X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=cfffbb9e1bbb57a3746a8c8e5eec82cbab0680d7;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=3420993f9e753f49bb7102e185fa47fdf9dc6448;hpb=ce728f87f1f43be3041ef02f7f2cc2e39314711a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3420993..cfffbb9 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,1057 +1,1759 @@
- /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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 showFullId = false;
-    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;
-    int wrappedWidth;
-    Font font = new Font("SansSerif", Font.PLAIN, 10);
-    AlignmentI alignment;
-    ColumnSelection colSel = new ColumnSelection();
-    int threshold;
-    int increment;
-    NJTree currentTree = null;
-    boolean scaleAboveWrapped = false;
-    boolean scaleLeftWrapped = true;
-    boolean scaleRightWrapped = true;
-
-    /** DOCUMENT ME!! */
-    public Vector vconsensus;
-    AlignmentAnnotation consensus;
-    AlignmentAnnotation conservation;
-    AlignmentAnnotation quality;
-
-    /** 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;
-
-    /**
-     * Creates a new AlignViewport object.
-     *
-     * @param al DOCUMENT ME!
-     */
-    public AlignViewport(AlignmentI al)
-    {
-        setAlignment(al);
-        this.startRes = 0;
-        this.endRes = al.getWidth() - 1;
-        this.startSeq = 0;
-        this.endSeq = al.getHeight() - 1;
-
-        updateFromPreferences();
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateFromPreferences()
-    {
-      showFullId = Cache.getDefault("SHOW_FULL_ID", 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);
-
-       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
-        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 showSequenceFeatures(boolean b)
-    {
-        showSequenceFeatures = b;
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConservation()
-    {
-      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()
-                                                 1);
-
-          if (showConservation)
-          {
-            alignment.addAnnotation(conservation);
-          }
-
-          quality = new AlignmentAnnotation("Quality",
-                                            "Alignment Quality based on Blosum62 scores",
-                                            qannotations,
-                                            cons.qualityRange[0].floatValue(),
-                                            cons.qualityRange[1].floatValue(),
-                                            1);
-
-          if (showQuality)
-          {
-            alignment.addAnnotation(quality);
-          }
-        }
-        else
-        {
-          conservation.annotations = annotations;
-          quality.annotations = qannotations;
-          quality.graphMax = cons.qualityRange[1].floatValue();
-        }
-      }
-      catch (OutOfMemoryError error)
-      {
-        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, 1);
-
-          if (showIdentity)
-          {
-            alignment.addAnnotation(consensus);
-          }
-        }
-        else
-        {
-          consensus.annotations = annotations;
-        }
-
-        if (globalColourScheme != null)
-          globalColourScheme.setConsensus(vconsensus);
-
-      }catch(OutOfMemoryError error)
-      {
-        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();
-      }
-
-    }
-
-    /**
-     * 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'));
-    }
-
-    /**
-     * 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!
-     *
-     * @param y DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getIndex(int y)
-    {
-        int y1 = 0;
-        int starty = getStartSeq();
-        int endy = getEndSeq();
-
-        for (int i = starty; i <= endy; i++)
-        {
-            if ((i < alignment.getHeight()) &&
-                    (alignment.getSequenceAt(i) != null))
-            {
-                int y2 = y1 + getCharHeight();
-
-                if ((y >= y1) && (y <= y2))
-                {
-                    return i;
-                }
-
-                y1 = y2;
-            }
-            else
-            {
-                return -1;
-            }
-        }
-
-        return -1;
-    }
-
-    /**
-     * 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 getShowFullId()
-    {
-        return showFullId;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowFullId(boolean b)
-    {
-        showFullId = 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;
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * 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 java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+/**
+ * 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 colourAppliesToAllGroups = true;
+  ColourSchemeI globalColourScheme = null;
+  boolean conservationColourSelected = false;
+  boolean abovePIDThreshold = false;
+  SequenceGroup selectionGroup;
+  int charHeight;
+  int charWidth;
+  boolean validCharWidth;
+  int wrappedWidth;
+  Font font;
+  boolean seqNameItalics;
+  AlignmentI alignment;
+  ColumnSelection colSel = new ColumnSelection();
+  int threshold;
+  int increment;
+  NJTree currentTree = null;
+  boolean scaleAboveWrapped = false;
+  boolean scaleLeftWrapped = true;
+  boolean scaleRightWrapped = true;
+  boolean hasHiddenColumns = false;
+  boolean hasHiddenRows = false;
+  boolean showHiddenMarkers = true;
+
+  boolean cursorMode = false;
+
+  // The following vector holds the features which are
+  // currently visible, in the correct order or rendering
+  Hashtable featuresDisplayed = null;
+
+  /** DOCUMENT ME!! */
+  public Hashtable[] hconsensus;
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+  boolean autoCalculateConsensus = true;
+
+  /** DOCUMENT ME!! */
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+  // JBPNote Prolly only need this in the applet version.
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+      PropertyChangeSupport(this);
+
+  boolean ignoreGapsInConsensusCalculation = false;
+
+  boolean isDataset = false;
+
+  boolean antiAlias = false;
+
+  boolean padGaps = false;
+
+  Rectangle explodedPosition;
+
+  String viewName;
+
+  String sequenceSetID;
+
+  boolean gatherViewsHere = false;
+
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
+
+  Hashtable sequenceColours;
+
+  int thresholdTextColour = 0;
+  Color textColour = Color.black;
+  Color textColour2 = Color.white;
+
+  boolean rightAlignIds = false;
+
+  Hashtable hiddenRepSequences;
+
+  /**
+   * Creates a new AlignViewport object.
+   *
+   * @param al DOCUMENT ME!
+   */
+  public AlignViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    init();
+  }
+
+  /**
+   * Create a new AlignViewport with hidden regions
+   * @param al AlignmentI
+   * @param hiddenColumns ColumnSelection
+   */
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+  {
+    setAlignment(al);
+    if (hiddenColumns != null)
+    {
+      this.colSel = hiddenColumns;
+      if (hiddenColumns.getHiddenColumns() != null)
+      {
+        hasHiddenColumns = true;
+      }
+    }
+    init();
+  }
+
+  void init()
+  {
+    this.startRes = 0;
+    this.endRes = alignment.getWidth() - 1;
+    this.startSeq = 0;
+    this.endSeq = alignment.getHeight() - 1;
+
+    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
+    showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+
+    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+
+    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+    padGaps = Cache.getDefault("PAD_GAPS", true);
+
+    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+    String fontSize = Cache.getDefault("FONT_SIZE", "10");
+
+    seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
+    int style = 0;
+
+    if (fontStyle.equals("bold"))
+    {
+      style = 1;
+    }
+    else if (fontStyle.equals("italic"))
+    {
+      style = 2;
+    }
+
+    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 (hconsensus == null && !isDataset)
+    {
+      if (!alignment.isNucleotide())
+      {
+        conservation = new AlignmentAnnotation("Conservation",
+                                               "Conservation of total alignment less than " +
+                                               ConsPercGaps + "% gaps",
+                                               new Annotation[1], 0f,
+                                               11f,
+                                               AlignmentAnnotation.BAR_GRAPH);
+        conservation.hasText = true;
+        conservation.autoCalculated = true;
+
+        if (Cache.getDefault("SHOW_CONSERVATION", true))
+        {
+          alignment.addAnnotation(conservation);
+        }
+
+        if (Cache.getDefault("SHOW_QUALITY", true))
+        {
+          quality = new AlignmentAnnotation("Quality",
+                                            "Alignment Quality based on Blosum62 scores",
+                                            new Annotation[1],
+                                            0f,
+                                            11f,
+                                            AlignmentAnnotation.BAR_GRAPH);
+          quality.hasText = true;
+          quality.autoCalculated = true;
+
+          alignment.addAnnotation(quality);
+        }
+      }
+
+      consensus = new AlignmentAnnotation("Consensus", "PID",
+                                          new Annotation[1], 0f, 100f,
+                                          AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
+
+      if (Cache.getDefault("SHOW_IDENTITY", true))
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
+
+    if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+    {
+      globalColourScheme = ColourSchemeProperty.getColour(alignment,
+          jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+
+      if (globalColourScheme instanceof UserColourScheme)
+      {
+        globalColourScheme = UserDefinedColours.loadDefaultColours();
+        ( (UserColourScheme) globalColourScheme).setThreshold(0,
+            getIgnoreGapsConsensus());
+      }
+
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(hconsensus);
+      }
+    }
+
+    wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setShowSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
+
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
+
+  class ConservationThread
+      extends Thread
+  {
+    AlignmentPanel ap;
+    public ConservationThread(AlignmentPanel ap)
+    {
+      this.ap = ap;
+    }
+
+    public void run()
+    {
+      try
+      {
+        updatingConservation = true;
+
+        while (UPDATING_CONSERVATION)
+        {
+          try
+          {
+            if (ap != null)
+            {
+              ap.repaint();
+            }
+            Thread.sleep(200);
+          }
+          catch (Exception ex)
+          {
+            ex.printStackTrace();
+          }
+        }
+
+        UPDATING_CONSERVATION = true;
+
+        int alWidth = alignment.getWidth();
+        if (alWidth < 0)
+        {
+          return;
+        }
+
+        Conservation cons = new jalview.analysis.Conservation("All",
+            jalview.schemes.ResidueProperties.propHash, 3,
+            alignment.getSequences(), 0, alWidth - 1);
+
+        cons.calculate();
+        cons.verdict(false, ConsPercGaps);
+
+        if (quality != null)
+        {
+          cons.findQuality();
+        }
+
+        char[] sequence = cons.getConsSequence().getSequence();
+        float minR;
+        float minG;
+        float minB;
+        float maxR;
+        float maxG;
+        float maxB;
+        minR = 0.3f;
+        minG = 0.0f;
+        minB = 0f;
+        maxR = 1.0f - minR;
+        maxG = 0.9f - minG;
+        maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+
+        float min = 0f;
+        float max = 11f;
+        float qmin = 0f;
+        float qmax = 0f;
+
+        char c;
+
+        conservation.annotations = new Annotation[alWidth];
+
+        if (quality != null)
+        {
+          quality.graphMax = cons.qualityRange[1].floatValue();
+          quality.annotations = new Annotation[alWidth];
+          qmin = cons.qualityRange[0].floatValue();
+          qmax = cons.qualityRange[1].floatValue();
+        }
+
+        for (int i = 0; i < alWidth; i++)
+        {
+          float value = 0;
+
+          c = sequence[i];
+
+          if (Character.isDigit(c))
+          {
+            value = (int) (c - '0');
+          }
+          else if (c == '*')
+          {
+            value = 11;
+          }
+          else if (c == '+')
+          {
+            value = 10;
+          }
+
+          float vprop = value - min;
+          vprop /= max;
+          conservation.annotations[i] =
+              new Annotation(String.valueOf(c),
+                             String.valueOf(value), ' ', value,
+                             new Color(minR + (maxR * vprop),
+                                       minG + (maxG * vprop),
+                                       minB + (maxB * vprop)));
+
+          // Quality calc
+          if (quality != null)
+          {
+            value = ( (Double) cons.quality.get(i)).floatValue();
+            vprop = value - qmin;
+            vprop /= qmax;
+            quality.annotations[i] = new Annotation(" ", String.valueOf(value),
+                ' ',
+                value,
+                new Color(minR + (maxR * vprop),
+                          minG + (maxG * vprop),
+                          minB + (maxB * vprop)));
+          }
+        }
+      }
+      catch (OutOfMemoryError error)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calculating conservation!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
+        conservation = null;
+        quality = null;
+
+        System.out.println("Conservation calculation: " + error);
+        System.gc();
+
+      }
+
+      UPDATING_CONSERVATION = false;
+      updatingConservation = false;
+
+      if (ap != null)
+      {
+        ap.repaint();
+      }
+
+    }
+  }
+
+  ConservationThread conservationThread;
+
+  ConsensusThread consensusThread;
+
+  boolean consUpdateNeeded = false;
+
+  static boolean UPDATING_CONSENSUS = false;
+
+  static boolean UPDATING_CONSERVATION = false;
+
+  boolean updatingConsensus = false;
+
+  boolean updatingConservation = false;
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateConservation(final AlignmentPanel ap)
+  {
+    if (alignment.isNucleotide() || conservation == null)
+    {
+      return;
+    }
+
+    conservationThread = new ConservationThread(ap);
+    conservationThread.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateConsensus(final AlignmentPanel ap)
+  {
+    consensusThread = new ConsensusThread(ap);
+    consensusThread.start();
+  }
+
+  class ConsensusThread
+      extends Thread
+  {
+    AlignmentPanel ap;
+    public ConsensusThread(AlignmentPanel ap)
+    {
+      this.ap = ap;
+    }
+
+    public void run()
+    {
+      updatingConsensus = true;
+      while (UPDATING_CONSENSUS)
+      {
+        try
+        {
+          if (ap != null)
+          {
+            ap.repaint();
+          }
+
+          Thread.sleep(200);
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+
+      UPDATING_CONSENSUS = true;
+
+      try
+      {
+        int aWidth = alignment.getWidth();
+        if (aWidth < 0)
+        {
+          return;
+        }
+
+        consensus.annotations = null;
+        consensus.annotations = new Annotation[aWidth];
+
+        hconsensus = new Hashtable[aWidth];
+        AAFrequency.calculate(alignment.getSequencesArray(),
+                              0,
+                              alignment.getWidth(),
+                              hconsensus);
+
+        for (int i = 0; i < aWidth; i++)
+        {
+          float value = 0;
+          if (ignoreGapsInConsensusCalculation)
+          {
+            value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
+                floatValue();
+          }
+          else
+          {
+            value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
+                floatValue();
+          }
+
+          String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+          String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+
+          if (maxRes.length() > 1)
+          {
+            mouseOver = "[" + maxRes + "] ";
+            maxRes = "+";
+          }
+
+          mouseOver += ( (int) value + "%");
+          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+              value);
+        }
+
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(hconsensus);
+        }
+
+      }
+      catch (OutOfMemoryError error)
+      {
+        alignment.deleteAnnotation(consensus);
+
+        consensus = null;
+        hconsensus = null;
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calculating consensus!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
+        System.out.println("Consensus calculation: " + error);
+        System.gc();
+      }
+      UPDATING_CONSENSUS = false;
+      updatingConsensus = false;
+
+      if (ap != null)
+      {
+        ap.repaint();
+      }
+    }
+  }
+
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation row.
+   * @return consensus sequence as a new sequence object
+   */
+  public SequenceI getConsensusSeq()
+  {
+    if (consensus == null)
+    {
+      updateConsensus(null);
+    }
+    if (consensus == null)
+    {
+      return null;
+    }
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
+    {
+      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, AlignmentPanel ap)
+  {
+    ignoreGapsInConsensusCalculation = b;
+    updateConsensus(ap);
+    if (globalColourScheme != null)
+    {
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+                                      ignoreGapsInConsensusCalculation);
+    }
+  }
+
+  public boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensusCalculation;
+  }
+
+  public void setDataset(boolean b)
+  {
+    isDataset = b;
+  }
+
+  public boolean isDataset()
+  {
+    return isDataset;
+  }
+
+  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 hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+  {
+    int sSize = sg.getSize();
+    if (sSize < 2)
+    {
+      return;
+    }
+
+    if (hiddenRepSequences == null)
+    {
+      hiddenRepSequences = new Hashtable();
+    }
+
+    hiddenRepSequences.put(repSequence, sg);
+
+    //Hide all sequences except the repSequence
+    SequenceI[] seqs = new SequenceI[sSize - 1];
+    int index = 0;
+    for (int i = 0; i < sSize; i++)
+    {
+      if (sg.getSequenceAt(i) != repSequence)
+      {
+        if (index == sSize - 1)
+        {
+          return;
+        }
+
+        seqs[index++] = sg.getSequenceAt(i);
+      }
+    }
+
+    hideSequence(seqs);
+
+  }
+
+  public void hideAllSelectedSeqs()
+  {
+    if (selectionGroup == null)
+    {
+      return;
+    }
+
+    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+
+    hideSequence(seqs);
+
+    setSelectionGroup(null);
+  }
+
+  public void hideSequence(SequenceI[] seq)
+  {
+    if (seq != null)
+    {
+      for (int i = 0; i < seq.length; i++)
+      {
+        alignment.getHiddenSequences().hideSequence(seq[i]);
+      }
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
+    }
+  }
+
+  public void showSequence(int index)
+  {
+    Vector tmp = alignment.getHiddenSequences().showSequence(index
+        , hiddenRepSequences);
+    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(hiddenRepSequences);
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence(
+            (SequenceI) tmp.elementAt(t), false
+            );
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      hasHiddenRows = false;
+      hiddenRepSequences = null;
+    }
+  }
+
+  public void invertColumnSelection()
+  {
+    for (int i = 0; i < alignment.getWidth(); i++)
+    {
+      if (colSel.contains(i))
+      {
+        colSel.removeElement(i);
+      }
+      else
+      {
+        if (!hasHiddenColumns || colSel.isVisible(i))
+        {
+          colSel.addElement(i);
+        }
+      }
+    }
+  }
+
+  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();
+      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 + 1);
+      }
+    }
+    else
+    {
+      selection.addOperation(CigarArray.M, end - start + 1);
+    }
+    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,
+                               (selectedOnly && selectionGroup != null) ?
+                               selectionGroup.getStartRes() : 0);
+    }
+    return null;
+  }
+
+  /**
+   * This method returns the visible alignment as text, as
+   * seen on the GUI, ie if columns are hidden they will not
+   * be returned in the result.
+   * Use this for calculating trees, PCA, redundancy etc on views
+   * which contain hidden columns.
+   * @return String[]
+   */
+  public String[] getViewAsString(boolean selectedRegionOnly)
+  {
+    String[] selection = null;
+    SequenceI[] seqs = null;
+    int i, iSize;
+    int start = 0, end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
+    {
+      iSize = selectionGroup.getSize();
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
+    }
+    else
+    {
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth();
+    }
+
+    selection = new String[iSize];
+    if (hasHiddenColumns)
+    {
+      selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+    }
+    else
+    {
+      for (i = 0; i < iSize; i++)
+      {
+        selection[i] = seqs[i].getSequenceAsString(start, end);
+      }
+
+    }
+    return selection;
+  }
+
+  public boolean getShowHiddenMarkers()
+  {
+    return showHiddenMarkers;
+  }
+
+  public void setShowHiddenMarkers(boolean show)
+  {
+    showHiddenMarkers = show;
+  }
+
+  public String getSequenceSetId()
+  {
+    if (sequenceSetID == null)
+    {
+      sequenceSetID = alignment.hashCode() + "";
+    }
+
+    return sequenceSetID;
+  }
+
+  public void alignmentChanged(AlignmentPanel ap)
+  {
+    if (padGaps)
+    {
+      alignment.padGaps();
+    }
+
+    if (hconsensus != null && autoCalculateConsensus)
+    {
+      updateConsensus(ap);
+      updateConservation(ap);
+    }
+
+    //Reset endRes of groups if beyond alignment width
+    int alWidth = alignment.getWidth();
+    Vector groups = alignment.getGroups();
+    if (groups != null)
+    {
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+        if (sg.getEndRes() > alWidth)
+        {
+          sg.setEndRes(alWidth - 1);
+        }
+      }
+    }
+
+    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
+    {
+      selectionGroup.setEndRes(alWidth - 1);
+    }
+
+    resetAllColourSchemes();
+
+    // alignment.adjustSequenceAnnotations();
+  }
+
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = globalColourScheme;
+    if (cs != null)
+    {
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) cs).
+            resetClustalX(alignment.getSequences(),
+                          alignment.getWidth());
+      }
+
+      cs.setConsensus(hconsensus);
+      if (cs.conservationApplied())
+      {
+        Alignment al = (Alignment) alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, ConsPercGaps);
+
+        cs.setConservation(c);
+      }
+    }
+
+    int s, sSize = alignment.getGroups().size();
+    for (s = 0; s < sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
+      if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) sg.cs).resetClustalX(
+            sg.getSequences(hiddenRepSequences), sg.getWidth());
+      }
+      sg.recalcConservation();
+    }
+  }
+
+  public Color getSequenceColour(SequenceI seq)
+  {
+    if (sequenceColours == null || !sequenceColours.containsKey(seq))
+    {
+      return Color.white;
+    }
+    else
+    {
+      return (Color) sequenceColours.get(seq);
+    }
+  }
+
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+
+    if (col == null)
+    {
+      sequenceColours.remove(seq);
+    }
+    else
+    {
+      sequenceColours.put(seq, col);
+    }
+  }
+
+}