-{
-  int startRes;
-  int endRes;
-
-  int startSeq;
-  int endSeq;
-
-
-  boolean cursorMode = false;
-
-  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 showConservation = true;
-  boolean showQuality = true;
-  boolean showConsensus = true;
-
-  boolean colourAppliesToAllGroups = true;
-  ColourSchemeI globalColourScheme = null;
-  boolean conservationColourSelected = false;
-  boolean abovePIDThreshold = false;
-
-  SequenceGroup selectionGroup;
-
-  int charHeight;
-  int charWidth;
-  int wrappedWidth;
-
-  Font font = new Font("SansSerif", Font.PLAIN, 10);
-  boolean validCharWidth = true;
-  AlignmentI alignment;
-
-  ColumnSelection colSel = new ColumnSelection();
-
-  int threshold;
-  int increment;
-
-  NJTree currentTree = null;
-
-  boolean scaleAboveWrapped = true;
-  boolean scaleLeftWrapped = true;
-  boolean scaleRightWrapped = true;
-
-  // The following vector holds the features which are
- // currently visible, in the correct order or rendering
-  Hashtable featuresDisplayed;
-
-  boolean hasHiddenColumns = false;
-  boolean hasHiddenRows = false;
-  boolean showHiddenMarkers = true;
-
-
-  public Vector vconsensus;
-  AlignmentAnnotation consensus;
-  AlignmentAnnotation conservation;
-  AlignmentAnnotation quality;
-
-  boolean autocalculateConsensus = true;
-
-  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
-
-  boolean ignoreGapsInConsensusCalculation = false;
-
-  jalview.bin.JalviewLite applet;
-
-  boolean MAC = false;
-
-  public AlignViewport(AlignmentI al, JalviewLite applet)
-  {
-    this.applet = applet;
-    setAlignment(al);
-    this.startRes = 0;
-    this.endRes = al.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = al.getHeight() - 1;
-    setFont(font);
-
-    if(System.getProperty("os.name").startsWith("Mac"))
-      MAC = true;
-
-    if (applet != null)
-    {
-      String param = applet.getParameter("showFullId");
-      if (param != null)
-      {
-        showJVSuffix = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showAnnotation");
-      if (param != null)
-      {
-        showAnnotation = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showConservation");
-      if (param != null)
-      {
-        showConservation = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showQuality");
-      if (param != null)
-      {
-        showQuality = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showConsensus");
-      if (param != null)
-      {
-        showConsensus = Boolean.valueOf(param).booleanValue();
-      }
-    }
-    // We must set conservation and consensus before setting colour,
-    // as Blosum and Clustal require this to be done
-    updateConservation();
-    updateConsensus();
-
-
-    if (applet != null)
-    {
-      String colour = applet.getParameter("defaultColour");
-
-      if(colour == null)
-      {
-        colour = applet.getParameter("userDefinedColour");
-        if(colour !=null)
-          colour = "User Defined";
-      }
-
-      if(colour != null)
-      {
-        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
-        if (globalColourScheme != null)
-        {
-          globalColourScheme.setConsensus(vconsensus);
-        }
-      }
-
-      if(applet.getParameter("userDefinedColour")!=null)
-      {
-        ((UserColourScheme)globalColourScheme).parseAppletParameter(
-            applet.getParameter("userDefinedColour"));
-      }
-
-
-    }
-  }
-
-  public void showSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
-
-  public void updateConservation()
-  {
-    if(alignment.isNucleotide())
-          return;
-
-    Conservation cons = new jalview.analysis.Conservation("All",
-        jalview.schemes.ResidueProperties.propHash, 3,
-        alignment.getSequences(), 0,
-        alignment.getWidth() - 1);
-    cons.calculate();
-    cons.verdict(false, ConsPercGaps);
-    cons.findQuality();
-    int alWidth = alignment.getWidth();
-    Annotation[] annotations = new Annotation[alWidth];
-    Annotation[] qannotations = new Annotation[alWidth];
-    String sequence = cons.getConsSequence().getSequence();
-    float minR, minG, minB, maxR, maxG, 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 = cons.qualityRange[0].floatValue();
-    float qmax = cons.qualityRange[1].floatValue();
-
-    for (int i = 0; i < alWidth; i++)
-    {
-      float value = 0;
-      try
-      {
-        value = Integer.parseInt(sequence.charAt(i) + "");
-      }
-      catch (Exception ex)
-      {
-        if (sequence.charAt(i) == '*')
-        {
-          value = 11;
-        }
-        if (sequence.charAt(i) == '+')
-        {
-          value = 10;
-        }
-      }
-      float vprop = value - min;
-      vprop /= max;
-
-      annotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      "", ' ', value,
-                                      new Color(minR + maxR * vprop,
-                                                minG + maxG * vprop,
-                                                minB + maxB * vprop));
-      // Quality calc
-      value = ( (Double) cons.quality.elementAt(i)).floatValue();
-      vprop = value - qmin;
-      vprop /= qmax;
-      qannotations[i] = new Annotation(" ",
-                                       String.valueOf(value), ' ', value,
-                                       new
-                                       Color(minR + maxR * vprop,
-                                             minG + maxG * vprop,
-                                             minB + maxB * vprop));
-    }
-
-    if (conservation == null)
-    {
-      conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than " +
-                                             ConsPercGaps + "% gaps",
-                                             annotations,
-                                             0f, // cons.qualityRange[0].floatValue(),
-                                             11f, // cons.qualityRange[1].floatValue()
-                                             AlignmentAnnotation.BAR_GRAPH);
-      if (showConservation)
-      {
-        alignment.addAnnotation(conservation);
-      }
-      quality = new AlignmentAnnotation("Quality",
-                                        "Alignment Quality based on Blosum62 scores",
-                                        qannotations,
-                                        cons.qualityRange[0].floatValue(),
-                                        cons.qualityRange[1].floatValue(),
-                                        AlignmentAnnotation.BAR_GRAPH);
-      if (showQuality)
-      {
-        alignment.addAnnotation(quality);
-      }
-    }
-    else
-    {
-      conservation.annotations = annotations;
-      quality.annotations = qannotations;
-      quality.graphMax = cons.qualityRange[1].floatValue();
-    }
-
-  }
-
-  public void updateConsensus()
-  {
-    Annotation[] annotations = new Annotation[alignment.getWidth()];
-
-    // this routine prevents vconsensus becoming a new object each time
-    // consenus is calculated. Important for speed of Blosum62
-    // and PID colouring of alignment
-    if (vconsensus == null)
-    {
-      vconsensus = alignment.getAAFrequency();
-    }
-    else
-    {
-      Vector temp = alignment.getAAFrequency();
-      vconsensus.removeAllElements();
-      Enumeration e = temp.elements();
-      while (e.hasMoreElements())
-      {
-        vconsensus.addElement(e.nextElement());
-      }
-    }
-    Hashtable hash = null;
-    for (int i = 0; i < alignment.getWidth(); i++)
-    {
-      hash = (Hashtable) vconsensus.elementAt(i);
-      float value = 0;
-      if(ignoreGapsInConsensusCalculation)
-        value = ((Float)hash.get("pid_nogaps")).floatValue();
-      else
-        value = ((Float)hash.get("pid_gaps")).floatValue();
-
-      String maxRes = hash.get("maxResidue").toString();
-      String mouseOver = hash.get("maxResidue") + " ";
-      if (maxRes.length() > 1)
-      {
-        mouseOver = "[" + maxRes + "] ";
-        maxRes = "+";
-      }
-
-
-      mouseOver += (int) value + "%";
-      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-
-    }
-
-    if (consensus == null)
-    {
-      consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      if (showConsensus)
-      {
-        alignment.addAnnotation(consensus);
-      }
-    }
-    else
-    {
-      consensus.annotations = annotations;
-    }
-
-    if(globalColourScheme!=null)
-          globalColourScheme.setConsensus(vconsensus);
-
-  }
-
-  public SequenceGroup getSelectionGroup()
-  {
-    return selectionGroup;
-  }
-
-  public void setSelectionGroup(SequenceGroup sg)
-  {
-    selectionGroup = sg;
-  }
-
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
-
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
-
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
-
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
-
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
-
-  public void setGlobalColourScheme(ColourSchemeI cs)
-  {
-    globalColourScheme = cs;
-  }
-
-  public ColourSchemeI getGlobalColourScheme()
-  {
-    return globalColourScheme;
-  }
-
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
-
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
-
-  public void setEndRes(int res)
-  {
-    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;
-  }
-
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
-    {
-      seq = alignment.getHeight();
-    }
-    if (seq < 0)
-    {
-      seq = 0;
-    }
-    this.endSeq = seq;
-  }
-
-  public int getEndSeq()
-  {
-    return endSeq;
-  }
-
-  java.awt.Frame nullFrame;
-  public void setFont(Font f)
-  {
-    font = f;
-    if(nullFrame == null)
-    {
-      nullFrame = new java.awt.Frame();
-      nullFrame.addNotify();
-    }
-
-    java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
-    setCharHeight(fm.getHeight());
-    charWidth = fm.charWidth('M');
-  }
-
-  public Font getFont()
-  {
-    return font;
-  }
-
-  public int getCharWidth()
-  {
-    return charWidth;
-  }
-
-  public void setCharHeight(int h)
-  {
-    this.charHeight = h;
-  }
-
-  public int getCharHeight()
-  {
-    return charHeight;
-  }
-
-  public void setWrappedWidth(int w)
-  {
-    this.wrappedWidth = w;
-  }
-
-  public int getwrappedWidth()
-  {
-    return wrappedWidth;
-  }
-
-  public AlignmentI getAlignment()
-  {
-    return alignment;
-  }
-
-  public void setAlignment(AlignmentI align)
-  {
-    this.alignment = align;
-  }
-
-  public void setWrapAlignment(boolean state)
-  {
-    wrapAlignment = state;
-  }
-
-  public void setShowText(boolean state)
-  {
-    showText = state;
-  }
-
-  public void setRenderGaps(boolean state)
-  {
-    renderGaps = state;
-  }
-
-  public boolean getColourText()
-  {
-    return showColourText;
-  }
-
-  public void setColourText(boolean state)
-  {
-    showColourText = state;
-  }
-
-  public void setShowBoxes(boolean state)
-  {
-    showBoxes = state;
-  }
-
-  public boolean getWrapAlignment()
-  {
-    return wrapAlignment;
-  }
-
-  public boolean getShowText()
-  {
-    return showText;
-  }
-
-  public boolean getShowBoxes()
-  {
-    return showBoxes;
-  }
-
-  public char getGapCharacter()
-  {
-    return getAlignment().getGapCharacter();
-  }
-
-  public void setGapCharacter(char gap)
-  {
-    if (getAlignment() != null)
-    {
-      getAlignment().setGapCharacter(gap);
-    }
-  }
-
-  public void setThreshold(int thresh)
-  {
-    threshold = thresh;
-  }
-
-  public int getThreshold()
-  {
-    return threshold;
-  }
-
-  public void setIncrement(int inc)
-  {
-    increment = inc;
-  }
-
-  public int getIncrement()
-  {
-    return increment;
-  }
-
-  public void setHiddenColumns(ColumnSelection colsel)
-  {
-    this.colSel = colsel;
-    if(colSel.getHiddenColumns()!=null)
-      hasHiddenColumns = true;
-  }
-
-  public ColumnSelection getColumnSelection()
-  {
-    return colSel;
-  }
-
-  public void resetSeqLimits(int height)
-  {
-    setEndSeq(height / getCharHeight());
-  }
-
-  public void setCurrentTree(NJTree tree)
-  {
-    currentTree = tree;
-  }
-
-  public NJTree getCurrentTree()
-  {
-    return currentTree;
-  }
-
-  public void setColourAppliesToAllGroups(boolean b)
-  {
-    colourAppliesToAllGroups = b;
-  }
-
-  public boolean getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
-
-  public boolean getShowJVSuffix()
-  {
-    return showJVSuffix;
-  }
-
-  public void setShowJVSuffix(boolean b)
-  {
-    showJVSuffix = b;
-  }
-
-  public boolean getShowAnnotation()
-  {
-    return showAnnotation;
-  }
-
-  public void setShowAnnotation(boolean b)
-  {
-    showAnnotation = b;
-  }
-
-  public boolean getScaleAboveWrapped()
-  {
-    return scaleAboveWrapped;
-  }
-
-  public boolean getScaleLeftWrapped()
-  {
-    return scaleLeftWrapped;
-  }
-
-  public boolean getScaleRightWrapped()
-  {
-    return scaleRightWrapped;
-  }
-
-  public void setScaleAboveWrapped(boolean b)
-  {
-    scaleAboveWrapped = b;
-  }
-
-  public void setScaleLeftWrapped(boolean b)
-  {
-    scaleLeftWrapped = b;
-  }
-
-  public void setScaleRightWrapped(boolean b)
-  {
-    scaleRightWrapped = b;
-  }
-
-  public void setIgnoreGapsConsensus(boolean b)
-  {
-    ignoreGapsInConsensusCalculation = b;
-    updateConsensus();
-    if (globalColourScheme!=null)
-    {
-      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-          ignoreGapsInConsensusCalculation);
-
-    }
-  }
-
-  /**
-   * 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 boolean getIgnoreGapsConsensus()
-  {
-    return ignoreGapsInConsensusCalculation;
-  }
-  public void hideSelectedColumns()
-  {
-    if (colSel.size() < 1)
-      return;
-
-    colSel.hideSelectedColumns();
-    setSelectionGroup(null);
-
-    hasHiddenColumns = true;
-  }
-
-  public void invertColumnSelection()
-  {
-    int column;
-    for (int i = 0; i < alignment.getWidth(); i++)
-    {
-      column = i;
-
-      if (colSel.contains(column))
-        colSel.removeElement(column);
-      else
-        colSel.addElement(column);
-
-    }
-  }
-
-
-  public void hideColumns(int start, int end)
-  {
-    if(start==end)
-      colSel.hideColumns(start);
-    else
-      colSel.hideColumns(start, end);
-
-    hasHiddenColumns = true;
-  }
-
-  public void hideSequence(SequenceI seq)
-  {
-    if(seq!=null)
-    {
-      alignment.getHiddenSequences().hideSequence(seq);
-      hasHiddenRows = true;
-      firePropertyChange("alignment", null, alignment.getSequences());
-    }
-  }
-
-  public void hideAllSelectedSeqs()
-  {
-    if (selectionGroup == null)
-      return;
-
-    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
-    for (int i = 0; i < seqs.length; i++)
-    {
-      alignment.getHiddenSequences().hideSequence(seqs[i]);
-    }
-    firePropertyChange("alignment", null, alignment.getSequences());
-    hasHiddenRows = true;
-    setSelectionGroup(null);
-  }
-
-  public void showColumn(int col)
-  {
-    colSel.revealHiddenColumns(col);
-    if(colSel.getHiddenColumns()==null)
-      hasHiddenColumns = false;
-  }
-
-  public void showAllHiddenColumns()
-  {
-    colSel.revealAllHiddenColumns();
-    hasHiddenColumns = false;
-  }
-
-  public void showAllHiddenSeqs()
-  {
-    if(alignment.getHiddenSequences().getSize()>0)
-    {
-      if(selectionGroup==null)
-      {
-        selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth()-1);
-      }
-      Vector tmp = alignment.getHiddenSequences().showAll();
-      for(int t=0; t<tmp.size(); t++)
-      {
-        selectionGroup.addSequence(
-            (SequenceI)tmp.elementAt(t), false
-            );
-      }
-      firePropertyChange("alignment", null, alignment.getSequences());
-      hasHiddenRows = false;
-    }
-  }
-
-  public int adjustForHiddenSeqs(int alignmentIndex)
-  {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
-  }
-
-  /**
-   * This method returns the a new SequenceI [] with
-   * the selection sequence and start and end points adjusted
-   * @return String[]
-   */
-  public SequenceI[] getSelectionAsNewSequence()
-  {
-    SequenceI[] sequences;
-
-    if (selectionGroup == null)
-      sequences = alignment.getSequencesArray();
-    else
-      sequences = selectionGroup.getSelectionAsNewSequences(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[]
-   */
-  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(false);
-      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;
-        }
-
-        if (hideStart>end)
-          break;
-
-        if (hideEnd>end)
-          hideEnd=end;
-
-        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);
-    } else {
-      selection.addOperation(CigarArray.M, end-start);
-    }
-    return selection;
-  }
-  /**
-   * 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)
-      return new AlignmentView(aligview);
-    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)
-  {
-    String [] selection = null;
-    SequenceI [] seqs= null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
-    {
-      iSize = selectionGroup.getSize(false);
-      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];
-
-
-    for(i=0; i<iSize; i++)
-    {
-      if (hasHiddenColumns)
-      {
-           StringBuffer visibleSeq = new StringBuffer();
-           Vector regions = colSel.getHiddenColumns();
-
-           int blockStart = start, blockEnd=end;
-           int [] region;
-           int hideStart, hideEnd;
-
-           for (int j = 0; j < regions.size(); j++)
-           {
-             region = (int[]) regions.elementAt(j);
-             hideStart = region[0];
-             hideEnd = region[1];
-
-             if(hideStart < start)
-             {
-               continue;
-             }
-
-             blockStart = Math.min(blockStart, hideEnd+1);
-             blockEnd = Math.min(blockEnd, hideStart);
-
-             if(blockStart>blockEnd)
-             {
-                break;
-             }
-
-
-             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
-             blockStart = hideEnd+1;
-             blockEnd = end;
-           }
-
-           if(end>blockStart)
-             visibleSeq.append(seqs[i].getSequence(blockStart, end));
-
-           selection[i] = visibleSeq.toString();
-      }
-      else
-      {
-        selection[i] = seqs[i].getSequence(start, end);
-      }
-    }
-
-    return selection;
-  }
-
-  public boolean getShowHiddenMarkers()
-  {
-    return showHiddenMarkers;
-  }
-
-  public void setShowHiddenMarkers(boolean show)
-  {
-    showHiddenMarkers = show;
-  }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
+ * 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.
+ *
+ * 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
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class AlignViewport
+{
+  int startRes;
+  int endRes;
+
+  int startSeq;
+  int endSeq;
+
+
+  boolean cursorMode = false;
+
+  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 showConservation = true;
+  boolean showQuality = true;
+  boolean showConsensus = true;
+
+  boolean colourAppliesToAllGroups = true;
+  ColourSchemeI globalColourScheme = null;
+  boolean conservationColourSelected = false;
+  boolean abovePIDThreshold = false;
+
+  SequenceGroup selectionGroup;
+
+  int charHeight;
+  int charWidth;
+  int wrappedWidth;
+
+  Font font = new Font("SansSerif", Font.PLAIN, 10);
+  boolean validCharWidth = true;
+  AlignmentI alignment;
+
+  ColumnSelection colSel = new ColumnSelection();
+
+  int threshold;
+  int increment;
+
+  NJTree currentTree = null;
+
+  boolean scaleAboveWrapped = true;
+  boolean scaleLeftWrapped = true;
+  boolean scaleRightWrapped = true;
+
+  // The following vector holds the features which are
+ // currently visible, in the correct order or rendering
+  Hashtable featuresDisplayed;
+
+  boolean hasHiddenColumns = false;
+  boolean hasHiddenRows = false;
+  boolean showHiddenMarkers = true;
+
+
+  public Vector vconsensus;
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+
+  boolean autocalculateConsensus = true;
+
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+
+  boolean ignoreGapsInConsensusCalculation = false;
+
+  jalview.bin.JalviewLite applet;
+
+  boolean MAC = false;
+
+  public AlignViewport(AlignmentI al, JalviewLite applet)
+  {
+    this.applet = applet;
+    setAlignment(al);
+    this.startRes = 0;
+    this.endRes = al.getWidth() - 1;
+    this.startSeq = 0;
+    this.endSeq = al.getHeight() - 1;
+    setFont(font);
+
+    if(System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
+    if (applet != null)
+    {
+      String param = applet.getParameter("showFullId");
+      if (param != null)
+      {
+        showJVSuffix = Boolean.valueOf(param).booleanValue();
+      }
+
+      param = applet.getParameter("showAnnotation");
+      if (param != null)
+      {
+        showAnnotation = Boolean.valueOf(param).booleanValue();
+      }
+
+      param = applet.getParameter("showConservation");
+      if (param != null)
+      {
+        showConservation = Boolean.valueOf(param).booleanValue();
+      }
+
+      param = applet.getParameter("showQuality");
+      if (param != null)
+      {
+        showQuality = Boolean.valueOf(param).booleanValue();
+      }
+
+      param = applet.getParameter("showConsensus");
+      if (param != null)
+      {
+        showConsensus = Boolean.valueOf(param).booleanValue();
+      }
+    }
+    // We must set conservation and consensus before setting colour,
+    // as Blosum and Clustal require this to be done
+    updateConservation();
+    updateConsensus();
+
+
+    if (applet != null)
+    {
+      String colour = applet.getParameter("defaultColour");
+
+      if(colour == null)
+      {
+        colour = applet.getParameter("userDefinedColour");
+        if(colour !=null)
+          colour = "User Defined";
+      }
+
+      if(colour != null)
+      {
+        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(vconsensus);
+        }
+      }
+
+      if(applet.getParameter("userDefinedColour")!=null)
+      {
+        ((UserColourScheme)globalColourScheme).parseAppletParameter(
+            applet.getParameter("userDefinedColour"));
+      }
+
+
+    }
+  }
+
+  public void showSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
+
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
+
+
+  public void updateConservation()
+  {
+    if(alignment.isNucleotide())
+          return;
+
+    Conservation cons = new jalview.analysis.Conservation("All",
+        jalview.schemes.ResidueProperties.propHash, 3,
+        alignment.getSequences(), 0,
+        alignment.getWidth() - 1);
+    cons.calculate();
+    cons.verdict(false, ConsPercGaps);
+    cons.findQuality();
+    int alWidth = alignment.getWidth();
+    Annotation[] annotations = new Annotation[alWidth];
+    Annotation[] qannotations = new Annotation[alWidth];
+    String sequence = cons.getConsSequence().getSequence();
+    float minR, minG, minB, maxR, maxG, 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 = cons.qualityRange[0].floatValue();
+    float qmax = cons.qualityRange[1].floatValue();
+
+    for (int i = 0; i < alWidth; i++)
+    {
+      float value = 0;
+      try
+      {
+        value = Integer.parseInt(sequence.charAt(i) + "");
+      }
+      catch (Exception ex)
+      {
+        if (sequence.charAt(i) == '*')
+        {
+          value = 11;
+        }
+        if (sequence.charAt(i) == '+')
+        {
+          value = 10;
+        }
+      }
+      float vprop = value - min;
+      vprop /= max;
+
+      annotations[i] = new Annotation(sequence.charAt(i) + "",
+                                      "", ' ', value,
+                                      new Color(minR + maxR * vprop,
+                                                minG + maxG * vprop,
+                                                minB + maxB * vprop));
+      // Quality calc
+      value = ( (Double) cons.quality.elementAt(i)).floatValue();
+      vprop = value - qmin;
+      vprop /= qmax;
+      qannotations[i] = new Annotation(" ",
+                                       String.valueOf(value), ' ', value,
+                                       new
+                                       Color(minR + maxR * vprop,
+                                             minG + maxG * vprop,
+                                             minB + maxB * vprop));
+    }
+
+    if (conservation == null)
+    {
+      conservation = new AlignmentAnnotation("Conservation",
+                                             "Conservation of total alignment less than " +
+                                             ConsPercGaps + "% gaps",
+                                             annotations,
+                                             0f, // cons.qualityRange[0].floatValue(),
+                                             11f, // cons.qualityRange[1].floatValue()
+                                             AlignmentAnnotation.BAR_GRAPH);
+      if (showConservation)
+      {
+        alignment.addAnnotation(conservation);
+      }
+      quality = new AlignmentAnnotation("Quality",
+                                        "Alignment Quality based on Blosum62 scores",
+                                        qannotations,
+                                        cons.qualityRange[0].floatValue(),
+                                        cons.qualityRange[1].floatValue(),
+                                        AlignmentAnnotation.BAR_GRAPH);
+      if (showQuality)
+      {
+        alignment.addAnnotation(quality);
+      }
+    }
+    else
+    {
+      conservation.annotations = annotations;
+      quality.annotations = qannotations;
+      quality.graphMax = cons.qualityRange[1].floatValue();
+    }
+
+  }
+
+  public void updateConsensus()
+  {
+    Annotation[] annotations = new Annotation[alignment.getWidth()];
+
+    // this routine prevents vconsensus becoming a new object each time
+    // consenus is calculated. Important for speed of Blosum62
+    // and PID colouring of alignment
+    if (vconsensus == null)
+    {
+      vconsensus = alignment.getAAFrequency();
+    }
+    else
+    {
+      Vector temp = alignment.getAAFrequency();
+      vconsensus.removeAllElements();
+      Enumeration e = temp.elements();
+      while (e.hasMoreElements())
+      {
+        vconsensus.addElement(e.nextElement());
+      }
+    }
+    Hashtable hash = null;
+    for (int i = 0; i < alignment.getWidth(); i++)
+    {
+      hash = (Hashtable) vconsensus.elementAt(i);
+      float value = 0;
+      if(ignoreGapsInConsensusCalculation)
+        value = ((Float)hash.get("pid_nogaps")).floatValue();
+      else
+        value = ((Float)hash.get("pid_gaps")).floatValue();
+
+      String maxRes = hash.get("maxResidue").toString();
+      String mouseOver = hash.get("maxResidue") + " ";
+      if (maxRes.length() > 1)
+      {
+        mouseOver = "[" + maxRes + "] ";
+        maxRes = "+";
+      }
+
+
+      mouseOver += (int) value + "%";
+      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+
+    }
+
+    if (consensus == null)
+    {
+      consensus = new AlignmentAnnotation("Consensus",
+                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+      if (showConsensus)
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
+    else
+    {
+      consensus.annotations = annotations;
+    }
+
+    if(globalColourScheme!=null)
+          globalColourScheme.setConsensus(vconsensus);
+
+  }
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation row.
+   * @return consensus sequence as a new sequence object
+   */
+  /**
+   * 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();
+    if (consensus==null)
+      return null;
+    StringBuffer seqs=new StringBuffer();
+    for (int i=0; i<consensus.annotations.length; i++) {
+      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);          
+      }
+    }
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;
+  }
+  public SequenceGroup getSelectionGroup()
+  {
+    return selectionGroup;
+  }
+
+  public void setSelectionGroup(SequenceGroup sg)
+  {
+    selectionGroup = sg;
+  }
+
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
+
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
+
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
+
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
+
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  public int getStartSeq()
+  {
+    return startSeq;
+  }
+
+  public void setGlobalColourScheme(ColourSchemeI cs)
+  {
+    globalColourScheme = cs;
+  }
+
+  public ColourSchemeI getGlobalColourScheme()
+  {
+    return globalColourScheme;
+  }
+
+  public void setStartRes(int res)
+  {
+    this.startRes = res;
+  }
+
+  public void setStartSeq(int seq)
+  {
+    this.startSeq = seq;
+  }
+
+  public void setEndRes(int res)
+  {
+    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;
+  }
+
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
+    {
+      seq = alignment.getHeight();
+    }
+    if (seq < 0)
+    {
+      seq = 0;
+    }
+    this.endSeq = seq;
+  }
+
+  public int getEndSeq()
+  {
+    return endSeq;
+  }
+
+  java.awt.Frame nullFrame;
+  public void setFont(Font f)
+  {
+    font = f;
+    if(nullFrame == null)
+    {
+      nullFrame = new java.awt.Frame();
+      nullFrame.addNotify();
+    }
+
+    java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
+    setCharHeight(fm.getHeight());
+    charWidth = fm.charWidth('M');
+  }
+
+  public Font getFont()
+  {
+    return font;
+  }
+
+  public int getCharWidth()
+  {
+    return charWidth;
+  }
+
+  public void setCharHeight(int h)
+  {
+    this.charHeight = h;
+  }
+
+  public int getCharHeight()
+  {
+    return charHeight;
+  }
+
+  public void setWrappedWidth(int w)
+  {
+    this.wrappedWidth = w;
+  }
+
+  public int getwrappedWidth()
+  {
+    return wrappedWidth;
+  }
+
+  public AlignmentI getAlignment()
+  {
+    return alignment;
+  }
+
+  public void setAlignment(AlignmentI align)
+  {
+    this.alignment = align;
+  }
+
+  public void setWrapAlignment(boolean state)
+  {
+    wrapAlignment = state;
+  }
+
+  public void setShowText(boolean state)
+  {
+    showText = state;
+  }
+
+  public void setRenderGaps(boolean state)
+  {
+    renderGaps = state;
+  }
+
+  public boolean getColourText()
+  {
+    return showColourText;
+  }
+
+  public void setColourText(boolean state)
+  {
+    showColourText = state;
+  }
+
+  public void setShowBoxes(boolean state)
+  {
+    showBoxes = state;
+  }
+
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
+  }
+
+  public boolean getShowText()
+  {
+    return showText;
+  }
+
+  public boolean getShowBoxes()
+  {
+    return showBoxes;
+  }
+
+  public char getGapCharacter()
+  {
+    return getAlignment().getGapCharacter();
+  }
+
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
+    {
+      getAlignment().setGapCharacter(gap);
+    }
+  }
+
+  public void setThreshold(int thresh)
+  {
+    threshold = thresh;
+  }
+
+  public int getThreshold()
+  {
+    return threshold;
+  }
+
+  public void setIncrement(int inc)
+  {
+    increment = inc;
+  }
+
+  public int getIncrement()
+  {
+    return increment;
+  }
+
+  public void setHiddenColumns(ColumnSelection colsel)
+  {
+    this.colSel = colsel;
+    if(colSel.getHiddenColumns()!=null)
+      hasHiddenColumns = true;
+  }
+
+  public ColumnSelection getColumnSelection()
+  {
+    return colSel;
+  }
+
+  public void resetSeqLimits(int height)
+  {
+    setEndSeq(height / getCharHeight());
+  }
+
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
+  }
+
+  public NJTree getCurrentTree()
+  {
+    return currentTree;
+  }
+
+  public void setColourAppliesToAllGroups(boolean b)
+  {
+    colourAppliesToAllGroups = b;
+  }
+
+  public boolean getColourAppliesToAllGroups()
+  {
+    return colourAppliesToAllGroups;
+  }
+
+  public boolean getShowJVSuffix()
+  {
+    return showJVSuffix;
+  }
+
+  public void setShowJVSuffix(boolean b)
+  {
+    showJVSuffix = b;
+  }
+
+  public boolean getShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  public void setShowAnnotation(boolean b)
+  {
+    showAnnotation = b;
+  }
+
+  public boolean getScaleAboveWrapped()
+  {
+    return scaleAboveWrapped;
+  }
+
+  public boolean getScaleLeftWrapped()
+  {
+    return scaleLeftWrapped;
+  }
+
+  public boolean getScaleRightWrapped()
+  {
+    return scaleRightWrapped;
+  }
+
+  public void setScaleAboveWrapped(boolean b)
+  {
+    scaleAboveWrapped = b;
+  }
+
+  public void setScaleLeftWrapped(boolean b)
+  {
+    scaleLeftWrapped = b;
+  }
+
+  public void setScaleRightWrapped(boolean b)
+  {
+    scaleRightWrapped = b;
+  }
+
+  public void setIgnoreGapsConsensus(boolean b)
+  {
+    ignoreGapsInConsensusCalculation = b;
+    updateConsensus();
+    if (globalColourScheme!=null)
+    {
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+          ignoreGapsInConsensusCalculation);
+
+    }
+  }
+
+  /**
+   * 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 boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensusCalculation;
+  }
+  public void hideSelectedColumns()
+  {
+    if (colSel.size() < 1)
+      return;
+
+    colSel.hideSelectedColumns();
+    setSelectionGroup(null);
+
+    hasHiddenColumns = true;
+  }
+
+  public void invertColumnSelection()
+  {
+    int column;
+    for (int i = 0; i < alignment.getWidth(); i++)
+    {
+      column = i;
+
+      if (colSel.contains(column))
+        colSel.removeElement(column);
+      else
+        colSel.addElement(column);
+
+    }
+  }
+
+
+  public void hideColumns(int start, int end)
+  {
+    if(start==end)
+      colSel.hideColumns(start);
+    else
+      colSel.hideColumns(start, end);
+
+    hasHiddenColumns = true;
+  }
+
+  public void hideSequence(SequenceI seq)
+  {
+    if(seq!=null)
+    {
+      alignment.getHiddenSequences().hideSequence(seq);
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
+    }
+  }
+
+  public void hideAllSelectedSeqs()
+  {
+    if (selectionGroup == null)
+      return;
+
+    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+
+    for (int i = 0; i < seqs.length; i++)
+    {
+      alignment.getHiddenSequences().hideSequence(seqs[i]);
+    }
+    firePropertyChange("alignment", null, alignment.getSequences());
+    hasHiddenRows = true;
+    setSelectionGroup(null);
+  }
+
+  public void showColumn(int col)
+  {
+    colSel.revealHiddenColumns(col);
+    if(colSel.getHiddenColumns()==null)
+      hasHiddenColumns = false;
+  }
+
+  public void showAllHiddenColumns()
+  {
+    colSel.revealAllHiddenColumns();
+    hasHiddenColumns = false;
+  }
+
+  public void showAllHiddenSeqs()
+  {
+    if(alignment.getHiddenSequences().getSize()>0)
+    {
+      if(selectionGroup==null)
+      {
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth()-1);
+      }
+      Vector tmp = alignment.getHiddenSequences().showAll();
+      for(int t=0; t<tmp.size(); t++)
+      {
+        selectionGroup.addSequence(
+            (SequenceI)tmp.elementAt(t), false
+            );
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      hasHiddenRows = false;
+    }
+  }
+
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+  }
+
+  /**
+   * This method returns the a new SequenceI [] with
+   * the selection sequence and start and end points adjusted
+   * @return String[]
+   */
+  public SequenceI[] getSelectionAsNewSequence()
+  {
+    SequenceI[] sequences;
+
+    if (selectionGroup == null)
+      sequences = alignment.getSequencesArray();
+    else
+      sequences = selectionGroup.getSelectionAsNewSequences(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[]
+   */
+  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(false);
+      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;
+        }
+
+        if (hideStart>end)
+          break;
+
+        if (hideEnd>end)
+          hideEnd=end;
+
+        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);
+    } else {
+      selection.addOperation(CigarArray.M, end-start);
+    }
+    return selection;
+  }
+  /**
+   * 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)
+      return new AlignmentView(aligview);
+    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)
+  {
+    String [] selection = null;
+    SequenceI [] seqs= null;
+    int i, iSize;
+    int start = 0, end = 0;
+    if(selectedRegionOnly && selectionGroup!=null)
+    {
+      iSize = selectionGroup.getSize(false);
+      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];
+
+
+    for(i=0; i<iSize; i++)
+    {
+      if (hasHiddenColumns)
+      {
+           StringBuffer visibleSeq = new StringBuffer();
+           Vector regions = colSel.getHiddenColumns();
+
+           int blockStart = start, blockEnd=end;
+           int [] region;
+           int hideStart, hideEnd;
+
+           for (int j = 0; j < regions.size(); j++)
+           {
+             region = (int[]) regions.elementAt(j);
+             hideStart = region[0];
+             hideEnd = region[1];
+
+             if(hideStart < start)
+             {
+               continue;
+             }
+
+             blockStart = Math.min(blockStart, hideEnd+1);
+             blockEnd = Math.min(blockEnd, hideStart);
+
+             if(blockStart>blockEnd)
+             {
+                break;
+             }
+
+
+             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+             blockStart = hideEnd+1;
+             blockEnd = end;
+           }
+
+           if(end>blockStart)
+             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+           selection[i] = visibleSeq.toString();
+      }
+      else
+      {
+        selection[i] = seqs[i].getSequence(start, end);
+      }
+    }
+
+    return selection;
+  }
+
+  public boolean getShowHiddenMarkers()
+  {
+    return showHiddenMarkers;
+  }
+
+  public void setShowHiddenMarkers(boolean show)
+  {
+    showHiddenMarkers = show;
+  }
+
+
+}
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 0523d1f..ae6ef37 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,204 +1,243 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * 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.
- *
- * 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
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationLabels
-    extends Panel implements ActionListener
-{
-  boolean active = false;
-  AlignmentPanel ap;
-  AlignViewport av;
-  boolean resizing = false;
-  int oldY, mouseX;
-  static String ADDNEW = "Add new row";
-  static String HIDE = "Hide this row";
-  static String DELETE = "Delete this row";
-  static String SHOWALL = "Show all hidden rows";
-  static String OUTPUT_TEXT = "Show Values In Textbox";
-  int selectedRow = 0;
-  int scrollOffset = 0;
-
-  public AnnotationLabels(AlignmentPanel ap)
-  {
-    this.ap = ap;
-    this.av = ap.av;
-    setLayout(null);
-    addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      {
-        doMousePressed(evt);
-      }
-    });
-  }
-
-  public AnnotationLabels(AlignViewport av)
-{
-  this.av = av;
-}
-
-
-  public void setScrollOffset(int y)
-  {
-    scrollOffset = y;
-    repaint();
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
-    if (evt.getActionCommand().equals(HIDE))
-    {
-      aa[selectedRow].visible = false;
-    }
-    else if (evt.getActionCommand().equals(SHOWALL))
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        aa[i].visible = true;
-      }
-    }
-    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
-    {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
-      Frame frame = new Frame();
-      frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
-                                       ap.alignFrame.getTitle() + " - " +
-                                       aa[selectedRow].label, 500, 100);
-      cap.setText(aa[selectedRow].toString());
-    }
-
-    ap.annotationPanel.adjustPanelHeight();
-    setSize(getSize().width, ap.annotationPanel.getSize().height);
-    ap.validate();
-    ap.repaint();
-  }
-
-  public void doMousePressed(MouseEvent evt)
-  {
-    int y = evt.getY() - scrollOffset;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-    int height = 0;
-    for (int i = 0; i < aa.length; i++)
-    {
-      if (!aa[i].visible)
-      {
-        continue;
-      }
-
-      height += aa[i].height;
-      if (y < height)
-      {
-        selectedRow = i;
-        break;
-      }
-    }
-
-    PopupMenu pop = new PopupMenu("Annotations");
-    MenuItem item = new MenuItem(HIDE);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new MenuItem(SHOWALL);
-    item.addActionListener(this);
-    pop.add(item);
-    this.add(pop);
-    item = new MenuItem(OUTPUT_TEXT);
-    item.addActionListener(this);
-    pop.add(item);
-
-    if (aa[selectedRow].label.equals("Consensus"))
-    {
-      pop.addSeparator();
-      final CheckboxMenuItem cbmi = new CheckboxMenuItem(
-          "Ignore Gaps In Consensus",
-          ap.av.getIgnoreGapsConsensus());
-
-      cbmi.addItemListener(new ItemListener()
-      {
-        public void itemStateChanged(ItemEvent e)
-        {
-          ap.av.setIgnoreGapsConsensus(cbmi.getState());
-          ap.repaint();
-        }
-      });
-      pop.add(cbmi);
-    }
-
-     pop.show(this, evt.getX(), evt.getY());
-
-  }
-
-  public void paint(Graphics g)
-  {
-    drawComponent(g, getSize().width);
-  }
-
-  public void drawComponent(Graphics g, int width)
-  {
-    g.setFont(av.getFont());
-    FontMetrics fm = g.getFontMetrics(av.getFont());
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getSize().width, getSize().height);
-
-    g.translate(0, scrollOffset);
-    g.setColor(Color.black);
-
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    int y = g.getFont().getSize();
-    int x = 0;
-
-    if (aa != null)
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (!aa[i].visible)
-        {
-          continue;
-        }
-
-        x = width - fm.stringWidth(aa[i].label) - 3;
-
-        if (aa[i].graph>0)
-        {
-          y += (aa[i].height / 3);
-        }
-
-        g.drawString(aa[i].label, x, y);
-
-        if (aa[i].graph>0)
-        {
-          y += (2 * aa[i].height / 3);
-        }
-        else
-        {
-          y += aa[i].height;
-        }
-      }
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
+ * 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.
+ *
+ * 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
+ */
+
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.Vector;
+
+import jalview.datamodel.*;
+
+public class AnnotationLabels
+    extends Panel implements ActionListener
+{
+  boolean active = false;
+  AlignmentPanel ap;
+  AlignViewport av;
+  boolean resizing = false;
+  int oldY, mouseX;
+  static String ADDNEW = "Add new row";
+  static String HIDE = "Hide this row";
+  static String DELETE = "Delete this row";
+  static String SHOWALL = "Show all hidden rows";
+  static String OUTPUT_TEXT = "Show Values In Textbox";
+  static String COPYCONS_SEQ = "Copy Consensus Sequence";
+  
+  int selectedRow = 0;
+  int scrollOffset = 0;
+
+  public AnnotationLabels(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    this.av = ap.av;
+    setLayout(null);
+    addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        doMousePressed(evt);
+      }
+    });
+  }
+
+  public AnnotationLabels(AlignViewport av)
+{
+  this.av = av;
+}
+
+
+  public void setScrollOffset(int y)
+  {
+    scrollOffset = y;
+    repaint();
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+    if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
+    }
+    else if (evt.getActionCommand().equals(SHOWALL))
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        aa[i].visible = true;
+      }
+    }
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame,
+                                       ap.alignFrame.getTitle() + " - " +
+                                       aa[selectedRow].label, 500, 100);
+      cap.setText(aa[selectedRow].toString());
+    }
+    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+    {
+      SequenceI cons=av.getConsensusSeq();
+      if (cons!=null)
+        copy_annotseqtoclipboard(cons);
+      
+    }
+    ap.annotationPanel.adjustPanelHeight();
+    setSize(getSize().width, ap.annotationPanel.getSize().height);
+    ap.validate();
+    ap.repaint();
+  }
+
+  public void doMousePressed(MouseEvent evt)
+  {
+    int y = evt.getY() - scrollOffset;
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    int height = 0;
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (!aa[i].visible)
+      {
+        continue;
+      }
+
+      height += aa[i].height;
+      if (y < height)
+      {
+        selectedRow = i;
+        break;
+      }
+    }
+
+    PopupMenu pop = new PopupMenu("Annotations");
+    MenuItem item = new MenuItem(HIDE);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new MenuItem(SHOWALL);
+    item.addActionListener(this);
+    pop.add(item);
+    this.add(pop);
+    item = new MenuItem(OUTPUT_TEXT);
+    item.addActionListener(this);
+    pop.add(item);
+
+    if (aa[selectedRow].label.equals("Consensus"))
+    {
+      pop.addSeparator();
+      final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+          "Ignore Gaps In Consensus",
+          ap.av.getIgnoreGapsConsensus());
+
+      cbmi.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent e)
+        {
+          ap.av.setIgnoreGapsConsensus(cbmi.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cbmi);
+      final MenuItem cpcons=new MenuItem(COPYCONS_SEQ);
+      cpcons.addActionListener(this);
+      pop.add(cpcons);
+    }
+
+     pop.show(this, evt.getX(), evt.getY());
+
+  }
+/**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void copy_annotseqtoclipboard(SequenceI sq)
+    {
+      if (sq==null || sq.getLength()<1)
+        return;
+      jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
+      jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
+          sq.getStart() + "\t" +
+          sq.getEnd() + "\t" +
+          sq.getSequence() + "\n");
+      if (av.hasHiddenColumns)
+      {
+        jalview.appletgui.AlignFrame.copiedHiddenColumns=new Vector();
+        for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
+        {
+          int[] region = (int[])
+              av.getColumnSelection().getHiddenColumns().elementAt(i);
+
+          jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]{region[0],
+                            region[1]});
+        }
+      }
+    }
+
+  public void paint(Graphics g)
+  {
+    drawComponent(g, getSize().width);
+  }
+
+  public void drawComponent(Graphics g, int width)
+  {
+    g.setFont(av.getFont());
+    FontMetrics fm = g.getFontMetrics(av.getFont());
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getSize().width, getSize().height);
+
+    g.translate(0, scrollOffset);
+    g.setColor(Color.black);
+
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    int y = g.getFont().getSize();
+    int x = 0;
+
+    if (aa != null)
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
+
+        x = width - fm.stringWidth(aa[i].label) - 3;
+
+        if (aa[i].graph>0)
+        {
+          y += (aa[i].height / 3);
+        }
+
+        g.drawString(aa[i].label, x, y);
+
+        if (aa[i].graph>0)
+        {
+          y += (2 * aa[i].height / 3);
+        }
+        else
+        {
+          y += aa[i].height;
+        }
+      }
+    }
+  }
+
+}
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index c7e8418..2d22231 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,671 +1,728 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * 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.
- *
- * 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
- */
-package jalview.datamodel;
-
-import jalview.util.ShiftList;
-
-import java.util.*;
-
-/**
- * NOTE: Columns are zero based.
- */
-public class ColumnSelection
-{
-    Vector selected = new Vector();
-
-    //Vector of int [] {startCol, endCol}
-    Vector hiddenColumns;
-
-    /**
-     * Add a column to the selection
-     *
-     * @param col index of column
-     */
-    public void addElement(int col)
-    {
-        Integer column = new Integer(col);
-        if (!selected.contains(column))
-        {
-            selected.addElement(column);
-        }
-    }
-
-    /**
-     * clears column selection
-     */
-    public void clear()
-    {
-        selected.removeAllElements();
-    }
-
-    /**
-     * removes col from selection
-     *
-     * @param col index of column to be removed
-     */
-    public void removeElement(int col)
-    {
-        Integer colInt = new Integer(col);
-
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
-    }
-
-    /**
-     * removes a range of columns from the selection
-     * @param start int - first column in range to be removed
-     * @param end int - last col
-     */
-    public void removeElements(int start, int end)
-    {
-      Integer colInt;
-      for(int i=start; i<end; i++)
-      {
-        colInt = new Integer(i);
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
-      }
-    }
-    /**
-     *
-     * @return Vector containing selected columns as Integers
-     */
-    public Vector getSelected()
-    {
-      return selected;
-    }
-
-    /**
-     *
-     * @param col index to search for in column selection
-     *
-     * @return true if Integer(col) is in selection.
-     */
-    public boolean contains(int col)
-    {
-        return selected.contains(new Integer(col));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int columnAt(int i)
-    {
-        return ((Integer) selected.elementAt(i)).intValue();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int size()
-    {
-        return selected.size();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMax()
-    {
-        int max = -1;
-
-        for (int i = 0; i < selected.size(); i++)
-        {
-            if (columnAt(i) > max)
-            {
-                max = columnAt(i);
-            }
-        }
-
-        return max;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMin()
-    {
-        int min = 1000000000;
-
-        for (int i = 0; i < selected.size(); i++)
-        {
-            if (columnAt(i) < min)
-            {
-                min = columnAt(i);
-            }
-        }
-
-        return min;
-    }
-
-
-    /**
-     * propagate shift in alignment columns to column selection
-     *
-     * @param start beginning of edit
-     * @param left shift in edit (+ve for removal, or -ve for inserts)
-     */
-    public void compensateForEdit(int start, int change)
-    {
-        for (int i = 0; i < size(); i++)
-        {
-            int temp = columnAt(i);
-
-            if (temp >= start)
-            {
-                selected.setElementAt(new Integer(temp - change), i);
-            }
-        }
-
-        if(hiddenColumns!=null)
-        {
-          for(int i=0; i<hiddenColumns.size(); i++)
-          {
-            int[] region = (int[]) hiddenColumns.elementAt(i);
-            if(region[0] > start)
-            {
-              region[0] -= change;
-              region[1] -= change;
-            }
-            if(region[0]<0)
-              region[0] = 0;
-            if(region[1] <0)
-             region[1] = 0;
-          }
-        }
-    }
-    /**
-     * propagate shift in alignment columns to column selection
-     * special version of compensateForEdit - allowing for edits within hidden regions
-     * @param start beginning of edit
-     * @param left shift in edit (+ve for removal, or -ve for inserts)
-     */
-    private void compensateForDelEdits(int start, int change)
-    {
-        for (int i = 0; i < size(); i++)
-        {
-            int temp = columnAt(i);
-
-            if (temp >= start)
-            {
-                selected.setElementAt(new Integer(temp - change), i);
-            }
-        }
-
-        if(hiddenColumns!=null)
-        {
-          for(int i=0; i<hiddenColumns.size(); i++)
-          {
-            int[] region = (int[]) hiddenColumns.elementAt(i);
-            if(region[0] >= start)
-            {
-              region[0] -= change;
-            }
-            if (region[1]>= start) {
-              region[1] -=change;
-            }
-            if (region[1]<region[0]) {
-              hiddenColumns.removeElementAt(i--);
-            }
-
-            if(region[0]<0)
-              region[0] = 0;
-            if(region[1] <0)
-             region[1] = 0;
-          }
-        }
-    }
-    /**
-     * Adjust hidden column boundaries based on a series of column
-     * additions or deletions in visible regions.
-     * @param shiftrecord
-     * @return
-     */
-    public ShiftList compensateForEdits(ShiftList shiftrecord) {
-      if (shiftrecord!=null) {
-        Vector shifts = shiftrecord.shifts;
-        if (shifts!=null && shifts.size()>0) {
-          int shifted=0;
-          for (int i=0,j=shifts.size(); i<j; i++) {
-            int[] sh = (int[]) shifts.elementAt(i);
-            //compensateForEdit(shifted+sh[0], sh[1]);
-            compensateForDelEdits(shifted+sh[0], sh[1]);
-            shifted-=sh[1];
-          }
-        }
-        return shiftrecord.getInverse();
-      }
-      return null;
-    }
-    /**
-     * removes intersection of position,length ranges in deletions
-     * from the start,end regions marked in intervals.
-     * @param deletions
-     * @param intervals
-     * @return
-     */
-    private boolean pruneIntervalVector(Vector deletions, Vector intervals) {
-      boolean pruned=false;
-      int i=0,j=intervals.size()-1, s=0, t=deletions.size()-1;
-      int hr[]=(int[]) intervals.elementAt(i);
-      int sr[]=(int[]) deletions.elementAt(s);
-      while (i<=j && s<=t) {
-        boolean trailinghn=hr[1]>=sr[0];
-        if (!trailinghn) {
-          if (i<j)
-            hr=(int[]) intervals.elementAt(++i);
-          else
-            i++;
-          continue;
-        }
-        int endshift=sr[0]+sr[1]; // deletion ranges - -ve means an insert
-        if (endshift<hr[0] || endshift<sr[0]) { // leadinghc disjoint or not a deletion
-          if (s<t)
-            sr=(int[]) deletions.elementAt(++s);
-          else
-            s++;
-          continue;
-        }
-        boolean leadinghn=hr[0]>=sr[0];
-        boolean leadinghc=hr[0]<endshift;
-        boolean trailinghc=hr[1]<endshift;
-        if (leadinghn) {
-          if (trailinghc) {// deleted hidden region.
-            intervals.removeElementAt(i);
-            pruned=true;
-            j--;
-            if (i<=j)
-              hr=(int[]) intervals.elementAt(i);
-            continue;
-          }
-          if (leadinghc) {
-            hr[0]=endshift; // clip c terminal region
-            leadinghn=!leadinghn;
-            pruned=true;
-          }
-        }
-        if (!leadinghn) {
-          if (trailinghc) {
-            if (trailinghn) {
-              hr[1]=sr[0]-1;
-              pruned=true;
-            }
-          } else {
-            // sr contained in hr
-            if (s<t)
-              sr=(int[]) deletions.elementAt(++s);
-            else
-              s++;
-            continue;
-          }
-        }
-      }
-      return pruned; // true if any interval was removed or modified by operations.
-    }
-    private boolean pruneColumnList(Vector deletion, Vector list) {
-      int s=0,t=deletion.size();
-      int[] sr=(int[])list.elementAt(s++);
-      boolean pruned=false;
-      int i=0, j=list.size();
-      while (i<j && s<=t) {
-        int c=((Integer)list.elementAt(i++)).intValue();
-        if (sr[0]<=c) {
-          if (sr[1]+sr[0]>=c) { // sr[1] -ve means inseriton.
-            list.removeElementAt(--i);
-            j--;
-          } else {
-            if (s<t)
-              sr = (int[])deletion.elementAt(s);
-            s++;
-          }
-        }
-      }
-      return pruned;
-    }
-    /**
-     * remove any hiddenColumns or selected columns and shift remaining
-     * based on a series of position, range deletions.
-     * @param deletions
-     */
-    public void pruneDeletions(ShiftList deletions) {
-      if (deletions!=null) {
-        Vector shifts=deletions.shifts;
-        if (shifts!=null && shifts.size()>0) {
-          // delete any intervals intersecting.
-          if (hiddenColumns!=null) {
-            pruneIntervalVector(shifts, hiddenColumns);
-            if (hiddenColumns!=null && hiddenColumns.size()==0) {
-              hiddenColumns=null;
-            }
-          }
-          if (selected!=null && selected.size()>0) {
-            pruneColumnList(shifts, selected);
-            if (selected!=null && selected.size()==0)
-              selected=null;
-          }
-          // and shift the rest.
-          this.compensateForEdits(deletions);
-        }
-      }
-    }
-    /**
-     * This Method is used to return all the HiddenColumn regions
-     * less than the given index.
-     * @param end int
-     * @return Vector
-     */
-    public Vector getHiddenColumns()
-    {
-      return hiddenColumns;
-    }
-    /**
-     * Return absolute column index for a visible column index
-     * @param column int column index in alignment view
-     * @return alignment column index for column
-     */
-    public int adjustForHiddenColumns(int column)
-    {
-      int result = column;
-      if (hiddenColumns != null)
-      {
-        for (int i = 0; i < hiddenColumns.size(); i++)
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          if (result >= region[0])
-          {
-            result += region[1] - region[0] + 1;
-          }
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Use this method to find out where a visible column is in the alignment
-     * when hidden columns exist
-     * @param hiddenColumn int
-     * @return int
-     */
-    public int findColumnPosition(int hiddenColumn)
-    {
-      int result = hiddenColumn;
-      if (hiddenColumns != null)
-      {
-        int index = 0;
-        int gaps = 0;
-        do
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if (hiddenColumn > region[1])
-          {
-            result -= region[1]+1-region[0];
-          }
-          index++;
-        }
-        while (index < hiddenColumns.size());
-
-        result -= gaps;
-      }
-
-      return result;
-    }
-
-    /**
-     * Use this method to determine where the next hiddenRegion starts
-    */
-    public int findHiddenRegionPosition(int hiddenRegion)
-    {
-      int result = 0;
-      if (hiddenColumns != null)
-      {
-        int index = 0;
-        int gaps = 0;
-        do
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(hiddenRegion==0)
-          {
-            return region[0];
-          }
-
-            gaps +=  region[1] +1 - region[0];
-            result = region[1] +1;
-            index++;
-        }
-        while(index < hiddenRegion+1);
-
-        result -= gaps;
-      }
-
-      return result;
-    }
-
-    /**
-     * THis method returns the rightmost limit of a
-     * region of an alignment with hidden columns.
-     * In otherwords, the next hidden column.
-     * @param index int
-     */
-    public int getHiddenBoundaryRight(int alPos)
-    {
-      if (hiddenColumns != null)
-      {
-        int index = 0;
-        do
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(alPos < region[0])
-            return region[0];
-
-          index++;
-        }
-        while(index < hiddenColumns.size());
-      }
-
-      return alPos;
-
-    }
-    /**
-     * THis method returns the rightmost limit of a
-     * region of an alignment with hidden columns.
-     * In otherwords, the next hidden column.
-     * @param index int
-     */
-    public int getHiddenBoundaryLeft(int alPos)
-    {
-      if (hiddenColumns != null)
-      {
-        int index = hiddenColumns.size()-1;
-        do
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(alPos > region[1])
-            return region[1];
-
-          index--;
-        }
-        while(index >-1);
-      }
-
-      return alPos;
-
-    }
-
-    public void hideSelectedColumns()
-    {
-      while (size() > 0)
-      {
-        int column = ( (Integer) getSelected().firstElement()).intValue();
-        hideColumns(column);
-      }
-
-    }
-
-    public void hideColumns(int start, int end)
-    {
-      if(hiddenColumns==null)
-        hiddenColumns = new Vector();
-
-      boolean added = false;
-      boolean overlap = false;
-
-      for (int i = 0; i < hiddenColumns.size(); i++)
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
-        if ( start<=region[1] && end>=region[0])
-        {
-          hiddenColumns.removeElementAt(i);
-          overlap = true;
-          break;
-        }
-        else if (end < region[0] && start < region[0])
-        {
-          hiddenColumns.insertElementAt(new int[]
-                                        {start, end}, i);
-          added = true;
-          break;
-        }
-      }
-
-      if(overlap)
-      {
-         hideColumns(start, end);
-      }
-      else if (!added)
-        hiddenColumns.addElement(new int[] {start, end});
-
-    }
-
-    /**
-     * This method will find a range of selected columns
-     * around the column specified
-     * @param res int
-     */
-    public void hideColumns(int col)
-    {
-      // First find out range of columns to hide
-      int min = col, max = col+1;
-      while( contains(min) )
-      {  removeElement(min); min --;  }
-
-      while( contains(max) )
-      { removeElement(max);  max ++;  }
-
-      min++; max--;
-
-      hideColumns(min, max);
-    }
-
-    public void revealAllHiddenColumns()
-    {
-      if(hiddenColumns!=null)
-      {
-        for (int i = 0; i < hiddenColumns.size(); i++)
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          for (int j = region[0]; j < region[1]+1; j++)
-          {
-            addElement(j);
-          }
-        }
-      }
-
-      hiddenColumns = null;
-    }
-
-    public void revealHiddenColumns(int res)
-    {
-      for(int i=0; i<hiddenColumns.size(); i++)
-      {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        if( res == region[0])
-        {
-          for (int j = region[0]; j < region[1]+1; j++)
-          {
-            addElement(j);
-          }
-
-          hiddenColumns.removeElement(region);
-          break;
-        }
-      }
-      if(hiddenColumns.size()==0)
-        hiddenColumns = null;
-    }
-
-    public boolean isVisible(int column)
-    {
-      for(int i=0; i<hiddenColumns.size(); i++)
-      {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        if( column >= region[0] && column <= region[1])
-        {
-          return false;
-        }
-      }
-      return true;
-    }
-    /**
-     * Copy constructor
-     * @param copy
-     */
-    public ColumnSelection(ColumnSelection copy) {
-      if (copy!=null) {
-        if (copy.selected!=null) {
-          selected = new Vector();
-          for (int i=0,j=copy.selected.size(); i<j; i++) {
-            selected.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
-          }
-        }
-        if (copy.hiddenColumns!=null) {
-          hiddenColumns=new Vector();
-          for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
-            int[] rh,cp;
-            rh = (int[])copy.hiddenColumns.elementAt(i);
-            if (rh!=null) {
-              cp = new int[rh.length];
-              System.arraycopy(rh, 0, cp, 0, rh.length);
-              hiddenColumns.setElementAt(cp, i);
-            }
-          }
-        }
-      }
-    }
-
-  /**
-   * ColumnSelection
-   */
-  public ColumnSelection()
-  {
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
+ * 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.
+ *
+ * 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
+ */
+package jalview.datamodel;
+
+import jalview.util.ShiftList;
+
+import java.util.*;
+
+/**
+ * NOTE: Columns are zero based.
+ */
+public class ColumnSelection
+{
+    Vector selected = new Vector();
+
+    //Vector of int [] {startCol, endCol}
+    Vector hiddenColumns;
+
+    /**
+     * Add a column to the selection
+     *
+     * @param col index of column
+     */
+    public void addElement(int col)
+    {
+        Integer column = new Integer(col);
+        if (!selected.contains(column))
+        {
+            selected.addElement(column);
+        }
+    }
+
+    /**
+     * clears column selection
+     */
+    public void clear()
+    {
+        selected.removeAllElements();
+    }
+
+    /**
+     * removes col from selection
+     *
+     * @param col index of column to be removed
+     */
+    public void removeElement(int col)
+    {
+        Integer colInt = new Integer(col);
+
+        if (selected.contains(colInt))
+        {
+            selected.removeElement(colInt);
+        }
+    }
+
+    /**
+     * removes a range of columns from the selection
+     * @param start int - first column in range to be removed
+     * @param end int - last col
+     */
+    public void removeElements(int start, int end)
+    {
+      Integer colInt;
+      for(int i=start; i<end; i++)
+      {
+        colInt = new Integer(i);
+        if (selected.contains(colInt))
+        {
+            selected.removeElement(colInt);
+        }
+      }
+    }
+    /**
+     *
+     * @return Vector containing selected columns as Integers
+     */
+    public Vector getSelected()
+    {
+      return selected;
+    }
+
+    /**
+     *
+     * @param col index to search for in column selection
+     *
+     * @return true if Integer(col) is in selection.
+     */
+    public boolean contains(int col)
+    {
+        return selected.contains(new Integer(col));
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int columnAt(int i)
+    {
+        return ((Integer) selected.elementAt(i)).intValue();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int size()
+    {
+        return selected.size();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMax()
+    {
+        int max = -1;
+
+        for (int i = 0; i < selected.size(); i++)
+        {
+            if (columnAt(i) > max)
+            {
+                max = columnAt(i);
+            }
+        }
+
+        return max;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMin()
+    {
+        int min = 1000000000;
+
+        for (int i = 0; i < selected.size(); i++)
+        {
+            if (columnAt(i) < min)
+            {
+                min = columnAt(i);
+            }
+        }
+
+        return min;
+    }
+
+
+    /**
+     * propagate shift in alignment columns to column selection
+     *
+     * @param start beginning of edit
+     * @param left shift in edit (+ve for removal, or -ve for inserts)
+     */
+    public void compensateForEdit(int start, int change)
+    {
+        for (int i = 0; i < size(); i++)
+        {
+            int temp = columnAt(i);
+
+            if (temp >= start)
+            {
+                selected.setElementAt(new Integer(temp - change), i);
+            }
+        }
+
+        if(hiddenColumns!=null)
+        {
+          for(int i=0; i<hiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) hiddenColumns.elementAt(i);
+            if(region[0] > start)
+            {
+              region[0] -= change;
+              region[1] -= change;
+            }
+            if(region[0]<0)
+              region[0] = 0;
+            if(region[1] <0)
+             region[1] = 0;
+          }
+        }
+    }
+    /**
+     * propagate shift in alignment columns to column selection
+     * special version of compensateForEdit - allowing for edits within hidden regions
+     * @param start beginning of edit
+     * @param left shift in edit (+ve for removal, or -ve for inserts)
+     */
+    private void compensateForDelEdits(int start, int change)
+    {
+        for (int i = 0; i < size(); i++)
+        {
+            int temp = columnAt(i);
+
+            if (temp >= start)
+            {
+                selected.setElementAt(new Integer(temp - change), i);
+            }
+        }
+
+        if(hiddenColumns!=null)
+        {
+          for(int i=0; i<hiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) hiddenColumns.elementAt(i);
+            if(region[0] >= start)
+            {
+              region[0] -= change;
+            }
+            if (region[1]>= start) {
+              region[1] -=change;
+            }
+            if (region[1]<region[0]) {
+              hiddenColumns.removeElementAt(i--);
+            }
+
+            if(region[0]<0)
+              region[0] = 0;
+            if(region[1] <0)
+             region[1] = 0;
+          }
+        }
+    }
+    /**
+     * Adjust hidden column boundaries based on a series of column
+     * additions or deletions in visible regions.
+     * @param shiftrecord
+     * @return
+     */
+    public ShiftList compensateForEdits(ShiftList shiftrecord) {
+      if (shiftrecord!=null) {
+        Vector shifts = shiftrecord.shifts;
+        if (shifts!=null && shifts.size()>0) {
+          int shifted=0;
+          for (int i=0,j=shifts.size(); i<j; i++) {
+            int[] sh = (int[]) shifts.elementAt(i);
+            //compensateForEdit(shifted+sh[0], sh[1]);
+            compensateForDelEdits(shifted+sh[0], sh[1]);
+            shifted-=sh[1];
+          }
+        }
+        return shiftrecord.getInverse();
+      }
+      return null;
+    }
+    /**
+     * removes intersection of position,length ranges in deletions
+     * from the start,end regions marked in intervals.
+     * @param deletions
+     * @param intervals
+     * @return
+     */
+    private boolean pruneIntervalVector(Vector deletions, Vector intervals) {
+      boolean pruned=false;
+      int i=0,j=intervals.size()-1, s=0, t=deletions.size()-1;
+      int hr[]=(int[]) intervals.elementAt(i);
+      int sr[]=(int[]) deletions.elementAt(s);
+      while (i<=j && s<=t) {
+        boolean trailinghn=hr[1]>=sr[0];
+        if (!trailinghn) {
+          if (i<j)
+            hr=(int[]) intervals.elementAt(++i);
+          else
+            i++;
+          continue;
+        }
+        int endshift=sr[0]+sr[1]; // deletion ranges - -ve means an insert
+        if (endshift<hr[0] || endshift<sr[0]) { // leadinghc disjoint or not a deletion
+          if (s<t)
+            sr=(int[]) deletions.elementAt(++s);
+          else
+            s++;
+          continue;
+        }
+        boolean leadinghn=hr[0]>=sr[0];
+        boolean leadinghc=hr[0]<endshift;
+        boolean trailinghc=hr[1]<endshift;
+        if (leadinghn) {
+          if (trailinghc) {// deleted hidden region.
+            intervals.removeElementAt(i);
+            pruned=true;
+            j--;
+            if (i<=j)
+              hr=(int[]) intervals.elementAt(i);
+            continue;
+          }
+          if (leadinghc) {
+            hr[0]=endshift; // clip c terminal region
+            leadinghn=!leadinghn;
+            pruned=true;
+          }
+        }
+        if (!leadinghn) {
+          if (trailinghc) {
+            if (trailinghn) {
+              hr[1]=sr[0]-1;
+              pruned=true;
+            }
+          } else {
+            // sr contained in hr
+            if (s<t)
+              sr=(int[]) deletions.elementAt(++s);
+            else
+              s++;
+            continue;
+          }
+        }
+      }
+      return pruned; // true if any interval was removed or modified by operations.
+    }
+    private boolean pruneColumnList(Vector deletion, Vector list) {
+      int s=0,t=deletion.size();
+      int[] sr=(int[])list.elementAt(s++);
+      boolean pruned=false;
+      int i=0, j=list.size();
+      while (i<j && s<=t) {
+        int c=((Integer)list.elementAt(i++)).intValue();
+        if (sr[0]<=c) {
+          if (sr[1]+sr[0]>=c) { // sr[1] -ve means inseriton.
+            list.removeElementAt(--i);
+            j--;
+          } else {
+            if (s<t)
+              sr = (int[])deletion.elementAt(s);
+            s++;
+          }
+        }
+      }
+      return pruned;
+    }
+    /**
+     * remove any hiddenColumns or selected columns and shift remaining
+     * based on a series of position, range deletions.
+     * @param deletions
+     */
+    public void pruneDeletions(ShiftList deletions) {
+      if (deletions!=null) {
+        Vector shifts=deletions.shifts;
+        if (shifts!=null && shifts.size()>0) {
+          // delete any intervals intersecting.
+          if (hiddenColumns!=null) {
+            pruneIntervalVector(shifts, hiddenColumns);
+            if (hiddenColumns!=null && hiddenColumns.size()==0) {
+              hiddenColumns=null;
+            }
+          }
+          if (selected!=null && selected.size()>0) {
+            pruneColumnList(shifts, selected);
+            if (selected!=null && selected.size()==0)
+              selected=null;
+          }
+          // and shift the rest.
+          this.compensateForEdits(deletions);
+        }
+      }
+    }
+    /**
+     * This Method is used to return all the HiddenColumn regions
+     * less than the given index.
+     * @param end int
+     * @return Vector
+     */
+    public Vector getHiddenColumns()
+    {
+      return hiddenColumns;
+    }
+    /**
+     * Return absolute column index for a visible column index
+     * @param column int column index in alignment view
+     * @return alignment column index for column
+     */
+    public int adjustForHiddenColumns(int column)
+    {
+      int result = column;
+      if (hiddenColumns != null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          if (result >= region[0])
+          {
+            result += region[1] - region[0] + 1;
+          }
+        }
+      }
+      return result;
+    }
+
+    /**
+     * Use this method to find out where a visible column is in the alignment
+     * when hidden columns exist
+     * @param hiddenColumn int
+     * @return int
+     */
+    public int findColumnPosition(int hiddenColumn)
+    {
+      int result = hiddenColumn;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int gaps = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if (hiddenColumn > region[1])
+          {
+            result -= region[1]+1-region[0];
+          }
+          index++;
+        }
+        while (index < hiddenColumns.size());
+
+        result -= gaps;
+      }
+
+      return result;
+    }
+
+    /**
+     * Use this method to determine where the next hiddenRegion starts
+    */
+    public int findHiddenRegionPosition(int hiddenRegion)
+    {
+      int result = 0;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int gaps = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(hiddenRegion==0)
+          {
+            return region[0];
+          }
+
+            gaps +=  region[1] +1 - region[0];
+            result = region[1] +1;
+            index++;
+        }
+        while(index < hiddenRegion+1);
+
+        result -= gaps;
+      }
+
+      return result;
+    }
+
+    /**
+     * THis method returns the rightmost limit of a
+     * region of an alignment with hidden columns.
+     * In otherwords, the next hidden column.
+     * @param index int
+     */
+    public int getHiddenBoundaryRight(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos < region[0])
+            return region[0];
+
+          index++;
+        }
+        while(index < hiddenColumns.size());
+      }
+
+      return alPos;
+
+    }
+    /**
+     * THis method returns the rightmost limit of a
+     * region of an alignment with hidden columns.
+     * In otherwords, the next hidden column.
+     * @param index int
+     */
+    public int getHiddenBoundaryLeft(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = hiddenColumns.size()-1;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos > region[1])
+            return region[1];
+
+          index--;
+        }
+        while(index >-1);
+      }
+
+      return alPos;
+
+    }
+
+    public void hideSelectedColumns()
+    {
+      while (size() > 0)
+      {
+        int column = ( (Integer) getSelected().firstElement()).intValue();
+        hideColumns(column);
+      }
+
+    }
+
+    public void hideColumns(int start, int end)
+    {
+      if(hiddenColumns==null)
+        hiddenColumns = new Vector();
+
+      boolean added = false;
+      boolean overlap = false;
+
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if ( start<=region[1] && end>=region[0])
+        {
+          hiddenColumns.removeElementAt(i);
+          overlap = true;
+          break;
+        }
+        else if (end < region[0] && start < region[0])
+        {
+          hiddenColumns.insertElementAt(new int[]
+                                        {start, end}, i);
+          added = true;
+          break;
+        }
+      }
+
+      if(overlap)
+      {
+         hideColumns(start, end);
+      }
+      else if (!added)
+        hiddenColumns.addElement(new int[] {start, end});
+
+    }
+
+    /**
+     * This method will find a range of selected columns
+     * around the column specified
+     * @param res int
+     */
+    public void hideColumns(int col)
+    {
+      // First find out range of columns to hide
+      int min = col, max = col+1;
+      while( contains(min) )
+      {  removeElement(min); min --;  }
+
+      while( contains(max) )
+      { removeElement(max);  max ++;  }
+
+      min++; max--;
+
+      hideColumns(min, max);
+    }
+
+    public void revealAllHiddenColumns()
+    {
+      if(hiddenColumns!=null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          for (int j = region[0]; j < region[1]+1; j++)
+          {
+            addElement(j);
+          }
+        }
+      }
+
+      hiddenColumns = null;
+    }
+
+    public void revealHiddenColumns(int res)
+    {
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( res == region[0])
+        {
+          for (int j = region[0]; j < region[1]+1; j++)
+          {
+            addElement(j);
+          }
+
+          hiddenColumns.removeElement(region);
+          break;
+        }
+      }
+      if(hiddenColumns.size()==0)
+        hiddenColumns = null;
+    }
+
+    public boolean isVisible(int column)
+    {
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( column >= region[0] && column <= region[1])
+        {
+          return false;
+        }
+      }
+      return true;
+    }
+    /**
+     * Copy constructor
+     * @param copy
+     */
+    public ColumnSelection(ColumnSelection copy) {
+      if (copy!=null) {
+        if (copy.selected!=null) {
+          selected = new Vector();
+          for (int i=0,j=copy.selected.size(); i<j; i++) {
+            selected.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
+          }
+        }
+        if (copy.hiddenColumns!=null) {
+          hiddenColumns=new Vector();
+          for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
+            int[] rh,cp;
+            rh = (int[])copy.hiddenColumns.elementAt(i);
+            if (rh!=null) {
+              cp = new int[rh.length];
+              System.arraycopy(rh, 0, cp, 0, rh.length);
+              hiddenColumns.setElementAt(cp, i);
+            }
+          }
+        }
+      }
+    }
+
+  /**
+   * ColumnSelection
+   */
+  public ColumnSelection()
+  {
+  }
+
+  public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) {
+    int i,iSize=seqs.length;
+    String selection[] = new String[iSize];
+    if (hiddenColumns!=null && hiddenColumns.size()>0)
+      {
+      for (i=0; i<iSize; i++) {
+        StringBuffer visibleSeq = new StringBuffer();
+        Vector regions = getHiddenColumns();
+
+        int blockStart = start, blockEnd=end;
+        int [] region;
+           int hideStart, hideEnd;
+
+           for (int j = 0; j < regions.size(); j++)
+           {
+             region = (int[]) regions.elementAt(j);
+             hideStart = region[0];
+             hideEnd = region[1];
+
+             if(hideStart < start)
+             {
+               continue;
+             }
+
+             blockStart = Math.min(blockStart, hideEnd+1);
+             blockEnd = Math.min(blockEnd, hideStart);
+
+             if(blockStart>blockEnd)
+             {
+                break;
+             }
+
+
+             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+             blockStart = hideEnd+1;
+             blockEnd = end;
+           }
+
+           if(end>blockStart)
+             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+           selection[i] = visibleSeq.toString();
+        }
+      }
+      else
+      {
+        for(i=0; i<iSize; i++)
+        {
+        selection[i] = seqs[i].getSequence(start, end);
+        }
+      }
+      
+    return selection;
+    }
+  
+}
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index dd01647..5edb65b 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,1431 +1,1411 @@
- /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * 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.
- *
- * 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
- */
-package jalview.gui;
-
-import jalview.analysis.*;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AlignViewport
-{
-    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 showConservation = true;
-    boolean showQuality = true;
-    boolean showIdentity = 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;
-    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 Vector vconsensus;
-    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;
-
-
-    public AlignViewport(AlignmentI al, boolean dataset)
-    {
-      isDataset = dataset;
-      setAlignment(al);
-      init();
-    }
-    /**
-     * 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);
-      showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
-
-      showQuality = Cache.getDefault("SHOW_QUALITY", true);
-      showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
-
-      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
-      padGaps = Cache.getDefault("PAD_GAPS", false);
-
-       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
-       String fontSize = Cache.getDefault("FONT_SIZE", "10");
-
-       int style = 0;
-
-       if (fontStyle.equals("bold"))
-       {
-         style = 1;
-       }
-       else if (fontStyle.equals("italic"))
-       {
-         style = 2;
-       }
-
-       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
-
-
-       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
-
-
-        // We must set conservation and consensus before setting colour,
-        // as Blosum and Clustal require this to be done
-        if(vconsensus==null && !isDataset)
-        {
-          updateConservation();
-          updateConsensus();
-        }
-
-        if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
-        {
-          globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
-
-            if (globalColourScheme instanceof UserColourScheme)
-            {
-                globalColourScheme = UserDefinedColours.loadDefaultColours();
-                ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
-            }
-
-            if (globalColourScheme != null)
-            {
-                globalColourScheme.setConsensus(vconsensus);
-            }
-        }
-    }
-
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowSequenceFeatures(boolean b)
-    {
-        showSequenceFeatures = b;
-    }
-
-    public boolean getShowSequenceFeatures()
-    {
-      return showSequenceFeatures;
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConservation()
-    {
-      if(alignment.isNucleotide())
-          return;
-
-      try{
-        Conservation cons = new jalview.analysis.Conservation("All",
-            jalview.schemes.ResidueProperties.propHash, 3,
-            alignment.getSequences(), 0, alignment.getWidth() - 1);
-        cons.calculate();
-        cons.verdict(false, ConsPercGaps);
-        cons.findQuality();
-
-        int alWidth = alignment.getWidth();
-        Annotation[] annotations = new Annotation[alWidth];
-        Annotation[] qannotations = new Annotation[alWidth];
-        String 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 = cons.qualityRange[0].floatValue();
-        float qmax = cons.qualityRange[1].floatValue();
-
-        for (int i = 0; i < alWidth; i++)
-        {
-          float value = 0;
-
-          try
-          {
-            value = Integer.parseInt(sequence.charAt(i) + "");
-          }
-          catch (Exception ex)
-          {
-            if (sequence.charAt(i) == '*')
-            {
-              value = 11;
-            }
-
-            if (sequence.charAt(i) == '+')
-            {
-              value = 10;
-            }
-          }
-
-          float vprop = value - min;
-          vprop /= max;
-          annotations[i] = new Annotation(sequence.charAt(i) + "",
-                                          String.valueOf(value), ' ', value,
-                                          new Color(minR + (maxR * vprop),
-              minG + (maxG * vprop),
-              minB + (maxB * vprop)));
-
-          // Quality calc
-          value = ( (Double) cons.quality.get(i)).floatValue();
-          vprop = value - qmin;
-          vprop /= qmax;
-          qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
-                                           value,
-                                           new Color(minR + (maxR * vprop),
-              minG + (maxG * vprop),
-              minB + (maxB * vprop)));
-        }
-
-        if (conservation == null)
-        {
-          conservation = new AlignmentAnnotation("Conservation",
-                                                 "Conservation of total alignment less than " +
-                                                 ConsPercGaps + "% gaps",
-                                                 annotations, 0f, // cons.qualityRange[0].floatValue(),
-                                                 11f, // cons.qualityRange[1].floatValue()
-                                                 AlignmentAnnotation.BAR_GRAPH);
-
-          if (showConservation)
-          {
-            alignment.addAnnotation(conservation);
-          }
-
-          quality = new AlignmentAnnotation("Quality",
-                                            "Alignment Quality based on Blosum62 scores",
-                                            qannotations,
-                                            cons.qualityRange[0].floatValue(),
-                                            cons.qualityRange[1].floatValue(),
-                                            AlignmentAnnotation.BAR_GRAPH);
-
-          if (showQuality)
-          {
-            alignment.addAnnotation(quality);
-          }
-        }
-        else
-        {
-          conservation.annotations = annotations;
-          quality.annotations = qannotations;
-          quality.graphMax = cons.qualityRange[1].floatValue();
-        }
-      }
-      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);
-          }
-        });
-
-        System.out.println("Conservation calculation: " + error);
-        System.gc();
-
-      }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConsensus()
-    {
-      try{
-        Annotation[] annotations = new Annotation[alignment.getWidth()];
-
-        // this routine prevents vconsensus becoming a new object each time
-        // consenus is calculated. Important for speed of Blosum62
-        // and PID colouring of alignment
-        if (vconsensus == null)
-        {
-          vconsensus = alignment.getAAFrequency();
-        }
-        else
-        {
-          Vector temp = alignment.getAAFrequency();
-          vconsensus.clear();
-
-          Enumeration e = temp.elements();
-
-          while (e.hasMoreElements())
-          {
-            vconsensus.add(e.nextElement());
-          }
-        }
-
-        Hashtable hash = null;
-
-        for (int i = 0; i < alignment.getWidth(); i++)
-        {
-          hash = (Hashtable) vconsensus.elementAt(i);
-
-          float value = 0;
-          if (ignoreGapsInConsensusCalculation)
-            value = ( (Float) hash.get("pid_nogaps")).floatValue();
-          else
-            value = ( (Float) hash.get("pid_gaps")).floatValue();
-
-          String maxRes = hash.get("maxResidue").toString();
-          String mouseOver = hash.get("maxResidue") + " ";
-
-          if (maxRes.length() > 1)
-          {
-            mouseOver = "[" + maxRes + "] ";
-            maxRes = "+";
-          }
-
-          mouseOver += ( (int) value + "%");
-          annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-        }
-
-        if (consensus == null)
-        {
-          consensus = new AlignmentAnnotation("Consensus", "PID",
-                                              annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
-
-          if (showIdentity)
-          {
-            alignment.addAnnotation(consensus);
-          }
-        }
-        else
-        {
-          consensus.annotations = annotations;
-        }
-
-        if (globalColourScheme != null)
-          globalColourScheme.setConsensus(vconsensus);
-
-      }catch(OutOfMemoryError error)
-      {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "Out of memory calc45ulating 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();
-      }
-
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceGroup getSelectionGroup()
-    {
-        return selectionGroup;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void setSelectionGroup(SequenceGroup sg)
-    {
-        selectionGroup = sg;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getConservationSelected()
-    {
-        return conservationColourSelected;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setConservationSelected(boolean b)
-    {
-        conservationColourSelected = b;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getAbovePIDThreshold()
-    {
-        return abovePIDThreshold;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setAbovePIDThreshold(boolean b)
-    {
-        abovePIDThreshold = b;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
-    {
-        return startRes;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
-    {
-        return endRes;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartSeq()
-    {
-        return startSeq;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     */
-    public void setGlobalColourScheme(ColourSchemeI cs)
-    {
-        globalColourScheme = cs;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColourSchemeI getGlobalColourScheme()
-    {
-        return globalColourScheme;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setStartRes(int res)
-    {
-        this.startRes = res;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setStartSeq(int seq)
-    {
-        this.startSeq = seq;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setEndRes(int res)
-    {
-        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;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setEndSeq(int seq)
-    {
-        if (seq > alignment.getHeight())
-        {
-            seq = alignment.getHeight();
-        }
-
-        if (seq < 0)
-        {
-            seq = 0;
-        }
-
-        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;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentI getAlignment()
-    {
-        return alignment;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param align DOCUMENT ME!
-     */
-    public void setAlignment(AlignmentI align)
-    {
-        this.alignment = align;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setWrapAlignment(boolean state)
-    {
-        wrapAlignment = state;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowText(boolean state)
-    {
-        showText = state;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setRenderGaps(boolean state)
-    {
-        renderGaps = state;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
-    {
-        return showColourText;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
-    {
-        showColourText = state;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowBoxes(boolean state)
-    {
-        showBoxes = state;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getWrapAlignment()
-    {
-        return wrapAlignment;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowText()
-    {
-        return showText;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowBoxes()
-    {
-        return showBoxes;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
-    {
-        return getAlignment().getGapCharacter();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gap DOCUMENT ME!
-     */
-    public void setGapCharacter(char gap)
-    {
-        if (getAlignment() != null)
-        {
-            getAlignment().setGapCharacter(gap);
-        }
-    }
-
-    /**
-     * 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)
-    {
-      ignoreGapsInConsensusCalculation = b;
-      updateConsensus();
-      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;
-    }
-
-
-    public void hideSelectedColumns()
-    {
-      if (colSel.size() < 1)
-        return;
-
-      colSel.hideSelectedColumns();
-      setSelectionGroup(null);
-
-      hasHiddenColumns = true;
-    }
-
-
-    public void hideColumns(int start, int end)
-    {
-      if(start==end)
-        colSel.hideColumns(start);
-      else
-        colSel.hideColumns(start, end);
-
-      hasHiddenColumns = true;
-    }
-
-    public void hideAllSelectedSeqs()
-    {
-      if (selectionGroup == null)
-        return;
-
-      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
-      for (int i = 0; i < seqs.length; i++)
-      {
-        alignment.getHiddenSequences().hideSequence(seqs[i]);
-      }
-      firePropertyChange("alignment", null, alignment.getSequences());
-      hasHiddenRows = true;
-      setSelectionGroup(null);
-    }
-
-    public void hideSequence(SequenceI seq)
-    {
-      if(seq!=null)
-      {
-        alignment.getHiddenSequences().hideSequence(seq);
-        hasHiddenRows = true;
-        firePropertyChange("alignment", null, alignment.getSequences());
-      }
-    }
-
-    public void showSequence(int index)
-    {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index);
-      if(tmp.size()>0)
-      {
-        if(selectionGroup==null)
-        {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
-        }
-
-        for (int t = 0; t < tmp.size(); t++)
-        {
-          selectionGroup.addSequence(
-              (SequenceI) tmp.elementAt(t), false
-              );
-        }
-        firePropertyChange("alignment", null, alignment.getSequences());
-      }
-
-      if(alignment.getHiddenSequences().getSize()<1)
-        hasHiddenRows = false;
-    }
-
-    public void showColumn(int col)
-    {
-      colSel.revealHiddenColumns(col);
-      if(colSel.getHiddenColumns()==null)
-        hasHiddenColumns = false;
-    }
-
-    public void showAllHiddenColumns()
-    {
-      colSel.revealAllHiddenColumns();
-      hasHiddenColumns = false;
-    }
-
-    public void showAllHiddenSeqs()
-    {
-      if(alignment.getHiddenSequences().getSize()>0)
-      {
-        if(selectionGroup==null)
-        {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
-        }
-        Vector tmp = alignment.getHiddenSequences().showAll();
-        for(int t=0; t<tmp.size(); t++)
-        {
-          selectionGroup.addSequence(
-              (SequenceI)tmp.elementAt(t), false
-              );
-        }
-        firePropertyChange("alignment", null, alignment.getSequences());
-        hasHiddenRows = false;
-      }
-    }
-
-    public void invertColumnSelection()
-    {
-      int column;
-      for(int i=0; i<alignment.getWidth(); i++)
-      {
-        column = i;
-
-        if(colSel.contains(column))
-          colSel.removeElement(column);
-        else
-          colSel.addElement(column);
-
-      }
-
-    }
-
-    public int adjustForHiddenSeqs(int alignmentIndex)
-    {
-      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
-    }
-
-    /**
-     * This method returns the a new SequenceI [] with
-     * the selection sequence and start and end points adjusted
-     * @return String[]
-     */
-    public SequenceI[] getSelectionAsNewSequence()
-    {
-      SequenceI[] sequences;
-
-      if (selectionGroup == null)
-        sequences = alignment.getSequencesArray();
-      else
-        sequences = selectionGroup.getSelectionAsNewSequences(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[]
-     */
-    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(false);
-        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;
-          }
-
-          if (hideStart>end)
-            break;
-
-          if (hideEnd>end)
-            hideEnd=end;
-
-          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);
-      } else {
-        selection.addOperation(CigarArray.M, end-start);
-      }
-      return selection;
-    }
-    /**
-     * 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)
-        return new AlignmentView(aligview);
-      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)
-    {
-      String [] selection = null;
-      SequenceI [] seqs= null;
-      int i, iSize;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
-      {
-        iSize = selectionGroup.getSize(false);
-        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];
-
-
-      for(i=0; i<iSize; i++)
-      {
-        if (hasHiddenColumns)
-        {
-             StringBuffer visibleSeq = new StringBuffer();
-             Vector regions = colSel.getHiddenColumns();
-
-             int blockStart = start, blockEnd=end;
-             int [] region;
-             int hideStart, hideEnd;
-
-             for (int j = 0; j < regions.size(); j++)
-             {
-               region = (int[]) regions.elementAt(j);
-               hideStart = region[0];
-               hideEnd = region[1];
-
-               if(hideStart < start)
-               {
-                 continue;
-               }
-
-               blockStart = Math.min(blockStart, hideEnd+1);
-               blockEnd = Math.min(blockEnd, hideStart);
-
-               if(blockStart>blockEnd)
-               {
-                  break;
-               }
-
-
-               visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
-               blockStart = hideEnd+1;
-               blockEnd = end;
-             }
-
-             if(end>blockStart)
-               visibleSeq.append(seqs[i].getSequence(blockStart, end));
-
-             selection[i] = visibleSeq.toString();
-        }
-        else
-        {
-          selection[i] = seqs[i].getSequence(start, end);
-        }
-      }
-
-      return selection;
-    }
-
-    public boolean getShowHiddenMarkers()
-    {
-      return showHiddenMarkers;
-    }
-
-    public void setShowHiddenMarkers(boolean show)
-    {
-      showHiddenMarkers = show;
-    }
-}
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
+ * 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.
+ *
+ * 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
+ */
+package jalview.gui;
+
+import jalview.analysis.*;
+
+import jalview.bin.*;
+
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
+
+import java.awt.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignViewport
+{
+    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 showConservation = true;
+    boolean showQuality = true;
+    boolean showIdentity = 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;
+    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 Vector vconsensus;
+    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;
+
+
+    public AlignViewport(AlignmentI al, boolean dataset)
+    {
+      isDataset = dataset;
+      setAlignment(al);
+      init();
+    }
+    /**
+     * 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);
+      showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+
+      showQuality = Cache.getDefault("SHOW_QUALITY", true);
+      showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
+
+      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+      padGaps = Cache.getDefault("PAD_GAPS", false);
+
+       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
+       String fontSize = Cache.getDefault("FONT_SIZE", "10");
+
+       int style = 0;
+
+       if (fontStyle.equals("bold"))
+       {
+         style = 1;
+       }
+       else if (fontStyle.equals("italic"))
+       {
+         style = 2;
+       }
+
+       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+
+
+       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
+
+
+        // We must set conservation and consensus before setting colour,
+        // as Blosum and Clustal require this to be done
+        if(vconsensus==null && !isDataset)
+        {
+          updateConservation();
+          updateConsensus();
+        }
+
+        if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+        {
+          globalColourScheme = ColourSchemeProperty.getColour(alignment,
+              jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+
+            if (globalColourScheme instanceof UserColourScheme)
+            {
+                globalColourScheme = UserDefinedColours.loadDefaultColours();
+                ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
+            }
+
+            if (globalColourScheme != null)
+            {
+                globalColourScheme.setConsensus(vconsensus);
+            }
+        }
+    }
+
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setShowSequenceFeatures(boolean b)
+    {
+        showSequenceFeatures = b;
+    }
+
+    public boolean getShowSequenceFeatures()
+    {
+      return showSequenceFeatures;
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void updateConservation()
+    {
+      if(alignment.isNucleotide())
+          return;
+
+      try{
+        Conservation cons = new jalview.analysis.Conservation("All",
+            jalview.schemes.ResidueProperties.propHash, 3,
+            alignment.getSequences(), 0, alignment.getWidth() - 1);
+        cons.calculate();
+        cons.verdict(false, ConsPercGaps);
+        cons.findQuality();
+
+        int alWidth = alignment.getWidth();
+        Annotation[] annotations = new Annotation[alWidth];
+        Annotation[] qannotations = new Annotation[alWidth];
+        String 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 = cons.qualityRange[0].floatValue();
+        float qmax = cons.qualityRange[1].floatValue();
+
+        for (int i = 0; i < alWidth; i++)
+        {
+          float value = 0;
+
+          try
+          {
+            value = Integer.parseInt(sequence.charAt(i) + "");
+          }
+          catch (Exception ex)
+          {
+            if (sequence.charAt(i) == '*')
+            {
+              value = 11;
+            }
+
+            if (sequence.charAt(i) == '+')
+            {
+              value = 10;
+            }
+          }
+
+          float vprop = value - min;
+          vprop /= max;
+          annotations[i] = new Annotation(sequence.charAt(i) + "",
+                                          String.valueOf(value), ' ', value,
+                                          new Color(minR + (maxR * vprop),
+              minG + (maxG * vprop),
+              minB + (maxB * vprop)));
+
+          // Quality calc
+          value = ( (Double) cons.quality.get(i)).floatValue();
+          vprop = value - qmin;
+          vprop /= qmax;
+          qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
+                                           value,
+                                           new Color(minR + (maxR * vprop),
+              minG + (maxG * vprop),
+              minB + (maxB * vprop)));
+        }
+
+        if (conservation == null)
+        {
+          conservation = new AlignmentAnnotation("Conservation",
+                                                 "Conservation of total alignment less than " +
+                                                 ConsPercGaps + "% gaps",
+                                                 annotations, 0f, // cons.qualityRange[0].floatValue(),
+                                                 11f, // cons.qualityRange[1].floatValue()
+                                                 AlignmentAnnotation.BAR_GRAPH);
+
+          if (showConservation)
+          {
+            alignment.addAnnotation(conservation);
+          }
+
+          quality = new AlignmentAnnotation("Quality",
+                                            "Alignment Quality based on Blosum62 scores",
+                                            qannotations,
+                                            cons.qualityRange[0].floatValue(),
+                                            cons.qualityRange[1].floatValue(),
+                                            AlignmentAnnotation.BAR_GRAPH);
+
+          if (showQuality)
+          {
+            alignment.addAnnotation(quality);
+          }
+        }
+        else
+        {
+          conservation.annotations = annotations;
+          quality.annotations = qannotations;
+          quality.graphMax = cons.qualityRange[1].floatValue();
+        }
+      }
+      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);
+          }
+        });
+
+        System.out.println("Conservation calculation: " + error);
+        System.gc();
+
+      }
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void updateConsensus()
+    {
+      try{
+        Annotation[] annotations = new Annotation[alignment.getWidth()];
+
+        // this routine prevents vconsensus becoming a new object each time
+        // consenus is calculated. Important for speed of Blosum62
+        // and PID colouring of alignment
+        if (vconsensus == null)
+        {
+          vconsensus = alignment.getAAFrequency();
+        }
+        else
+        {
+          Vector temp = alignment.getAAFrequency();
+          vconsensus.clear();
+
+          Enumeration e = temp.elements();
+
+          while (e.hasMoreElements())
+          {
+            vconsensus.add(e.nextElement());
+          }
+        }
+
+        Hashtable hash = null;
+
+        for (int i = 0; i < alignment.getWidth(); i++)
+        {
+          hash = (Hashtable) vconsensus.elementAt(i);
+
+          float value = 0;
+          if (ignoreGapsInConsensusCalculation)
+            value = ( (Float) hash.get("pid_nogaps")).floatValue();
+          else
+            value = ( (Float) hash.get("pid_gaps")).floatValue();
+
+          String maxRes = hash.get("maxResidue").toString();
+          String mouseOver = hash.get("maxResidue") + " ";
+
+          if (maxRes.length() > 1)
+          {
+            mouseOver = "[" + maxRes + "] ";
+            maxRes = "+";
+          }
+
+          mouseOver += ( (int) value + "%");
+          annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+        }
+
+        if (consensus == null)
+        {
+          consensus = new AlignmentAnnotation("Consensus", "PID",
+                                              annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
+
+          if (showIdentity)
+          {
+            alignment.addAnnotation(consensus);
+          }
+        }
+        else
+        {
+          consensus.annotations = annotations;
+        }
+
+        if (globalColourScheme != null)
+          globalColourScheme.setConsensus(vconsensus);
+
+      }catch(OutOfMemoryError error)
+      {
+        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();
+      }
+
+    }
+    /**
+     * 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();
+      if (consensus==null)
+        return null;
+      StringBuffer seqs=new StringBuffer();
+      for (int i=0; i<consensus.annotations.length; i++) {
+        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);          
+        }
+      }
+      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;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void setSelectionGroup(SequenceGroup sg)
+    {
+        selectionGroup = sg;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getConservationSelected()
+    {
+        return conservationColourSelected;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setConservationSelected(boolean b)
+    {
+        conservationColourSelected = b;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getAbovePIDThreshold()
+    {
+        return abovePIDThreshold;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAbovePIDThreshold(boolean b)
+    {
+        abovePIDThreshold = b;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartRes()
+    {
+        return startRes;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndRes()
+    {
+        return endRes;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartSeq()
+    {
+        return startSeq;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     */
+    public void setGlobalColourScheme(ColourSchemeI cs)
+    {
+        globalColourScheme = cs;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public ColourSchemeI getGlobalColourScheme()
+    {
+        return globalColourScheme;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     */
+    public void setStartRes(int res)
+    {
+        this.startRes = res;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setStartSeq(int seq)
+    {
+        this.startSeq = seq;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     */
+    public void setEndRes(int res)
+    {
+        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;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setEndSeq(int seq)
+    {
+        if (seq > alignment.getHeight())
+        {
+            seq = alignment.getHeight();
+        }
+
+        if (seq < 0)
+        {
+            seq = 0;
+        }
+
+        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;
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public AlignmentI getAlignment()
+    {
+        return alignment;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param align DOCUMENT ME!
+     */
+    public void setAlignment(AlignmentI align)
+    {
+        this.alignment = align;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setWrapAlignment(boolean state)
+    {
+        wrapAlignment = state;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowText(boolean state)
+    {
+        showText = state;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setRenderGaps(boolean state)
+    {
+        renderGaps = state;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getColourText()
+    {
+        return showColourText;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setColourText(boolean state)
+    {
+        showColourText = state;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowBoxes(boolean state)
+    {
+        showBoxes = state;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getWrapAlignment()
+    {
+        return wrapAlignment;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowText()
+    {
+        return showText;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowBoxes()
+    {
+        return showBoxes;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getGapCharacter()
+    {
+        return getAlignment().getGapCharacter();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gap DOCUMENT ME!
+     */
+    public void setGapCharacter(char gap)
+    {
+        if (getAlignment() != null)
+        {
+            getAlignment().setGapCharacter(gap);
+        }
+    }
+
+    /**
+     * 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)
+    {
+      ignoreGapsInConsensusCalculation = b;
+      updateConsensus();
+      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;
+    }
+
+
+    public void hideSelectedColumns()
+    {
+      if (colSel.size() < 1)
+        return;
+
+      colSel.hideSelectedColumns();
+      setSelectionGroup(null);
+
+      hasHiddenColumns = true;
+    }
+
+
+    public void hideColumns(int start, int end)
+    {
+      if(start==end)
+        colSel.hideColumns(start);
+      else
+        colSel.hideColumns(start, end);
+
+      hasHiddenColumns = true;
+    }
+
+    public void hideAllSelectedSeqs()
+    {
+      if (selectionGroup == null)
+        return;
+
+      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+
+      for (int i = 0; i < seqs.length; i++)
+      {
+        alignment.getHiddenSequences().hideSequence(seqs[i]);
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      hasHiddenRows = true;
+      setSelectionGroup(null);
+    }
+
+    public void hideSequence(SequenceI seq)
+    {
+      if(seq!=null)
+      {
+        alignment.getHiddenSequences().hideSequence(seq);
+        hasHiddenRows = true;
+        firePropertyChange("alignment", null, alignment.getSequences());
+      }
+    }
+
+    public void showSequence(int index)
+    {
+      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      if(tmp.size()>0)
+      {
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
+
+        for (int t = 0; t < tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI) tmp.elementAt(t), false
+              );
+        }
+        firePropertyChange("alignment", null, alignment.getSequences());
+      }
+
+      if(alignment.getHiddenSequences().getSize()<1)
+        hasHiddenRows = false;
+    }
+
+    public void showColumn(int col)
+    {
+      colSel.revealHiddenColumns(col);
+      if(colSel.getHiddenColumns()==null)
+        hasHiddenColumns = false;
+    }
+
+    public void showAllHiddenColumns()
+    {
+      colSel.revealAllHiddenColumns();
+      hasHiddenColumns = false;
+    }
+
+    public void showAllHiddenSeqs()
+    {
+      if(alignment.getHiddenSequences().getSize()>0)
+      {
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
+        Vector tmp = alignment.getHiddenSequences().showAll();
+        for(int t=0; t<tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI)tmp.elementAt(t), false
+              );
+        }
+        firePropertyChange("alignment", null, alignment.getSequences());
+        hasHiddenRows = false;
+      }
+    }
+
+    public void invertColumnSelection()
+    {
+      int column;
+      for(int i=0; i<alignment.getWidth(); i++)
+      {
+        column = i;
+
+        if(colSel.contains(column))
+          colSel.removeElement(column);
+        else
+          colSel.addElement(column);
+
+      }
+
+    }
+
+    public int adjustForHiddenSeqs(int alignmentIndex)
+    {
+      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+    }
+
+    /**
+     * This method returns the a new SequenceI [] with
+     * the selection sequence and start and end points adjusted
+     * @return String[]
+     */
+    public SequenceI[] getSelectionAsNewSequence()
+    {
+      SequenceI[] sequences;
+
+      if (selectionGroup == null)
+        sequences = alignment.getSequencesArray();
+      else
+        sequences = selectionGroup.getSelectionAsNewSequences(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[]
+     */
+    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(false);
+        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;
+          }
+
+          if (hideStart>end)
+            break;
+
+          if (hideEnd>end)
+            hideEnd=end;
+
+          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);
+      } else {
+        selection.addOperation(CigarArray.M, end-start);
+      }
+      return selection;
+    }
+    /**
+     * 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)
+        return new AlignmentView(aligview);
+      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)
+    {
+      String [] selection = null;
+      SequenceI [] seqs= null;
+      int i, iSize;
+      int start = 0, end = 0;
+      if(selectedRegionOnly && selectionGroup!=null)
+      {
+        iSize = selectionGroup.getSize(false);
+        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) {
+        selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+      } else {
+        for(i=0; i<iSize; i++)
+        {
+          selection[i] = seqs[i].getSequence(start, end);
+        }
+        
+      }
+      return selection;
+    }
+
+    public boolean getShowHiddenMarkers()
+    {
+      return showHiddenMarkers;
+    }
+
+    public void setShowHiddenMarkers(boolean show)
+    {
+      showHiddenMarkers = show;
+    }
+}
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index c537550..63d7c53 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,543 +1,602 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * 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.
- *
- * 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
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AnnotationLabels extends JPanel implements MouseListener,
-    MouseMotionListener, ActionListener
-{
-    static String ADDNEW = "Add New Row";
-    static String HIDE = "Hide This Row";
-    static String DELETE = "Delete This Row";
-    static String SHOWALL = "Show All Hidden Rows";
-    static String OUTPUT_TEXT = "Export Annotation";
-    boolean resizePanel = false;
-    Image image;
-    AlignmentPanel ap;
-    AlignViewport av;
-    boolean resizing = false;
-    MouseEvent dragEvent;
-    int oldY;
-    int selectedRow;
-    int scrollOffset = 0;
-    Font font = new Font("Arial", Font.PLAIN, 11);
-
-
-    /**
-     * Creates a new AnnotationLabels object.
-     *
-     * @param ap DOCUMENT ME!
-     */
-    public AnnotationLabels(AlignmentPanel ap)
-    {
-        this.ap = ap;
-        av = ap.av;
-
-        java.net.URL url = getClass().getResource("/images/idwidth.gif");
-        Image temp = null;
-
-        if (url != null)
-        {
-            temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        }
-
-        try
-        {
-            MediaTracker mt = new MediaTracker(this);
-            mt.addImage(temp, 0);
-            mt.waitForID(0);
-        }
-        catch (Exception ex)
-        {
-        }
-
-        BufferedImage bi = new BufferedImage(temp.getHeight(this),
-                temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
-        Graphics2D g = (Graphics2D) bi.getGraphics();
-        g.rotate(Math.toRadians(90));
-        g.drawImage(temp, 0, -bi.getWidth(this), this);
-        image = (Image) bi;
-
-        addMouseListener(this);
-        addMouseMotionListener(this);
-    }
-
-    public AnnotationLabels(AlignViewport av)
-    {
-      this.av = av;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param y DOCUMENT ME!
-     */
-    public void setScrollOffset(int y)
-    {
-        scrollOffset = y;
-        repaint();
-    }
-
-    void getSelectedRow(int y)
-    {
-      int height = 0;
-      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-      if(aa!=null)
-      {
-        for (int i = 0; i < aa.length; i++)
-        {
-          if (!aa[i].visible)
-          {
-            continue;
-          }
-
-          height += aa[i].height;
-
-          if (y < height)
-          {
-            selectedRow = i;
-
-            break;
-          }
-        }
-      }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void actionPerformed(ActionEvent evt)
-    {
-        int dif = 0;
-        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-        if (evt.getActionCommand().equals(ADDNEW))
-        {
-            String label = JOptionPane.showInputDialog(this,
-                    "Label for annotation");
-
-            if (label == null)
-            {
-                label = "";
-            }
-
-            AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,
-                    "New description",
-                    new Annotation[ap.av.alignment.getWidth()]);
-
-            ap.av.alignment.addAnnotation(newAnnotation);
-            ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
-            if (aa != null)
-              dif = aa[aa.length - 1].height;
-        }
-        else if (evt.getActionCommand().equals(HIDE))
-        {
-            aa[selectedRow].visible = false;
-
-            if (aa[selectedRow].label.equals("Conservation"))
-            {
-                ap.av.showConservation = false;
-            }
-
-            if (aa[selectedRow].label.equals("Quality"))
-            {
-                ap.av.showQuality = false;
-            }
-
-            if (aa[selectedRow].label.equals("Consensus"))
-            {
-                ap.av.showIdentity = false;
-            }
-
-            dif = aa[selectedRow].height * -1;
-        }
-        else if (evt.getActionCommand().equals(DELETE))
-        {
-            ap.av.alignment.deleteAnnotation(aa[selectedRow]);
-            dif = aa[selectedRow].height * -1;
-        }
-        else if (evt.getActionCommand().equals(SHOWALL))
-        {
-            for (int i = 0; i < aa.length; i++)
-            {
-                if (!aa[i].visible)
-                {
-                    dif += aa[i].height;
-                    aa[i].visible = true;
-                }
-            }
-        }
-        else if (evt.getActionCommand().equals(OUTPUT_TEXT))
-        {
-          new AnnotationExporter().exportAnnotations(
-              ap,
-              new AlignmentAnnotation[]
-              {aa[selectedRow]}
-              );
-        }
-
-
-        ap.annotationPanel.adjustPanelHeight();
-        ap.annotationScroller.validate();
-        ap.repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
-    {
-        getSelectedRow(evt.getY() - scrollOffset);
-        oldY = evt.getY();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
-    {
-        int start = selectedRow;
-        getSelectedRow(evt.getY() - scrollOffset);
-        int end = selectedRow;
-
-        if(start!=end)
-        {
-          //Swap these annotations
-          AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
-          AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
-
-
-          ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
-          ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
-        }
-
-        resizePanel = false;
-        dragEvent = null;
-        repaint();
-        ap.annotationPanel.repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent evt)
-    {
-      if(evt.getY()<10)
-      {
-        resizePanel = true;
-        repaint();
-      }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseExited(MouseEvent evt)
-    {
-      if(dragEvent == null)
-      {
-        resizePanel = false;
-        repaint();
-      }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
-    {
-      dragEvent = evt;
-
-      if (resizePanel)
-      {
-        Dimension d = ap.annotationScroller.getPreferredSize();
-        int dif = evt.getY() - oldY;
-
-        dif /= ap.av.charHeight;
-        dif *= ap.av.charHeight;
-
-        if ( (d.height - dif) > 20)
-        {
-          ap.annotationScroller.setPreferredSize(new Dimension(d.width,
-              d.height - dif));
-          d = ap.annotationSpaceFillerHolder.getPreferredSize();
-          ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-              d.width, d.height - dif));
-          ap.repaint();
-        }
-
-        ap.addNotify();
-      }
-      else
-        repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseMoved(MouseEvent evt)
-    {
-      resizePanel = evt.getY()<10;
-
-      repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent evt)
-    {
-       if(!SwingUtilities.isRightMouseButton(evt))
-         return;
-
-        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-        if ((aa == null) || (aa.length == 0))
-        {
-            JPopupMenu pop = new JPopupMenu("Annotations");
-            JMenuItem item = new JMenuItem(ADDNEW);
-            item.addActionListener(this);
-            pop.add(item);
-            pop.show(this, evt.getX(), evt.getY());
-
-            return;
-        }
-
-
-        JPopupMenu pop = new JPopupMenu("Annotations");
-        JMenuItem item = new JMenuItem(ADDNEW);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(HIDE);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(DELETE);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(SHOWALL);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(OUTPUT_TEXT);
-        item.addActionListener(this);
-        pop.add(item);
-
-        if (aa[selectedRow].label.equals("Consensus"))
-        {
-          pop.addSeparator();
-          final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-              "Ignore Gaps In Consensus",
-              ap.av.getIgnoreGapsConsensus());
-          cbmi.addActionListener(new ActionListener()
-              {public void actionPerformed(ActionEvent e)
-               {
-                 ap.av.setIgnoreGapsConsensus(cbmi.getState());
-                 ap.repaint();
-               }
-              });
-          pop.add(cbmi);
-
-        }
-
-        pop.show(this, evt.getX(), evt.getY());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g1 DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
-    {
-
-        int width = getWidth();
-        if(width==0)
-         width = ap.calculateIdWidth().width + 4;
-
-       Graphics2D g2 = (Graphics2D) g;
-       if(av.antiAlias)
-        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-            RenderingHints.VALUE_ANTIALIAS_ON);
-
-       drawComponent(g2, width);
-
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void drawComponent(Graphics g, int width)
-    {
-        if(av.getFont().getSize()<10)
-          g.setFont(font);
-        else
-          g.setFont(av.getFont());
-
-        FontMetrics fm = g.getFontMetrics(g.getFont());
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
-
-        g.translate(0, scrollOffset);
-        g.setColor(Color.black);
-
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-        int fontHeight = g.getFont().getSize();
-        int y = fontHeight;
-        int x = 0;
-        int graphExtras = 0;
-
-
-
-        if (aa != null)
-        {
-            for (int i = 0; i < aa.length; i++)
-            {
-                if (!aa[i].visible)
-                {
-                    continue;
-                }
-
-                x = width - fm.stringWidth(aa[i].label) - 3;
-
-                if (aa[i].graph>0 && aa[i].graphHeight>0)
-                {
-                    graphExtras = y;
-
-                    y += (aa[i].height / 3);
-
-                    if(aa[i].graphGroup<0)
-                        graphExtras = y + fontHeight;
-                }
-
-                if(aa[i].graphGroup>-1)
-                {
-                  int groupSize = 0;
-                  for (int gg = 0; gg < aa.length; gg++)
-                  {
-                    if (aa[gg].graphGroup == aa[i].graphGroup)
-                      groupSize++;
-                  }
-
-                  if(groupSize * (fontHeight+8) < aa[i].height)
-                    graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;
-
-                 for(int gg=0; gg<aa.length; gg++)
-                 {
-                   if(aa[gg].graphGroup==aa[i].graphGroup)
-                   {
-                     x = width - fm.stringWidth(aa[gg].label) - 3;
-                     g.drawString(aa[gg].label, x, graphExtras );
-                     if(aa[gg].annotations[0]!=null)
-                       g.setColor(aa[gg].annotations[0].colour);
-
-                     g.drawLine( x, graphExtras+3,
-                                 x+fm.stringWidth(aa[gg].label),
-                                 graphExtras+3);
-
-                     g.setColor(Color.black);
-                     graphExtras += fontHeight+8;
-                   }
-                 }
-                }
-                else
-                  g.drawString(aa[i].label, x, y);
-
-                if (aa[i].graph>0)
-                {
-                /*  if (aa[i].graphLines != null)
-                  {
-                    for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
-                    {
-                       x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
-                      g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
-                      g.setColor(aa[i].getGraphLine(gl).colour);
-                      Graphics2D g2 = (Graphics2D) g;
-                      g2.setStroke(new BasicStroke(1,
-                          BasicStroke.CAP_SQUARE,
-                          BasicStroke.JOIN_ROUND, 3f,
-                          new float[]
-                          {5f, 3f}, 0f));
-
-                      graphExtras += 3;
-
-                      g.drawLine(x, graphExtras,
-                                 x+fm.stringWidth(aa[i].label),
-                                 graphExtras);
-                      g2.setStroke(new BasicStroke());
-                    }
-                  }*/
-                    y += ((2 * aa[i].height) / 3);
-                }
-                else
-                {
-                    y += aa[i].height;
-                }
-            }
-        }
-
-        if (resizePanel)
-        {
-          g.drawImage(image, 2, 0 - scrollOffset, this);
-        }
-        else if (dragEvent != null && aa!=null)
-        {
-          g.setColor(Color.lightGray);
-          g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
-        }
-
-
-        if ((aa == null) || (aa.length < 1))
-        {
-            g.drawString("Right click", 2, 8);
-            g.drawString("to add annotation", 2, 18);
-        }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
+ * 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.
+ *
+ * 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
+ */
+package jalview.gui;
+
+import jalview.datamodel.*;
+import jalview.io.FormatAdapter;
+
+import java.awt.*;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.*;
+import java.awt.image.*;
+import java.util.Vector;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationLabels extends JPanel implements MouseListener,
+    MouseMotionListener, ActionListener
+{
+    static String ADDNEW = "Add New Row";
+    static String HIDE = "Hide This Row";
+    static String DELETE = "Delete This Row";
+    static String SHOWALL = "Show All Hidden Rows";
+    static String OUTPUT_TEXT = "Export Annotation";
+    static String COPYCONS_SEQ = "Copy Consensus Sequence";
+    boolean resizePanel = false;
+    Image image;
+    AlignmentPanel ap;
+    AlignViewport av;
+    boolean resizing = false;
+    MouseEvent dragEvent;
+    int oldY;
+    int selectedRow;
+    int scrollOffset = 0;
+    Font font = new Font("Arial", Font.PLAIN, 11);
+
+
+    /**
+     * Creates a new AnnotationLabels object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public AnnotationLabels(AlignmentPanel ap)
+    {
+        this.ap = ap;
+        av = ap.av;
+
+        java.net.URL url = getClass().getResource("/images/idwidth.gif");
+        Image temp = null;
+
+        if (url != null)
+        {
+            temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+        }
+
+        try
+        {
+            MediaTracker mt = new MediaTracker(this);
+            mt.addImage(temp, 0);
+            mt.waitForID(0);
+        }
+        catch (Exception ex)
+        {
+        }
+
+        BufferedImage bi = new BufferedImage(temp.getHeight(this),
+                temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
+        Graphics2D g = (Graphics2D) bi.getGraphics();
+        g.rotate(Math.toRadians(90));
+        g.drawImage(temp, 0, -bi.getWidth(this), this);
+        image = (Image) bi;
+
+        addMouseListener(this);
+        addMouseMotionListener(this);
+    }
+
+    public AnnotationLabels(AlignViewport av)
+    {
+      this.av = av;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param y DOCUMENT ME!
+     */
+    public void setScrollOffset(int y)
+    {
+        scrollOffset = y;
+        repaint();
+    }
+
+    void getSelectedRow(int y)
+    {
+      int height = 0;
+      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+      if(aa!=null)
+      {
+        for (int i = 0; i < aa.length; i++)
+        {
+          if (!aa[i].visible)
+          {
+            continue;
+          }
+
+          height += aa[i].height;
+
+          if (y < height)
+          {
+            selectedRow = i;
+
+            break;
+          }
+        }
+      }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void actionPerformed(ActionEvent evt)
+    {
+        int dif = 0;
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+        if (evt.getActionCommand().equals(ADDNEW))
+        {
+            String label = JOptionPane.showInputDialog(this,
+                    "Label for annotation");
+
+            if (label == null)
+            {
+                label = "";
+            }
+
+            AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,
+                    "New description",
+                    new Annotation[ap.av.alignment.getWidth()]);
+
+            ap.av.alignment.addAnnotation(newAnnotation);
+            ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+            if (aa != null)
+              dif = aa[aa.length - 1].height;
+        }
+        else if (evt.getActionCommand().equals(HIDE))
+        {
+            aa[selectedRow].visible = false;
+
+            if (aa[selectedRow].label.equals("Conservation"))
+            {
+                ap.av.showConservation = false;
+            }
+
+            if (aa[selectedRow].label.equals("Quality"))
+            {
+                ap.av.showQuality = false;
+            }
+
+            if (aa[selectedRow].label.equals("Consensus"))
+            {
+                ap.av.showIdentity = false;
+            }
+
+            dif = aa[selectedRow].height * -1;
+        }
+        else if (evt.getActionCommand().equals(DELETE))
+        {
+            ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+            dif = aa[selectedRow].height * -1;
+        }
+        else if (evt.getActionCommand().equals(SHOWALL))
+        {
+            for (int i = 0; i < aa.length; i++)
+            {
+                if (!aa[i].visible)
+                {
+                    dif += aa[i].height;
+                    aa[i].visible = true;
+                }
+            }
+        }
+        else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+        {
+          new AnnotationExporter().exportAnnotations(
+              ap,
+              new AlignmentAnnotation[]
+              {aa[selectedRow]}
+              );
+        }
+        else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+        {
+          SequenceI cons=av.getConsensusSeq();
+          if (cons!=null)
+            copy_annotseqtoclipboard(cons);
+          
+        }
+
+        ap.annotationPanel.adjustPanelHeight();
+        ap.annotationScroller.validate();
+        ap.repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
+    {
+        getSelectedRow(evt.getY() - scrollOffset);
+        oldY = evt.getY();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
+    {
+        int start = selectedRow;
+        getSelectedRow(evt.getY() - scrollOffset);
+        int end = selectedRow;
+
+        if(start!=end)
+        {
+          //Swap these annotations
+          AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
+          AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+
+
+          ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
+          ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+        }
+
+        resizePanel = false;
+        dragEvent = null;
+        repaint();
+        ap.annotationPanel.repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
+    {
+      if(evt.getY()<10)
+      {
+        resizePanel = true;
+        repaint();
+      }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
+    {
+      if(dragEvent == null)
+      {
+        resizePanel = false;
+        repaint();
+      }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
+    {
+      dragEvent = evt;
+
+      if (resizePanel)
+      {
+        Dimension d = ap.annotationScroller.getPreferredSize();
+        int dif = evt.getY() - oldY;
+
+        dif /= ap.av.charHeight;
+        dif *= ap.av.charHeight;
+
+        if ( (d.height - dif) > 20)
+        {
+          ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+              d.height - dif));
+          d = ap.annotationSpaceFillerHolder.getPreferredSize();
+          ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+              d.width, d.height - dif));
+          ap.repaint();
+        }
+
+        ap.addNotify();
+      }
+      else
+        repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
+    {
+      resizePanel = evt.getY()<10;
+
+      repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
+    {
+       if(!SwingUtilities.isRightMouseButton(evt))
+         return;
+
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+        if ((aa == null) || (aa.length == 0))
+        {
+            JPopupMenu pop = new JPopupMenu("Annotations");
+            JMenuItem item = new JMenuItem(ADDNEW);
+            item.addActionListener(this);
+            pop.add(item);
+            pop.show(this, evt.getX(), evt.getY());
+
+            return;
+        }
+
+
+        JPopupMenu pop = new JPopupMenu("Annotations");
+        JMenuItem item = new JMenuItem(ADDNEW);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(HIDE);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(DELETE);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(SHOWALL);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(OUTPUT_TEXT);
+        item.addActionListener(this);
+        pop.add(item);
+        // annotation object should be typed
+        if (aa[selectedRow].label.equals("Consensus"))
+        {
+          pop.addSeparator();
+          final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+              "Ignore Gaps In Consensus",
+              ap.av.getIgnoreGapsConsensus());
+          cbmi.addActionListener(new ActionListener()
+              {public void actionPerformed(ActionEvent e)
+               {
+                 ap.av.setIgnoreGapsConsensus(cbmi.getState());
+                 ap.repaint();
+               }
+              });
+          pop.add(cbmi);
+          final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+          consclipbrd.addActionListener(this);
+          pop.add(consclipbrd);
+        }
+
+        pop.show(this, evt.getX(), evt.getY());
+    }
+    /**
+     * do a single sequence copy to jalview and the system clipboard
+     *
+     * @param sq sequence to be copied to clipboard
+     */
+    protected void copy_annotseqtoclipboard(SequenceI sq)
+    {
+      SequenceI [] seqs = new SequenceI[] { sq };
+      String[] omitHidden = null;
+      SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()};
+      if (dseqs[0]==null) {
+        dseqs[0] = new Sequence(sq);
+        dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sq.getSequence()));
+        sq.setDatasetSequence(dseqs[0]);
+      }
+      Alignment ds=new Alignment(dseqs);
+      if (av.hasHiddenColumns)
+      {
+        omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs);
+      }
+
+      String output = new FormatAdapter().formatSequences(
+          "Fasta",
+          seqs,
+          omitHidden);
+
+
+      Toolkit.getDefaultToolkit().getSystemClipboard()
+          .setContents(new StringSelection(output), Desktop.instance);
+
+      Vector hiddenColumns = null;
+      if(av.hasHiddenColumns)
+      {
+        hiddenColumns =new Vector();
+        for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
+        {
+          int[] region = (int[])
+              av.getColumnSelection().getHiddenColumns().elementAt(i);
+
+          hiddenColumns.addElement(new int[]{region[0],
+                            region[1]});
+        }
+      }
+      
+      Desktop.jalviewClipboard = new Object[]{ seqs,
+          ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
+          hiddenColumns};
+    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g1 DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
+    {
+
+        int width = getWidth();
+        if(width==0)
+         width = ap.calculateIdWidth().width + 4;
+
+       Graphics2D g2 = (Graphics2D) g;
+       if(av.antiAlias)
+        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
+
+       drawComponent(g2, width);
+
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void drawComponent(Graphics g, int width)
+    {
+        if(av.getFont().getSize()<10)
+          g.setFont(font);
+        else
+          g.setFont(av.getFont());
+
+        FontMetrics fm = g.getFontMetrics(g.getFont());
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
+
+        g.translate(0, scrollOffset);
+        g.setColor(Color.black);
+
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        int fontHeight = g.getFont().getSize();
+        int y = fontHeight;
+        int x = 0;
+        int graphExtras = 0;
+
+
+
+        if (aa != null)
+        {
+            for (int i = 0; i < aa.length; i++)
+            {
+                if (!aa[i].visible)
+                {
+                    continue;
+                }
+
+                x = width - fm.stringWidth(aa[i].label) - 3;
+
+                if (aa[i].graph>0 && aa[i].graphHeight>0)
+                {
+                    graphExtras = y;
+
+                    y += (aa[i].height / 3);
+
+                    if(aa[i].graphGroup<0)
+                        graphExtras = y + fontHeight;
+                }
+
+                if(aa[i].graphGroup>-1)
+                {
+                  int groupSize = 0;
+                  for (int gg = 0; gg < aa.length; gg++)
+                  {
+                    if (aa[gg].graphGroup == aa[i].graphGroup)
+                      groupSize++;
+                  }
+
+                  if(groupSize * (fontHeight+8) < aa[i].height)
+                    graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;
+
+                 for(int gg=0; gg<aa.length; gg++)
+                 {
+                   if(aa[gg].graphGroup==aa[i].graphGroup)
+                   {
+                     x = width - fm.stringWidth(aa[gg].label) - 3;
+                     g.drawString(aa[gg].label, x, graphExtras );
+                     if(aa[gg].annotations[0]!=null)
+                       g.setColor(aa[gg].annotations[0].colour);
+
+                     g.drawLine( x, graphExtras+3,
+                                 x+fm.stringWidth(aa[gg].label),
+                                 graphExtras+3);
+
+                     g.setColor(Color.black);
+                     graphExtras += fontHeight+8;
+                   }
+                 }
+                }
+                else
+                  g.drawString(aa[i].label, x, y);
+
+                if (aa[i].graph>0)
+                {
+                /*  if (aa[i].graphLines != null)
+                  {
+                    for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
+                    {
+                       x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
+                      g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
+                      g.setColor(aa[i].getGraphLine(gl).colour);
+                      Graphics2D g2 = (Graphics2D) g;
+                      g2.setStroke(new BasicStroke(1,
+                          BasicStroke.CAP_SQUARE,
+                          BasicStroke.JOIN_ROUND, 3f,
+                          new float[]
+                          {5f, 3f}, 0f));
+
+                      graphExtras += 3;
+
+                      g.drawLine(x, graphExtras,
+                                 x+fm.stringWidth(aa[i].label),
+                                 graphExtras);
+                      g2.setStroke(new BasicStroke());
+                    }
+                  }*/
+                    y += ((2 * aa[i].height) / 3);
+                }
+                else
+                {
+                    y += aa[i].height;
+                }
+            }
+        }
+
+        if (resizePanel)
+        {
+          g.drawImage(image, 2, 0 - scrollOffset, this);
+        }
+        else if (dragEvent != null && aa!=null)
+        {
+          g.setColor(Color.lightGray);
+          g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
+        }
+
+
+        if ((aa == null) || (aa.length < 1))
+        {
+            g.drawString("Right click", 2, 8);
+            g.drawString("to add annotation", 2, 18);
+        }
+    }
+}