X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=4fd39a3d6e86290f371fb8210c5c99d6d8a1d49c;hb=04bb62b586382f183f08eb70131e7bf5f67cb47a;hp=44b7432745bf9ccfcc67e33fac60216613461d50;hpb=dc1ac2540d464c799ad67102cbddc77cf60c72be;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 44b7432..4fd39a3 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,4 +1,4 @@
-/*
+ /*
  * Jalview - A Sequence Alignment Editor and Viewer
  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
@@ -18,670 +18,1084 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-
 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 = new SequenceGroup();
-  int charHeight;
-  int charWidth;
-  int chunkWidth;
-  int chunkHeight;
-  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;
-  public Vector vconsensus;
-  AlignmentAnnotation consensus;
-  AlignmentAnnotation conservation;
-  AlignmentAnnotation quality;
-  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);
-
-  public AlignViewport(AlignmentI al)
-  {
-    setAlignment(al);
-    this.startRes = 0;
-    this.endRes = al.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = al.getHeight() - 1;
-
-    updateFromPreferences();
-  }
-
-  public void updateFromPreferences()
-  {
-    showFullId = Preferences.showFullId;
-    showAnnotation = Preferences.showAnnotation;
-    showConservation = Preferences.showConservation;
-    showQuality = Preferences.showQuality;
-    showIdentity = Preferences.showIdentity;
-    showFullId = Preferences.showFullId;
-
-    String fontName = Preferences.fontName;
-    String fontStyle = Preferences.fontStyle;
-    String fontSize = Cache.getProperty("FONT_SIZE");
-
-    if ( (fontName != null) && (fontStyle != null) && (fontSize != null))
-    {
-      int style = 0;
-
-      if (fontStyle.equals("bold"))
-      {
-        style = 1;
-      }
-      else if (fontStyle.equals("italic"))
-      {
-        style = 2;
-      }
-
-      setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+    int startRes;
+    int endRes;
+    int startSeq;
+    int endSeq;
+    boolean showDBPrefix = true;
+    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;
+    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;
+
+    boolean isDataset = false;
+
+
+    public AlignViewport(AlignmentI al, boolean dataset)
+    {
+      isDataset = dataset;
+      setAlignment(al);
+      init();
     }
-    else
+    /**
+     * Creates a new AlignViewport object.
+     *
+     * @param al DOCUMENT ME!
+     */
+    public AlignViewport(AlignmentI al)
     {
-      setFont(font);
+        setAlignment(al);
+        init();
     }
 
-    alignment.setGapCharacter(Preferences.gapSymbol);
+    void init()
+    {
+        this.startRes = 0;
+        this.endRes = alignment.getWidth() - 1;
+        this.startSeq = 0;
+        this.endSeq = alignment.getHeight() - 1;
+
+      showDBPrefix = Cache.getDefault("SHOW_DBPREFIX", true);
+      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);
 
-    // We must set conservation and consensus before setting colour,
-    // as Blosum and Clustal require this to be done
-    updateConservation();
-    updateConsensus();
+       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
+       String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
-    if (Preferences.defaultColour != null)
+       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 showSequenceFeatures(boolean b)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-          Preferences.defaultColour);
+        showSequenceFeatures = b;
+    }
 
-      if (globalColourScheme instanceof UserColourScheme)
-      {
-        globalColourScheme = UserDefinedColours.loadDefaultColours();
-      }
+    /**
+     * 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 (globalColourScheme != null)
-      {
-        globalColourScheme.setConsensus(vconsensus);
+        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();
+        }
       }
-    }
-  }
-
-  public void showSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public void updateConservation()
-  {
-    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
+      catch (OutOfMemoryError error)
       {
-        value = Integer.parseInt(sequence.charAt(i) + "");
+        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();
+
       }
-      catch (Exception ex)
-      {
-        if (sequence.charAt(i) == '*')
+    }
+
+    /**
+     * 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)
         {
-          value = 11;
+          vconsensus = alignment.getAAFrequency();
+        }
+        else
+        {
+          Vector temp = alignment.getAAFrequency();
+          vconsensus.clear();
+
+          Enumeration e = temp.elements();
+
+          while (e.hasMoreElements())
+          {
+            vconsensus.add(e.nextElement());
+          }
         }
 
-        if (sequence.charAt(i) == '+')
+        Hashtable hash = null;
+
+        for (int i = 0; i < alignment.getWidth(); i++)
         {
-          value = 10;
+          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);
         }
-      }
 
-      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);
-      }
+        if (consensus == null)
+        {
+          consensus = new AlignmentAnnotation("Consensus", "PID",
+                                              annotations, 0f, 100f, 1);
 
-      quality = new AlignmentAnnotation("Quality",
-                                        "Alignment Quality based on Blosum62 scores",
-                                        qannotations,
-                                        cons.qualityRange[0].floatValue(),
-                                        cons.qualityRange[1].floatValue(), 1);
+          if (showIdentity)
+          {
+            alignment.addAnnotation(consensus);
+          }
+        }
+        else
+        {
+          consensus.annotations = annotations;
+        }
+
+        if (globalColourScheme != null)
+          globalColourScheme.setConsensus(vconsensus);
 
-      if (showQuality)
+      }catch(OutOfMemoryError error)
       {
-        alignment.addAnnotation(quality);
+        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();
       }
+
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceGroup getSelectionGroup()
     {
-      conservation.annotations = annotations;
-      quality.annotations = qannotations;
-      quality.graphMax = cons.qualityRange[1].floatValue();
+        return selectionGroup;
     }
-  }
 
-  public void updateConsensus()
-  {
-    Annotation[] annotations = new Annotation[alignment.getWidth()];
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void setSelectionGroup(SequenceGroup sg)
+    {
+        selectionGroup = sg;
+    }
 
-    // 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)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getConservationSelected()
     {
-      vconsensus = alignment.getAAFrequency();
+        return conservationColourSelected;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setConservationSelected(boolean b)
     {
-      Vector temp = alignment.getAAFrequency();
-      vconsensus.clear();
+        conservationColourSelected = b;
+    }
 
-      Enumeration e = temp.elements();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getAbovePIDThreshold()
+    {
+        return abovePIDThreshold;
+    }
 
-      while (e.hasMoreElements())
-      {
-        vconsensus.add(e.nextElement());
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAbovePIDThreshold(boolean b)
+    {
+        abovePIDThreshold = b;
     }
 
-    Hashtable hash = null;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartRes()
+    {
+        return startRes;
+    }
 
-    for (int i = 0; i < alignment.getWidth(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndRes()
     {
-      hash = (Hashtable) vconsensus.elementAt(i);
+        return endRes;
+    }
 
-      float value = Float.parseFloat(hash.get("maxCount").toString());
-      value /= Float.parseFloat(hash.get("size").toString());
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartSeq()
+    {
+        return startSeq;
+    }
 
-      value *= 100;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     */
+    public void setGlobalColourScheme(ColourSchemeI cs)
+    {
+        globalColourScheme = cs;
+    }
 
-      String maxRes = hash.get("maxResidue") + " ";
-      String mouseOver = hash.get("maxResidue") + " ";
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public ColourSchemeI getGlobalColourScheme()
+    {
+        return globalColourScheme;
+    }
 
-      if (maxRes.length() > 2)
-      {
-        mouseOver = "[" + maxRes + "] ";
-        maxRes = "+ ";
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     */
+    public void setStartRes(int res)
+    {
+        this.startRes = res;
+    }
 
-      mouseOver += ( (int) value + "%");
-      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setStartSeq(int seq)
+    {
+        this.startSeq = seq;
     }
 
-    if (consensus == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     */
+    public void setEndRes(int res)
     {
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-                                          annotations, 0f, 100f, 1);
+        if (res > (alignment.getWidth() - 1))
+        {
+            // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
+            res = alignment.getWidth() - 1;
+        }
 
-      if (showIdentity)
-      {
-        alignment.addAnnotation(consensus);
-      }
+        if (res < 0)
+        {
+            res = 0;
+        }
+
+        this.endRes = res;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setEndSeq(int seq)
     {
-      consensus.annotations = annotations;
+        if (seq > alignment.getHeight())
+        {
+            seq = alignment.getHeight();
+        }
+
+        if (seq < 0)
+        {
+            seq = 0;
+        }
+
+        this.endSeq = seq;
     }
-  }
 
-  public SequenceGroup getSelectionGroup()
-  {
-    return selectionGroup;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndSeq()
+    {
+        return endSeq;
+    }
 
-  public void setSelectionGroup(SequenceGroup sg)
-  {
-    selectionGroup = sg;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param f DOCUMENT ME!
+     */
+    public void setFont(Font f)
+    {
+        font = f;
 
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
+        Container c = new Container();
 
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
+        java.awt.FontMetrics fm = c.getFontMetrics(font);
+        setCharHeight(fm.getHeight());
+        setCharWidth(fm.charWidth('M'));
+    }
 
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Font getFont()
+    {
+        return font;
+    }
 
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param w DOCUMENT ME!
+     */
+    public void setCharWidth(int w)
+    {
+        this.charWidth = w;
+    }
 
-  public int getStartRes()
-  {
-    return startRes;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getCharWidth()
+    {
+        return charWidth;
+    }
 
-  public int getEndRes()
-  {
-    return endRes;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param h DOCUMENT ME!
+     */
+    public void setCharHeight(int h)
+    {
+        this.charHeight = h;
+    }
 
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getCharHeight()
+    {
+        return charHeight;
+    }
 
-  public void setGlobalColourScheme(ColourSchemeI cs)
-  {
-    globalColourScheme = cs;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param w DOCUMENT ME!
+     */
+    public void setWrappedWidth(int w)
+    {
+        this.wrappedWidth = w;
+    }
 
-  public ColourSchemeI getGlobalColourScheme()
-  {
-    return globalColourScheme;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWrappedWidth()
+    {
+        return wrappedWidth;
+    }
 
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
 
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public AlignmentI getAlignment()
+    {
+        return alignment;
+    }
 
-  public void setEndRes(int res)
-  {
-    if (res > (alignment.getWidth() - 1))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param align DOCUMENT ME!
+     */
+    public void setAlignment(AlignmentI align)
     {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-      res = alignment.getWidth() - 1;
+        this.alignment = align;
     }
 
-    if (res < 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setWrapAlignment(boolean state)
     {
-      res = 0;
+        wrapAlignment = state;
     }
 
-    this.endRes = res;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowText(boolean state)
+    {
+        showText = state;
+    }
 
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setRenderGaps(boolean state)
     {
-      seq = alignment.getHeight();
+        renderGaps = state;
     }
 
-    if (seq < 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getColourText()
     {
-      seq = 0;
+        return showColourText;
     }
 
-    this.endSeq = seq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setColourText(boolean state)
+    {
+        showColourText = state;
+    }
 
-  public int getEndSeq()
-  {
-    return endSeq;
-  }
-
-  public void setFont(Font f)
-  {
-    font = f;
-
-    javax.swing.JFrame temp = new javax.swing.JFrame();
-    temp.addNotify();
-
-    java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);
-    setCharHeight(fm.getHeight());
-    setCharWidth(fm.charWidth('M'));
-  }
-
-  public Font getFont()
-  {
-    return font;
-  }
-
-  public void setCharWidth(int w)
-  {
-    this.charWidth = w;
-  }
-
-  public int getCharWidth()
-  {
-    return charWidth;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowBoxes(boolean state)
+    {
+        showBoxes = state;
+    }
 
-  public void setCharHeight(int h)
-  {
-    this.charHeight = h;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getWrapAlignment()
+    {
+        return wrapAlignment;
+    }
 
-  public int getCharHeight()
-  {
-    return charHeight;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowText()
+    {
+        return showText;
+    }
 
-  public void setChunkWidth(int w)
-  {
-    this.chunkWidth = w;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowBoxes()
+    {
+        return showBoxes;
+    }
 
-  public int getChunkWidth()
-  {
-    return chunkWidth;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getGapCharacter()
+    {
+        return getAlignment().getGapCharacter();
+    }
 
-  public void setChunkHeight(int h)
-  {
-    this.chunkHeight = h;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gap DOCUMENT ME!
+     */
+    public void setGapCharacter(char gap)
+    {
+        if (getAlignment() != null)
+        {
+            getAlignment().setGapCharacter(gap);
+        }
+    }
 
-  public int getChunkHeight()
-  {
-    return chunkHeight;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param thresh DOCUMENT ME!
+     */
+    public void setThreshold(int thresh)
+    {
+        threshold = thresh;
+    }
 
-  public AlignmentI getAlignment()
-  {
-    return alignment;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getThreshold()
+    {
+        return threshold;
+    }
 
-  public void setAlignment(AlignmentI align)
-  {
-    this.alignment = align;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param inc DOCUMENT ME!
+     */
+    public void setIncrement(int inc)
+    {
+        increment = inc;
+    }
 
-  public void setWrapAlignment(boolean state)
-  {
-    wrapAlignment = state;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getIncrement()
+    {
+        return increment;
+    }
 
-  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 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();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param y DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getIndex(int y)
+    {
+        int y1 = 0;
+        int starty = getStartSeq();
+        int endy = getEndSeq();
 
-        if ( (y >= y1) && (y <= y2))
+        for (int i = starty; i <= endy; i++)
         {
-          return 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;
+            }
         }
 
-        y1 = y2;
-      }
-      else
-      {
         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 getShowJVSuffix()
+    {
+        return showJVSuffix;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setShowJVSuffix(boolean b)
+    {
+        showJVSuffix = b;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowDBPrefix()
+    {
+        return showDBPrefix;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setShowDBPrefix(boolean b)
+    {
+        showDBPrefix = 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;
     }
 
-    return -1;
-  }
-
-  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 getShowFullId()
-  {
-    return showFullId;
-  }
-
-  public void setShowFullId(boolean b)
-  {
-    showFullId = 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 addPropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
-  {
-    changeSupport.addPropertyChangeListener(listener);
-  }
-
-  public void removePropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
-  {
-    changeSupport.removePropertyChangeListener(listener);
-  }
-
-  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
-  {
-    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
-  }
+    public void setDataset(boolean b)
+    {
+      isDataset = b;
+    }
+
+    public boolean isDataset()
+    {
+      return isDataset;
+    }
 }