From efc31b4a8d5cee63555586804a2b79c06bdb5a14 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 30 Jun 2005 14:46:58 +0000
Subject: [PATCH] Formatting changes

---
 src/jalview/analysis/AAFrequency.java              |  353 +--
 src/jalview/analysis/AlignSeq.java                 |  456 ++-
 src/jalview/analysis/AlignmentSorter.java          |  293 +-
 src/jalview/analysis/Conservation.java             |  293 +-
 src/jalview/analysis/NJTree.java                   |  688 ++++-
 src/jalview/analysis/PCA.java                      |  143 +-
 src/jalview/analysis/SeqsetUtils.java              |  264 +-
 src/jalview/analysis/SequenceIdMatcher.java        |  246 +-
 src/jalview/appletgui/AnnotationPanel.java         |    2 +-
 src/jalview/appletgui/IdCanvas.java                |   12 +-
 src/jalview/appletgui/SeqCanvas.java               |   12 +-
 src/jalview/bin/Cache.java                         |  139 +-
 src/jalview/bin/Jalview.java                       |  360 ++-
 src/jalview/bin/JalviewLite.java                   |  129 +-
 src/jalview/binding/Alignment.java                 |  145 +-
 src/jalview/binding/Annotation.java                |  724 ++---
 src/jalview/binding/AnnotationElement.java         |  213 +-
 src/jalview/binding/Colour.java                    |  145 +-
 src/jalview/binding/JGroup.java                    |  512 ++--
 src/jalview/binding/JSeq.java                      |  237 +-
 src/jalview/binding/JalviewModel.java              |  173 +-
 src/jalview/binding/JalviewModelSequence.java      | 1744 +++++------
 src/jalview/binding/JalviewModelSequence2.java     |  255 +-
 src/jalview/binding/JalviewModelSequence2Item.java |  361 +--
 src/jalview/binding/JalviewUserColours.java        |  236 +-
 src/jalview/binding/JalviewUserColoursItem.java    |   56 +-
 src/jalview/binding/Residue.java                   |  361 ++-
 src/jalview/binding/Sequence.java                  |  178 +-
 src/jalview/binding/SequenceSet.java               |  393 ++-
 src/jalview/binding/SequenceType.java              |  359 ++-
 src/jalview/binding/Tree.java                      |  471 +--
 src/jalview/binding/UserColour.java                |  362 +--
 src/jalview/binding/UserColourScheme.java          |  178 +-
 src/jalview/binding/UserColours.java               |  308 +-
 src/jalview/binding/VAMSAS.java                    | 1133 ++++----
 src/jalview/binding/VamsasModel.java               |  113 +-
 src/jalview/binding/Viewport.java                  | 2805 +++++++++---------
 src/jalview/datamodel/Alignment.java               |  573 ++--
 src/jalview/datamodel/AlignmentAnnotation.java     |  123 +-
 src/jalview/datamodel/AlignmentI.java              |  218 +-
 src/jalview/datamodel/AlignmentOrder.java          |  199 +-
 src/jalview/datamodel/Annotation.java              |   41 +-
 src/jalview/datamodel/BinaryNode.java              |  256 +-
 src/jalview/datamodel/BinarySequence.java          |  102 +-
 src/jalview/datamodel/HistoryItem.java             |   71 +-
 src/jalview/datamodel/Sequence.java                |  332 ++-
 src/jalview/datamodel/SequenceFeature.java         |  173 +-
 src/jalview/datamodel/SequenceGroup.java           |  660 +++--
 src/jalview/datamodel/SequenceI.java               |  199 +-
 src/jalview/datamodel/SequenceNode.java            |  117 +-
 src/jalview/datamodel/SequencePoint.java           |   55 +-
 src/jalview/datamodel/SuperGroup.java              |  110 +-
 src/jalview/gui/AlignFrame.java                    | 3049 ++++++++++++--------
 src/jalview/gui/AlignViewport.java                 | 1503 ++++++----
 src/jalview/gui/AlignmentPanel.java                | 1498 ++++++----
 src/jalview/gui/AnnotationLabels.java              |  570 ++--
 src/jalview/gui/AnnotationPanel.java               | 1282 ++++----
 src/jalview/gui/ColumnSelection.java               |  187 +-
 src/jalview/gui/CutAndPasteTransfer.java           |  208 +-
 src/jalview/gui/Desktop.java                       |  854 +++---
 src/jalview/gui/FeatureRenderer.java               |  171 +-
 src/jalview/gui/Finder.java                        |  560 ++--
 src/jalview/gui/FontChooser.java                   |  237 +-
 src/jalview/gui/IdCanvas.java                      |  422 +--
 src/jalview/gui/IdPanel.java                       |  538 ++--
 src/jalview/gui/IdwidthAdjuster.java               |  188 +-
 src/jalview/gui/Jalview2XML.java                   | 1261 ++++----
 src/jalview/gui/OverviewPanel.java                 |  545 ++--
 src/jalview/gui/PCAPanel.java                      |  245 +-
 src/jalview/gui/PaintRefresher.java                |   95 +-
 src/jalview/gui/PairwiseAlignPanel.java            |  171 +-
 src/jalview/gui/PopupMenu.java                     | 1387 +++++----
 src/jalview/gui/Preferences.java                   |  524 ++--
 src/jalview/gui/RedundancyPanel.java               |  253 +-
 src/jalview/gui/RotatableCanvas.java               | 1099 +++----
 src/jalview/gui/ScalePanel.java                    |  431 +--
 src/jalview/gui/SeqCanvas.java                     | 1009 ++++---
 src/jalview/gui/SeqPanel.java                      | 1439 ++++-----
 src/jalview/gui/SequenceRenderer.java              |  464 +--
 src/jalview/gui/SliderPanel.java                   |  492 ++--
 src/jalview/gui/SplashScreen.java                  |  176 +-
 src/jalview/gui/TreeCanvas.java                    | 1130 ++++----
 src/jalview/gui/TreePanel.java                     |  643 +++--
 src/jalview/gui/UserDefinedColours.java            |  624 ++--
 src/jalview/gui/WebserviceInfo.java                |  409 +--
 src/jalview/io/AlignFile.java                      |   62 +-
 src/jalview/io/BLCFile.java                        |  157 +-
 src/jalview/io/ClustalFile.java                    |  406 +--
 src/jalview/io/EBIFetchClient.java                 |  140 +-
 src/jalview/io/FastaFile.java                      |  186 +-
 src/jalview/io/FileParse.java                      |  107 +-
 src/jalview/io/FormatAdapter.java                  |  104 +-
 src/jalview/io/HTMLOutput.java                     |  587 ++--
 src/jalview/io/IdentifyFile.java                   |   70 +-
 src/jalview/io/JPredFile.java                      |  166 +-
 src/jalview/io/JalviewFileChooser.java             |  716 ++---
 src/jalview/io/JalviewFileFilter.java              |  280 +-
 src/jalview/io/JalviewFileView.java                |  166 +-
 src/jalview/io/MSFfile.java                        |  214 +-
 src/jalview/io/NewickFile.java                     |  416 ++-
 src/jalview/io/PIRFile.java                        |  276 +-
 src/jalview/io/PfamFile.java                       |  350 ++-
 src/jalview/io/PileUpfile.java                     |  511 ++--
 src/jalview/io/SequenceFeatureFetcher.java         |  306 +-
 src/jalview/io/WSWUBlastClient.java                |  114 +-
 src/jalview/jbappletgui/GAlignFrame.java           |   12 +-
 src/jalview/jbgui/GAlignFrame.java                 | 2183 +++++++-------
 src/jalview/jbgui/GAlignmentPanel.java             |  202 +-
 src/jalview/jbgui/GCutAndPasteTransfer.java        |  126 +-
 src/jalview/jbgui/GDesktop.java                    |  170 +-
 src/jalview/jbgui/GFinder.java                     |  179 +-
 src/jalview/jbgui/GFontChooser.java                |  114 +-
 src/jalview/jbgui/GPCAPanel.java                   |  184 +-
 src/jalview/jbgui/GPairwiseAlignPanel.java         |   44 +-
 src/jalview/jbgui/GPreferences.java                |  104 +-
 src/jalview/jbgui/GSliderPanel.java                |   86 +-
 src/jalview/jbgui/GTreePanel.java                  |  356 ++-
 src/jalview/jbgui/GUserDefinedColours.java         |  100 +-
 src/jalview/jbgui/GWebserviceInfo.java             |   44 +-
 src/jalview/math/Matrix.java                       |  422 ++-
 src/jalview/math/RotatableMatrix.java              |  120 +-
 src/jalview/schemes/Blosum62ColourScheme.java      |  115 +-
 src/jalview/schemes/BuriedColourScheme.java        |   25 +-
 src/jalview/schemes/ClustalxColourScheme.java      |  511 ++--
 src/jalview/schemes/ColourSchemeI.java             |   46 +-
 src/jalview/schemes/ColourSchemeProperty.java      |  231 +-
 src/jalview/schemes/Consensus.java                 |  114 +-
 src/jalview/schemes/ConservationColourScheme.java  |   93 +-
 src/jalview/schemes/HelixColourScheme.java         |   55 +-
 src/jalview/schemes/HydrophobicColourScheme.java   |   25 +-
 src/jalview/schemes/NucleotideColourScheme.java    |   50 +-
 src/jalview/schemes/PIDColourScheme.java           |  107 +-
 src/jalview/schemes/ResidueColourScheme.java       |   95 +-
 src/jalview/schemes/ResidueProperties.java         | 2294 ++++++++-------
 src/jalview/schemes/ScoreColourScheme.java         |   60 +-
 src/jalview/schemes/StrandColourScheme.java        |   25 +-
 src/jalview/schemes/TaylorColourScheme.java        |   45 +-
 src/jalview/schemes/TurnColourScheme.java          |   25 +-
 src/jalview/schemes/UserColourScheme.java          |   71 +-
 src/jalview/schemes/ZappoColourScheme.java         |   16 +-
 src/jalview/util/BrowserLauncher.java              | 1473 +++++-----
 src/jalview/util/Comparison.java                   |  131 +-
 src/jalview/util/Format.java                       |  478 ++-
 src/jalview/util/QuickSort.java                    |  215 +-
 src/jalview/ws/JPredClient.java                    |  779 ++---
 src/jalview/ws/MsaWSClient.java                    |  242 +-
 src/jalview/ws/MsaWServices.java                   |   17 +-
 src/jalview/ws/WSClient.java                       |   76 +-
 src/jalview/ws/WSClientI.java                      |   49 +-
 149 files changed, 34382 insertions(+), 24606 deletions(-)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 8110c48..4ef250b 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -25,44 +25,68 @@ import jalview.datamodel.*;
 import java.util.*;
 
 
-public class AAFrequency {
-    // Takes in a vector of sequences and column start and column end
-    // and returns a vector of size (end-start+1). Each element of the
-    // vector contains a hashtable with the keys being residues and
-    // the values being the count of each residue in that column.
-    // This class is used extensively in calculating alignment colourschemes
-    // that depend on the amount of conservation in each alignment column.
-    public static Vector calculate(Vector sequences, int start, int end) {
+/**
+ * Takes in a vector of sequences and column start and column end
+ * and returns a vector of size (end-start+1). Each element of the
+ * vector contains a hashtable with the keys being residues and
+ * the values being the count of each residue in that column.
+ * This class is used extensively in calculating alignment colourschemes
+ * that depend on the amount of conservation in each alignment column.
+ * @author $author$
+ * @version $Revision$
+ */
+public class AAFrequency
+{
+    /** Takes in a vector of sequences and column start and column end
+    * and returns a vector of size (end-start+1). Each element of the
+    * vector contains a hashtable with the keys being residues and
+    * the values being the count of each residue in that column.
+    * This class is used extensively in calculating alignment colourschemes
+    * that depend on the amount of conservation in each alignment column. */
+    public static Vector calculate(Vector sequences, int start, int end)
+    {
         Vector result = new Vector();
 
-        for (int i = start; i <= end; i++) {
+        for (int i = start; i <= end; i++)
+        {
             Hashtable residueHash = new Hashtable();
             int maxCount = 0;
             String maxResidue = "-";
             int nongap = 0;
 
-            for (int j = 0; j < sequences.size(); j++) {
-                if (sequences.elementAt(j) instanceof Sequence) {
+            for (int j = 0; j < sequences.size(); j++)
+            {
+                if (sequences.elementAt(j) instanceof Sequence)
+                {
                     Sequence s = (Sequence) sequences.elementAt(j);
 
-                    if (s.getSequence().length() > i) {
+                    if (s.getSequence().length() > i)
+                    {
                         String res = s.getSequence().charAt(i) + "";
 
-                        if (!jalview.util.Comparison.isGap(res.charAt(0))) {
+                        if (!jalview.util.Comparison.isGap(res.charAt(0)))
+                        {
                             nongap++;
-                        } else {
+                        }
+                        else
+                        {
                             res = "-"; // we always use this for gaps in the property vectors
                         }
 
-                        if (residueHash.containsKey(res)) {
+                        if (residueHash.containsKey(res))
+                        {
                             int count = ((Integer) residueHash.get(res)).intValue();
                             count++;
 
                             if (!jalview.util.Comparison.isGap(res.charAt(0)) &&
-                                    (count >= maxCount)) {
-                                if (count > maxCount) {
+                                    (count >= maxCount))
+                            {
+                                if (count > maxCount)
+                                {
                                     maxResidue = res;
-                                } else if (maxResidue.indexOf(res) == -1) {
+                                }
+                                else if (maxResidue.indexOf(res) == -1)
+                                {
                                     maxResidue += res;
                                 }
 
@@ -70,15 +94,22 @@ public class AAFrequency {
                             }
 
                             residueHash.put(res, new Integer(count));
-                        } else {
+                        }
+                        else
+                        {
                             residueHash.put(res, new Integer(1));
                         }
-                    } else {
-                        if (residueHash.containsKey("-")) {
+                    }
+                    else
+                    {
+                        if (residueHash.containsKey("-"))
+                        {
                             int count = ((Integer) residueHash.get("-")).intValue();
                             count++;
                             residueHash.put("-", new Integer(count));
-                        } else {
+                        }
+                        else
+                        {
                             residueHash.put("-", new Integer(1));
                         }
                     }
@@ -87,7 +118,8 @@ public class AAFrequency {
 
             residueHash.put("maxCount", new Integer(maxCount));
 
-            if (maxCount < 0) {
+            if (maxCount < 0)
+            {
                 System.out.println("asasa " + maxCount);
             }
 
@@ -99,279 +131,4 @@ public class AAFrequency {
 
         return result;
     }
-
-    public static Vector calculatePID(SequenceI refseq, Vector sequences,
-        int window, int start, int end) {
-        Vector result = new Vector();
-
-        boolean init = true;
-
-        Vector prev = null;
-
-        for (int i = start; i <= end; i++) {
-            Vector values = new Vector();
-
-            result.addElement(values);
-
-            // If start < window/2 then set value to zero.
-            if ((i < (window / 2)) ||
-                    (i >= (refseq.getSequence().length() - (window / 2)))) {
-                for (int j = 0; j < sequences.size(); j++) {
-                    values.addElement(new Integer(0));
-                }
-            } else if (init == true) {
-                init = false;
-
-                int winstart = i - (window / 2);
-                int winend = i + (window / 2);
-
-                if ((window % 2) != 0) {
-                    winend++;
-                }
-
-                for (int j = 0; j < sequences.size(); j++) {
-                    values.addElement(new Integer(0));
-                }
-
-                for (int k = winstart; k <= winend; k++) {
-                    String refchar = refseq.getSequence().substring(k, k + 1);
-
-                    if (jalview.util.Comparison.isGap(refchar.charAt(0))) {
-                        refchar = "-";
-                    } else {
-                        for (int j = 0; j < sequences.size(); j++) {
-                            Sequence s = (Sequence) sequences.elementAt(j);
-
-                            if (s.getSequence().length() > k) {
-                                String res = s.getSequence().substring(k, k +
-                                        1); // no gapchar test needed
-
-                                if (res.equals(refchar)) {
-                                    int val = ((Integer) values.elementAt(j)).intValue();
-                                    val++;
-                                    values.setElementAt(new Integer(val), j);
-                                }
-                            }
-                        }
-                    }
-                }
-
-                prev = values;
-            } else {
-                int winstart = i - (window / 2);
-                int winend = i + (window / 2);
-
-                if ((window % 2) != 0) {
-                    winend++;
-                }
-
-                // We need to take the previous set of values
-                // subtract the pid at winstart-1
-                // and add the pid at winend;
-                String pre_refchar = refseq.getSequence().substring(winstart -
-                        1, winstart);
-                String pos_refchar = "-";
-
-                if (refseq.getSequence().length() > winend) {
-                    pos_refchar = refseq.getSequence().substring(winend,
-                            winend + 1);
-                }
-
-                for (int j = 0; j < sequences.size(); j++) {
-                    // First copy the pid value from i-1
-                    int val = ((Integer) prev.elementAt(j)).intValue();
-
-                    Sequence s = (Sequence) sequences.elementAt(j);
-
-                    String pre_char = s.getSequence().substring(winstart - 1,
-                            winstart);
-
-                    String pos_char = "-";
-
-                    if (s.getSequence().length() > winend) {
-                        pos_char = s.getSequence().substring(winend, winend +
-                                1);
-                    }
-
-                    // Now substract 1 if the chars at winstart-1 match
-                    if ((jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false) &&
-                            pre_char.equals(pre_refchar)) {
-                        val--;
-                    }
-
-                    if ((jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false) &&
-                            pos_char.equals(pos_refchar)) {
-                        val++;
-                    }
-
-                    values.addElement(new Integer(val));
-                }
-
-                prev = values;
-            }
-        }
-
-        return result;
-    }
-
-    public static Hashtable findBlocks(Vector seqs, int start, int end,
-        Vector exc) {
-        // start and end are in real (not relative coords);
-        // The coords in the hashtable that is returned are in relative coords
-        // i.e. start from 0
-        Hashtable blocks = new Hashtable();
-
-        boolean prev = false;
-        int bstart = -1;
-
-        for (int i = start; i <= end; i++) {
-            SequenceI seq = (SequenceI) seqs.elementAt(0);
-
-            char c = seq.getCharAt(i);
-
-            boolean found = true;
-
-            int j = 1;
-
-            while ((j < seqs.size()) && (found == true)) {
-                SequenceI jseq = (SequenceI) seqs.elementAt(j);
-
-                if (!exc.contains(jseq)) {
-                    char cc = jseq.getCharAt(i);
-
-                    if (cc != c) {
-                        found = false;
-                    }
-                }
-
-                j++;
-            }
-
-            if ((prev == false) && (found == true)) {
-                bstart = i;
-            } else if ((prev == true) && (found == false) && (bstart != -1)) {
-                int blockstart = bstart - start;
-                int blocklen = i - bstart;
-
-                //System.out.println("Start len " + blockstart + " " + blocklen);
-                for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {
-                    blocks.put(new Integer(jj), new Integer(blocklen));
-                }
-
-                bstart = -1;
-            }
-
-            prev = found;
-        }
-
-        if (bstart != -1) {
-            int blockstart = bstart - start;
-            int blocklen = end - bstart;
-
-            //  System.out.println("Start len " + blockstart + " " + blocklen);
-            for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {
-                blocks.put(new Integer(blockstart), new Integer(blocklen));
-            }
-        }
-
-        return blocks;
-    }
-
-    public static Hashtable findKmerCount(SequenceI seq, int start, int end,
-        int window, int step, Vector kmers) {
-        int tmpstart = start;
-        Hashtable vals = new Hashtable();
-
-        while (tmpstart <= end) {
-            String tmpstr = seq.getSequence().substring(tmpstart -
-                    (window / 2), tmpstart + (window / 2));
-
-            int count = 0;
-
-            //System.out.println("Str " + tmpstr);
-            for (int ii = 0; ii < kmers.size(); ii++) {
-                String kmer = ((SequenceI) kmers.elementAt(ii)).getSequence();
-
-                int i = -1;
-
-                while (tmpstr.indexOf(kmer, i) != -1) {
-                    i = tmpstr.indexOf(kmer, i);
-
-                    i++;
-                    count++;
-                }
-
-                ii++;
-            }
-
-            vals.put(new Integer(tmpstart), new Integer(count));
-            tmpstart += step;
-        }
-
-        return vals;
-    }
-
-    public static Hashtable findBlockStarts(Vector seqs, int start, int end,
-        Vector exc) {
-        // start and end are in real (not relative coords);
-        // The coords in the hashtable that is returned are in relative coords
-        // i.e. start from 0
-        Hashtable blocks = new Hashtable();
-
-        boolean prev = false;
-        int bstart = -1;
-
-        for (int i = start; i <= end; i++) {
-            SequenceI seq = (SequenceI) seqs.elementAt(0);
-
-            char c = seq.getCharAt(i);
-
-            boolean found = true;
-
-            int j = 1;
-
-            while ((j < seqs.size()) && (found == true)) {
-                SequenceI jseq = (SequenceI) seqs.elementAt(j);
-
-                if (!exc.contains(jseq)) {
-                    char cc = jseq.getCharAt(i);
-
-                    if (cc != c) {
-                        found = false;
-                    }
-                }
-
-                j++;
-            }
-
-            if ((prev == false) && (found == true)) {
-                bstart = i;
-            } else if ((prev == true) && (found == false) && (bstart != -1)) {
-                int blockstart = bstart - start;
-                int blocklen = i - bstart;
-
-                //		System.out.println("Start len " + blockstart + " " + blocklen);
-                //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
-                blocks.put(new Integer(blockstart), new Integer(blocklen));
-
-                //	}
-                bstart = -1;
-            }
-
-            prev = found;
-        }
-
-        if (bstart != -1) {
-            int blockstart = bstart - start;
-            int blocklen = end - bstart;
-
-            //  System.out.println("Start len " + blockstart + " " + blocklen);
-            //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
-            blocks.put(new Integer(blockstart), new Integer(blocklen));
-
-            // }
-        }
-
-        return blocks;
-    }
 }
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 47c17a3..60ad85c 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,23 +20,28 @@ package jalview.analysis;
 
 import jalview.datamodel.SequenceI;
 
-import jalview.io.*;
-
 import jalview.schemes.*;
 
 import jalview.util.*;
 
 import java.awt.*;
 
-import java.io.*;
-
 import java.util.*;
 
 
-public class AlignSeq {
+/**
+ *
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignSeq
+{
+    /** DOCUMENT ME!! */
     public static java.util.Hashtable dnaHash = new java.util.Hashtable();
 
-    static {
+    static
+    {
         dnaHash.put("C", new Integer(0));
         dnaHash.put("T", new Integer(1));
         dnaHash.put("A", new Integer(2));
@@ -45,7 +50,8 @@ public class AlignSeq {
     }
 
     static String[] dna = { "C", "T", "A", "G", "-" };
-    static String[] pep = {
+    static String[] pep =
+    {
         "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
         "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-"
     };
@@ -65,11 +71,21 @@ public class AlignSeq {
     int[] aseq2;
     String astr1 = "";
     String astr2 = "";
+
+    /** DOCUMENT ME!! */
     public int seq1start;
+
+    /** DOCUMENT ME!! */
     public int seq1end;
+
+    /** DOCUMENT ME!! */
     public int seq2start;
+
+    /** DOCUMENT ME!! */
     public int seq2end;
     int count;
+
+    /** DOCUMENT ME!! */
     public int maxscore;
     float pid;
     int prev = 0;
@@ -82,84 +98,171 @@ public class AlignSeq {
     String type;
     Runtime rt;
 
-    public AlignSeq() {
-    }
 
-    public AlignSeq(SequenceI s1, SequenceI s2, String type) {
+    /**
+     * Creates a new AlignSeq object.
+     *
+     * @param s1 DOCUMENT ME!
+     * @param s2 DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     */
+    public AlignSeq(SequenceI s1, SequenceI s2, String type)
+    {
         rt = Runtime.getRuntime();
         SeqInit(s1, s2, type);
     }
 
-    public int getMaxScore() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMaxScore()
+    {
         return maxscore;
     }
 
-    public int getSeq2Start() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSeq2Start()
+    {
         return seq2start;
     }
 
-    public int getSeq2End() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSeq2End()
+    {
         return seq2end;
     }
 
-    public int getSeq1Start() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSeq1Start()
+    {
         return seq1start;
     }
 
-    public int getSeq1End() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSeq1End()
+    {
         return seq1end;
     }
 
-    public String getOutput() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getOutput()
+    {
         return output;
     }
 
-    public String getAStr1() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getAStr1()
+    {
         return astr1;
     }
 
-    public String getAStr2() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getAStr2()
+    {
         return astr2;
     }
 
-    public int[] getASeq1() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] getASeq1()
+    {
         return aseq1;
     }
 
-    public int[] getASeq2() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] getASeq2()
+    {
         return aseq2;
     }
 
-    public SequenceI getS1() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getS1()
+    {
         return s1;
     }
 
-    public SequenceI getS2() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getS2()
+    {
         return s2;
     }
 
-    public void SeqInit(SequenceI s1, SequenceI s2, String type) {
-        s1str = extractGaps(".", s1.getSequence());
-        s2str = extractGaps(".", s2.getSequence());
-        s1str = extractGaps("-", s1str);
-        s2str = extractGaps("-", s2str);
-        s1str = extractGaps(" ", s1str);
-        s2str = extractGaps(" ", s2str);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s1 DOCUMENT ME!
+     * @param s2 DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     */
+    public void SeqInit(SequenceI s1, SequenceI s2, String type)
+    {
+        s1str = extractGaps(jalview.util.Comparison.GapChars, s1.getSequence());
+        s2str = extractGaps(jalview.util.Comparison.GapChars, s2.getSequence());
 
         this.s1 = s1;
         this.s2 = s2;
 
         this.type = type;
 
-        if (type.equals("pep")) {
+        if (type.equals("pep"))
+        {
             lookup = ResidueProperties.getBLOSUM62();
             intToStr = pep;
             defInt = 23;
-        } else if (type.equals("dna")) {
+        }
+        else if (type.equals("dna"))
+        {
             lookup = ResidueProperties.getDNA();
             intToStr = dna;
             defInt = 4;
-        } else {
+        }
+        else
+        {
             output = output + ("Wrong type = dna or pep only");
             System.exit(0);
         }
@@ -205,20 +308,28 @@ public class AlignSeq {
         //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
     }
 
-    public void traceAlignment() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void traceAlignment()
+    {
         // Find the maximum score along the rhs or bottom row
         int max = -9999;
 
-        for (int i = 0; i < seq1.length; i++) {
-            if (score[i][seq2.length - 1] > max) {
+        for (int i = 0; i < seq1.length; i++)
+        {
+            if (score[i][seq2.length - 1] > max)
+            {
                 max = score[i][seq2.length - 1];
                 maxi = i;
                 maxj = seq2.length - 1;
             }
         }
 
-        for (int j = 0; j < seq2.length; j++) {
-            if (score[seq1.length - 1][j] > max) {
+        for (int j = 0; j < seq2.length; j++)
+        {
+            if (score[seq1.length - 1][j] > max)
+            {
                 max = score[seq1.length - 1][j];
                 maxi = seq1.length - 1;
                 maxj = j;
@@ -239,27 +350,35 @@ public class AlignSeq {
 
         count = (seq1.length + seq2.length) - 1;
 
-        while ((i > 0) && (j > 0)) {
-            if ((aseq1[count] != defInt) && (i >= 0)) {
+        while ((i > 0) && (j > 0))
+        {
+            if ((aseq1[count] != defInt) && (i >= 0))
+            {
                 aseq1[count] = seq1[i];
                 astr1 = intToStr[seq1[i]] + astr1;
             }
 
-            if ((aseq2[count] != defInt) && (j > 0)) {
+            if ((aseq2[count] != defInt) && (j > 0))
+            {
                 aseq2[count] = seq2[j];
                 astr2 = intToStr[seq2[j]] + astr2;
             }
 
             trace = findTrace(i, j);
 
-            if (trace == 0) {
+            if (trace == 0)
+            {
                 i--;
                 j--;
-            } else if (trace == 1) {
+            }
+            else if (trace == 1)
+            {
                 j--;
                 aseq1[count] = defInt;
                 astr1 = "-" + astr1.substring(1);
-            } else if (trace == -1) {
+            }
+            else if (trace == -1)
+            {
                 i--;
                 aseq2[count] = defInt;
                 astr2 = "-" + astr2.substring(1);
@@ -271,22 +390,29 @@ public class AlignSeq {
         seq1start = i + 1;
         seq2start = j + 1;
 
-        if (aseq1[count] != defInt) {
+        if (aseq1[count] != defInt)
+        {
             aseq1[count] = seq1[i];
             astr1 = intToStr[seq1[i]] + astr1;
         }
 
-        if (aseq2[count] != defInt) {
+        if (aseq2[count] != defInt)
+        {
             aseq2[count] = seq2[j];
             astr2 = intToStr[seq2[j]] + astr2;
         }
     }
 
-    public void printAlignment() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void printAlignment()
+    {
         // Find the biggest id length for formatting purposes
         int maxid = s1.getName().length();
 
-        if (s2.getName().length() > maxid) {
+        if (s2.getName().length() > maxid)
+        {
             maxid = s2.getName().length();
         }
 
@@ -294,8 +420,6 @@ public class AlignSeq {
         int nochunks = ((aseq1.length - count) / len) + 1;
         pid = 0;
 
-        int overlap = 0;
-
         output = output + ("Score = " + score[maxi][maxj] + "\n");
         output = output +
             ("Length of alignment = " + (aseq1.length - count) + "\n");
@@ -310,13 +434,16 @@ public class AlignSeq {
             (" :  " + seq2start + " - " + seq2end + " (Sequence length = " +
             s2str.length() + ")\n\n");
 
-        for (int j = 0; j < nochunks; j++) {
+        for (int j = 0; j < nochunks; j++)
+        {
             // Print the first aligned sequence
             output = output +
                 (new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
 
-            for (int i = 0; i < len; i++) {
-                if ((count + i + (j * len)) < aseq1.length) {
+            for (int i = 0; i < len; i++)
+            {
+                if ((count + i + (j * len)) < aseq1.length)
+                {
                     output = output +
                         (new Format("%s").form(intToStr[aseq1[count + i +
                             (j * len)]]));
@@ -328,22 +455,32 @@ public class AlignSeq {
                 (new Format("%" + (maxid) + "s").form(" ") + " ");
 
             // Print out the matching chars
-            for (int i = 0; i < len; i++) {
-                if ((count + i + (j * len)) < aseq1.length) {
+            for (int i = 0; i < len; i++)
+            {
+                if ((count + i + (j * len)) < aseq1.length)
+                {
                     if (intToStr[aseq1[count + i + (j * len)]].equals(
                                 intToStr[aseq2[count + i + (j * len)]]) &&
-                            !intToStr[aseq1[count + i + (j * len)]].equals("-")) {
+                            !intToStr[aseq1[count + i + (j * len)]].equals("-"))
+                    {
                         pid++;
                         output = output + ("|");
-                    } else if (type.equals("pep")) {
+                    }
+                    else if (type.equals("pep"))
+                    {
                         if (ResidueProperties.getPAM250(
                                     intToStr[aseq1[count + i + (j * len)]],
-                                    intToStr[aseq2[count + i + (j * len)]]) > 0) {
+                                    intToStr[aseq2[count + i + (j * len)]]) > 0)
+                        {
                             output = output + (".");
-                        } else {
+                        }
+                        else
+                        {
                             output = output + (" ");
                         }
-                    } else {
+                    }
+                    else
+                    {
                         output = output + (" ");
                     }
                 }
@@ -354,8 +491,10 @@ public class AlignSeq {
             output = output +
                 (new Format("%" + (maxid) + "s").form(s2.getName()) + " ");
 
-            for (int i = 0; i < len; i++) {
-                if ((count + i + (j * len)) < aseq1.length) {
+            for (int i = 0; i < len; i++)
+            {
+                if ((count + i + (j * len)) < aseq1.length)
+                {
                     output = output +
                         (new Format("%s").form(intToStr[aseq2[count + i +
                             (j * len)]]));
@@ -369,24 +508,35 @@ public class AlignSeq {
         output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));
     }
 
-    public void printScoreMatrix(int[][] mat) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param mat DOCUMENT ME!
+     */
+    public void printScoreMatrix(int[][] mat)
+    {
         int n = seq1.length;
         int m = seq2.length;
 
-        for (int i = 0; i < n; i++) {
+        for (int i = 0; i < n; i++)
+        {
             // Print the top sequence
-            if (i == 0) {
+            if (i == 0)
+            {
                 Format.print(System.out, "%8s", s2str.substring(0, 1));
 
-                for (int jj = 1; jj < m; jj++) {
+                for (int jj = 1; jj < m; jj++)
+                {
                     Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));
                 }
 
                 System.out.println();
             }
 
-            for (int j = 0; j < m; j++) {
-                if (j == 0) {
+            for (int j = 0; j < m; j++)
+            {
+                if (j == 0)
+                {
                     Format.print(System.out, "%3s", s1str.substring(i, i + 1));
                 }
 
@@ -397,25 +547,42 @@ public class AlignSeq {
         }
     }
 
-    public int findTrace(int i, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findTrace(int i, int j)
+    {
         int t = 0;
         int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
 
-        if (F[i][j] > max) {
+        if (F[i][j] > max)
+        {
             max = F[i][j];
             t = -1;
-        } else if (F[i][j] == max) {
-            if (prev == -1) {
+        }
+        else if (F[i][j] == max)
+        {
+            if (prev == -1)
+            {
                 max = F[i][j];
                 t = -1;
             }
         }
 
-        if (E[i][j] >= max) {
+        if (E[i][j] >= max)
+        {
             max = E[i][j];
             t = 1;
-        } else if (E[i][j] == max) {
-            if (prev == 1) {
+        }
+        else if (E[i][j] == max)
+        {
+            if (prev == 1)
+            {
                 max = E[i][j];
                 t = 1;
             }
@@ -426,7 +593,11 @@ public class AlignSeq {
         return t;
     }
 
-    public void calcScoreMatrix() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void calcScoreMatrix()
+    {
         int n = seq1.length;
         int m = seq2.length;
 
@@ -436,7 +607,8 @@ public class AlignSeq {
         F[0][0] = 0;
 
         // Calculate the top row first
-        for (int j = 1; j < m; j++) {
+        for (int j = 1; j < m; j++)
+        {
             // What should these values be? 0 maybe
             E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
             F[0][j] = -gapExtend;
@@ -448,7 +620,8 @@ public class AlignSeq {
         }
 
         // Now do the left hand column
-        for (int i = 1; i < n; i++) {
+        for (int i = 1; i < n; i++)
+        {
             E[i][0] = -gapOpen;
             F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
 
@@ -457,8 +630,10 @@ public class AlignSeq {
         }
 
         // Now do all the other rows
-        for (int i = 1; i < n; i++) {
-            for (int j = 1; j < m; j++) {
+        for (int i = 1; i < n; i++)
+        {
+            for (int j = 1; j < m; j++)
+            {
                 E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] -
                         gapExtend);
                 F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] -
@@ -471,72 +646,115 @@ public class AlignSeq {
         }
     }
 
-    public static String extractChars(String chars, String seq) {
-        String out = seq;
 
-        for (int i = 0; i < chars.length(); i++) {
-            String gap = chars.substring(i, i + 1);
-            out = extractGaps(gap, out);
-        }
-
-        return out;
-    }
 
-    public static String extractGaps(String gapChar, String seq) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gapChar DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String extractGaps(String gapChar, String seq)
+    {
         StringTokenizer str = new StringTokenizer(seq, gapChar);
         String newString = "";
 
-        while (str.hasMoreTokens()) {
+        while (str.hasMoreTokens())
+        {
             newString = newString + str.nextToken();
         }
 
         return newString;
     }
 
-    public int max(int i1, int i2, int i3) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i1 DOCUMENT ME!
+     * @param i2 DOCUMENT ME!
+     * @param i3 DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int max(int i1, int i2, int i3)
+    {
         int max = i1;
 
-        if (i2 > i1) {
+        if (i2 > i1)
+        {
             max = i2;
         }
 
-        if (i3 > max) {
+        if (i3 > max)
+        {
             max = i3;
         }
 
         return max;
     }
 
-    public int max(int i1, int i2) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i1 DOCUMENT ME!
+     * @param i2 DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int max(int i1, int i2)
+    {
         int max = i1;
 
-        if (i2 > i1) {
+        if (i2 > i1)
+        {
             max = i2;
         }
 
         return max;
     }
 
-    public int[] stringToInt(String s, String type) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] stringToInt(String s, String type)
+    {
         int[] seq1 = new int[s.length()];
 
-        for (int i = 0; i < s.length(); i++) {
+        for (int i = 0; i < s.length(); i++)
+        {
             String ss = s.substring(i, i + 1).toUpperCase();
 
-            try {
-                if (type.equals("pep")) {
+            try
+            {
+                if (type.equals("pep"))
+                {
                     seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();
-                } else if (type.equals("dna")) {
+                }
+                else if (type.equals("dna"))
+                {
                     seq1[i] = ((Integer) dnaHash.get(ss)).intValue();
                 }
 
-                if (seq1[i] > 23) {
+                if (seq1[i] > 23)
+                {
                     seq1[i] = 23;
                 }
-            } catch (Exception e) {
-                if (type.equals("dna")) {
+            }
+            catch (Exception e)
+            {
+                if (type.equals("dna"))
+                {
                     seq1[i] = 4;
-                } else {
+                }
+                else
+                {
                     seq1[i] = 23;
                 }
             }
@@ -545,18 +763,32 @@ public class AlignSeq {
         return seq1;
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param mat DOCUMENT ME!
+     * @param n DOCUMENT ME!
+     * @param m DOCUMENT ME!
+     * @param psize DOCUMENT ME!
+     */
     public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
-        int psize) {
+        int psize)
+    {
         int max = -1000;
         int min = 1000;
 
-        for (int i = 0; i < n; i++) {
-            for (int j = 0; j < m; j++) {
-                if (mat[i][j] >= max) {
+        for (int i = 0; i < n; i++)
+        {
+            for (int j = 0; j < m; j++)
+            {
+                if (mat[i][j] >= max)
+                {
                     max = mat[i][j];
                 }
 
-                if (mat[i][j] <= min) {
+                if (mat[i][j] <= min)
+                {
                     min = mat[i][j];
                 }
             }
@@ -564,8 +796,10 @@ public class AlignSeq {
 
         System.out.println(max + " " + min);
 
-        for (int i = 0; i < n; i++) {
-            for (int j = 0; j < m; j++) {
+        for (int i = 0; i < n; i++)
+        {
+            for (int j = 0; j < m; j++)
+            {
                 int x = psize * i;
                 int y = psize * j;
 
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index bdd6bce..20101dc 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -20,8 +20,6 @@ package jalview.analysis;
 
 import jalview.datamodel.*;
 
-import jalview.io.*;
-
 import jalview.util.*;
 
 import java.util.*;
@@ -29,8 +27,8 @@ import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
-public class AlignmentSorter {
-    /**    */
+public class AlignmentSorter
+{
     static boolean sortIdAscending = true;
     static int lastGroupHash = 0;
     static boolean sortGroupAscending = true;
@@ -45,13 +43,15 @@ public class AlignmentSorter {
      * @param align AlignmentI
      * @param s SequenceI
      */
-    public static void sortByPID(AlignmentI align, SequenceI s) {
+    public static void sortByPID(AlignmentI align, SequenceI s)
+    {
         int nSeq = align.getHeight();
 
         float[] scores = new float[nSeq];
         SequenceI[] seqs = new SequenceI[nSeq];
 
-        for (int i = 0; i < nSeq; i++) {
+        for (int i = 0; i < nSeq; i++)
+        {
             scores[i] = Comparison.PID(align.getSequenceAt(i), s);
             seqs[i] = align.getSequenceAt(i);
         }
@@ -61,129 +61,199 @@ public class AlignmentSorter {
         setReverseOrder(align, seqs);
     }
 
-    private static void setReverseOrder(AlignmentI align, SequenceI[] seqs) {
+    /**
+     * Reverse the order of the sort
+     *
+     * @param align DOCUMENT ME!
+     * @param seqs DOCUMENT ME!
+     */
+    private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
+    {
         int nSeq = seqs.length;
 
         int len = 0;
 
-        if ((nSeq % 2) == 0) {
+        if ((nSeq % 2) == 0)
+        {
             len = nSeq / 2;
-        } else {
+        }
+        else
+        {
             len = (nSeq + 1) / 2;
         }
 
         // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-        for (int i = 0; i < len; i++) {
+        for (int i = 0; i < len; i++)
+        {
             //SequenceI tmp = seqs[i];
             align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
             align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
         }
     }
 
-    private static void setOrder(AlignmentI align, Vector tmp) {
+    /**
+     * Sets the Alignment object with the given sequences
+     *
+     * @param align Alignment object to be updated
+     * @param tmp sequences as a vector
+     */
+    private static void setOrder(AlignmentI align, Vector tmp)
+    {
         setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
     }
 
-    private static void setOrder(AlignmentI align, SequenceI[] seqs) {
-
+    /**
+     * Sets the Alignment object with the given sequences
+     *
+     * @param align DOCUMENT ME!
+     * @param seqs sequences as an array
+     */
+    private static void setOrder(AlignmentI align, SequenceI[] seqs)
+    {
         // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
         Vector algn = align.getSequences();
+
         for (int i = 0; i < seqs.length; i++)
         {
-          algn.setElementAt(seqs[i], i);
+            algn.setElementAt(seqs[i], i);
         }
     }
 
-    public static void sortByID(AlignmentI align) {
+    /**
+     * Sorts by ID. Numbers are sorted before letters.
+     *
+     * @param align The alignment object to sort
+     */
+    public static void sortByID(AlignmentI align)
+    {
         int nSeq = align.getHeight();
 
         String[] ids = new String[nSeq];
         SequenceI[] seqs = new SequenceI[nSeq];
 
-        for (int i = 0; i < nSeq; i++) {
+        for (int i = 0; i < nSeq; i++)
+        {
             ids[i] = align.getSequenceAt(i).getName();
             seqs[i] = align.getSequenceAt(i);
         }
 
         QuickSort.sort(ids, seqs);
 
-        if (sortIdAscending) {
+        if (sortIdAscending)
+        {
             setReverseOrder(align, seqs);
-        } else {
+        }
+        else
+        {
             setOrder(align, seqs);
         }
 
         sortIdAscending = !sortIdAscending;
     }
 
-    public static void sortByGroup(AlignmentI align) {
-      //MAINTAINS ORIGNAL SEQUENCE ORDER,
-      //ORDERS BY GROUP SIZE
-
+    /**
+     * Sorts the alignment by size of group.
+     * <br>Maintains the order of sequences in each group
+     * by order in given alignment object.
+     *
+     * @param align sorts the given alignment object by group
+     */
+    public static void sortByGroup(AlignmentI align)
+    {
+        //MAINTAINS ORIGNAL SEQUENCE ORDER,
+        //ORDERS BY GROUP SIZE
         Vector groups = new Vector();
 
-        if (groups.hashCode() != lastGroupHash) {
+        if (groups.hashCode() != lastGroupHash)
+        {
             sortGroupAscending = true;
             lastGroupHash = groups.hashCode();
-        } else {
+        }
+        else
+        {
             sortGroupAscending = !sortGroupAscending;
         }
 
         //SORTS GROUPS BY SIZE
         //////////////////////
-        for(int i=0; i<align.getGroups().size(); i++)
+        for (int i = 0; i < align.getGroups().size(); i++)
         {
-           SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
-
-           for(int j=0; j<groups.size(); j++)
-           {
-             SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
-             if(sg.getSize() > sg2.getSize())
-             {
-               groups.insertElementAt(sg, j);
-               break;
-             }
-           }
-
-           if (!groups.contains(sg))
-           {
-             groups.addElement(sg);
-           }
+            SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
+
+            for (int j = 0; j < groups.size(); j++)
+            {
+                SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+
+                if (sg.getSize() > sg2.getSize())
+                {
+                    groups.insertElementAt(sg, j);
+
+                    break;
+                }
+            }
+
+            if (!groups.contains(sg))
+            {
+                groups.addElement(sg);
+            }
         }
 
         //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
         ///////////////////////////////////////////////
         Vector seqs = new Vector();
+
         for (int i = 0; i < groups.size(); i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            SequenceI [] orderedseqs = sg.getSequencesInOrder(align);
+            SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
+
             for (int j = 0; j < orderedseqs.length; j++)
             {
                 seqs.addElement(orderedseqs[j]);
             }
         }
 
-        if (sortGroupAscending) {
+        if (sortGroupAscending)
+        {
             setOrder(align, seqs);
-        } else {
+        }
+        else
+        {
             setReverseOrder(align,
                 vectorSubsetToArray(seqs, align.getSequences()));
         }
     }
 
-    private static SequenceI[] vectorToArray(Vector tmp) {
-
+    /**
+     * Converts Vector to array.
+     * java 1.18 does not have Vector.toArray()
+     *
+     * @param tmp Vector of SequenceI objects
+     *
+     * @return array of Sequence[]
+     */
+    private static SequenceI[] vectorToArray(Vector tmp)
+    {
         SequenceI[] seqs = new SequenceI[tmp.size()];
 
-        for (int i = 0; i < tmp.size(); i++) {
+        for (int i = 0; i < tmp.size(); i++)
+        {
             seqs[i] = (SequenceI) tmp.elementAt(i);
         }
 
         return seqs;
     }
 
-    private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tmp DOCUMENT ME!
+     * @param mask DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+    {
         Vector seqs = new Vector();
         int i;
         boolean[] tmask = new boolean[mask.size()];
@@ -191,8 +261,8 @@ public class AlignmentSorter {
         for (i = 0; i < mask.size(); i++)
             tmask[i] = true;
 
-        for (i = 0; i < tmp.size(); i++) {
-
+        for (i = 0; i < tmp.size(); i++)
+        {
             Object sq = tmp.elementAt(i);
 
             if (mask.contains(sq) && tmask[mask.indexOf(sq)])
@@ -203,47 +273,73 @@ public class AlignmentSorter {
         }
 
         for (i = 0; i < tmask.length; i++)
-            if (tmask[i]) {
+            if (tmask[i])
+            {
                 seqs.addElement(mask.elementAt(i));
             }
 
         return vectorToArray(seqs);
     }
 
-    public static void sortBy(AlignmentI align, AlignmentOrder order) {
+    /**
+     * Sorts by a given AlignmentOrder object
+     *
+     * @param align Alignment to order
+     * @param order specified order for alignment
+     */
+    public static void sortBy(AlignmentI align, AlignmentOrder order)
+    {
         // Get an ordered vector of sequences which may also be present in align
         Vector tmp = order.getOrder();
 
-        if (lastOrder == order) {
+        if (lastOrder == order)
+        {
             sortOrderAscending = !sortOrderAscending;
-        } else {
+        }
+        else
+        {
             sortOrderAscending = true;
         }
 
-        if (sortOrderAscending) {
+        if (sortOrderAscending)
+        {
             setOrder(align, tmp);
-        } else {
+        }
+        else
+        {
             setReverseOrder(align,
                 vectorSubsetToArray(tmp, align.getSequences()));
         }
     }
 
-    public static Vector getOrderByTree(AlignmentI align, NJTree tree) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param align alignment to order
+     * @param tree tree which has
+     *
+     * @return DOCUMENT ME!
+     */
+    private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+    {
         int nSeq = align.getHeight();
 
         Vector tmp = new Vector();
 
         tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
 
-        if (tmp.size() != nSeq) {
+        if (tmp.size() != nSeq)
+        {
             // TODO: JBPNote - decide if this is always an error
             // (eg. not when a tree is associated to another alignment which has more
             //  sequences)
-            if (tmp.size() < nSeq) {
+            if (tmp.size() < nSeq)
+            {
                 addStrays(align, tmp);
             }
 
-            if (tmp.size() != nSeq) {
+            if (tmp.size() != nSeq)
+            {
                 System.err.println("ERROR: tmp.size()=" + tmp.size() +
                     " != nseq=" + nSeq + " in getOrderByTree");
             }
@@ -252,60 +348,100 @@ public class AlignmentSorter {
         return tmp;
     }
 
-    public static void sortByTree(AlignmentI align, NJTree tree) {
+    /**
+     * Sorts the alignment by a given tree
+     *
+     * @param align alignment to order
+     * @param tree tree which has
+     */
+    public static void sortByTree(AlignmentI align, NJTree tree)
+    {
         Vector tmp = getOrderByTree(align, tree);
 
         // tmp should properly permute align with tree.
-        if (lastTree != tree) {
+        if (lastTree != tree)
+        {
             sortTreeAscending = true;
             lastTree = tree;
-        } else {
+        }
+        else
+        {
             sortTreeAscending = !sortTreeAscending;
         }
 
-        if (sortTreeAscending) {
+        if (sortTreeAscending)
+        {
             setOrder(align, tmp);
-        } else {
+        }
+        else
+        {
             setReverseOrder(align,
                 vectorSubsetToArray(tmp, align.getSequences()));
         }
     }
 
-    private static void addStrays(AlignmentI align, Vector seqs) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param align DOCUMENT ME!
+     * @param seqs DOCUMENT ME!
+     */
+    private static void addStrays(AlignmentI align, Vector seqs)
+    {
         int nSeq = align.getHeight();
 
-        for (int i = 0; i < nSeq; i++) {
-            if (!seqs.contains(align.getSequenceAt(i))) {
+        for (int i = 0; i < nSeq; i++)
+        {
+            if (!seqs.contains(align.getSequenceAt(i)))
+            {
                 seqs.addElement(align.getSequenceAt(i));
             }
         }
 
-        if (nSeq != seqs.size()) {
+        if (nSeq != seqs.size())
+        {
             System.err.println(
                 "ERROR: Size still not right even after addStrays");
         }
     }
 
-    public static Vector _sortByTree(SequenceNode node, Vector tmp,
-        Vector seqset) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param tmp DOCUMENT ME!
+     * @param seqset DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static Vector _sortByTree(SequenceNode node, Vector tmp,
+        Vector seqset)
+    {
+        if (node == null)
+        {
             return tmp;
         }
 
         SequenceNode left = (SequenceNode) node.left();
         SequenceNode right = (SequenceNode) node.right();
 
-        if ((left == null) && (right == null)) {
-            if (!node.isPlaceholder() && (node.element() != null)) {
-                if (node.element() instanceof SequenceI) {
-                    if (!tmp.contains(node.element())) {
+        if ((left == null) && (right == null))
+        {
+            if (!node.isPlaceholder() && (node.element() != null))
+            {
+                if (node.element() instanceof SequenceI)
+                {
+                    if (!tmp.contains(node.element()))
+                    {
                         tmp.addElement((SequenceI) node.element());
                     }
                 }
             }
 
             return tmp;
-        } else {
+        }
+        else
+        {
             _sortByTree(left, tmp, seqset);
             _sortByTree(right, tmp, seqset);
         }
@@ -321,7 +457,8 @@ public class AlignmentSorter {
      * recover the order of sequences given by the safe numbering scheme introducd
      * SeqsetUtils.uniquify.
      */
-    public static void recoverOrder(SequenceI[] alignment) {
+    public static void recoverOrder(SequenceI[] alignment)
+    {
         float[] ids = new float[alignment.length];
 
         for (int i = 0; i < alignment.length; i++)
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index bfb2e00..0fe4f5e 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -20,12 +20,17 @@ package jalview.analysis;
 
 import jalview.datamodel.*;
 
-import jalview.gui.*;
-
 import java.util.*;
 
 
-public class Conservation {
+/**
+ * Calculates conservation values for a given set of sequences
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Conservation
+{
     Vector sequences;
     int start;
     int end;
@@ -33,7 +38,11 @@ public class Conservation {
     int maxLength = 0; //  used by quality calcs
     boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
     Vector total = new Vector();
+
+    /** Stores calculated quality values */
     public Vector quality;
+
+    /** Stores maximum and minimum values of quality values  */
     public Double[] qualityRange = new Double[2];
     String consString = "";
     Sequence consSequence;
@@ -42,8 +51,19 @@ public class Conservation {
     String name = "";
     int[][] cons2;
 
+    /**
+     * Creates a new Conservation object.
+     *
+     * @param name Name of conservation
+     * @param propHash DOCUMENT ME!
+     * @param threshold to count the residues in residueHash(). commonly used value is 3
+     * @param sequences sequences to be used in calculation
+     * @param start start residue position
+     * @param end end residue position
+     */
     public Conservation(String name, Hashtable propHash, int threshold,
-        Vector sequences, int start, int end) {
+        Vector sequences, int start, int end)
+    {
         this.name = name;
         this.propHash = propHash;
         this.threshold = threshold;
@@ -54,81 +74,115 @@ public class Conservation {
         calcSeqNums();
     }
 
-    private void calcSeqNums() {
-        for (int i = 0; i < sequences.size(); i++) {
+    /**
+     * DOCUMENT ME!
+     */
+    private void calcSeqNums()
+    {
+        for (int i = 0; i < sequences.size(); i++)
+        {
             calcSeqNum(i);
         }
     }
 
-    private void calcSeqNum(int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    private void calcSeqNum(int i)
+    {
         String sq = null; // for dumb jbuilder not-inited exception warning
         int[] sqnum = null;
 
-        if ((i > -1) && (i < sequences.size())) {
+        if ((i > -1) && (i < sequences.size()))
+        {
             sq = ((SequenceI) sequences.elementAt(i)).getSequence();
 
-            if (seqNums.size() <= i) {
+            if (seqNums.size() <= i)
+            {
                 seqNums.addElement(new int[sq.length() + 1]);
             }
 
-            if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0]) {
+            if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
+            {
                 int j;
                 int len;
                 seqNumsChanged = true;
                 sq = ((SequenceI) sequences.elementAt(i)).getSequence();
                 len = sq.length();
 
-                if (maxLength < len) {
+                if (maxLength < len)
+                {
                     maxLength = len;
                 }
 
                 sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length
                 sqnum[0] = sq.hashCode();
 
-                for (j = 1; j <= len; j++) {
+                for (j = 1; j <= len; j++)
+                {
                     sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(
                                 sq.substring(j - 1, j)))).intValue(); // yuk
                 }
 
                 seqNums.setElementAt(sqnum, i);
             }
-        } else {
+        }
+        else
+        {
             // JBPNote INFO level debug
             System.err.println(
                 "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
         }
     }
 
-    public void calculate() {
-        for (int i = start; i <= end; i++) {
+    /**
+     * Calculates the conservation values for given set of sequences
+     */
+    public void calculate()
+    {
+        for (int i = start; i <= end; i++)
+        {
             Hashtable resultHash = null;
             Hashtable residueHash = null;
 
             resultHash = new Hashtable();
             residueHash = new Hashtable();
 
-            for (int j = 0; j < sequences.size(); j++) {
+            for (int j = 0; j < sequences.size(); j++)
+            {
                 // JBPNote - have to make sure elements of the sequences vector
                 //  are tested like this everywhere...
-                if (sequences.elementAt(j) instanceof Sequence) {
+                if (sequences.elementAt(j) instanceof Sequence)
+                {
                     Sequence s = (Sequence) sequences.elementAt(j);
 
-                    if (s.getLength() > i) {
+                    if (s.getLength() > i)
+                    {
                         String res = s.getSequence().substring(i, i + 1);
 
-                        if (residueHash.containsKey(res)) {
+                        if (residueHash.containsKey(res))
+                        {
                             int count = ((Integer) residueHash.get(res)).intValue();
                             count++;
                             residueHash.put(res, new Integer(count));
-                        } else {
+                        }
+                        else
+                        {
                             residueHash.put(res, new Integer(1));
                         }
-                    } else {
-                        if (residueHash.containsKey("-")) {
+                    }
+                    else
+                    {
+                        if (residueHash.containsKey("-"))
+                        {
                             int count = ((Integer) residueHash.get("-")).intValue();
                             count++;
                             residueHash.put("-", new Integer(count));
-                        } else {
+                        }
+                        else
+                        {
                             residueHash.put("-", new Integer(1));
                         }
                     }
@@ -141,26 +195,35 @@ public class Conservation {
             //loop over all the found residues
             Enumeration e = residueHash.keys();
 
-            while (e.hasMoreElements()) {
+            while (e.hasMoreElements())
+            {
                 String res = (String) e.nextElement();
 
-                if (((Integer) residueHash.get(res)).intValue() > thresh) {
+                if (((Integer) residueHash.get(res)).intValue() > thresh)
+                {
                     //Now loop over the properties
                     Enumeration e2 = propHash.keys();
 
-                    while (e2.hasMoreElements()) {
+                    while (e2.hasMoreElements())
+                    {
                         String type = (String) e2.nextElement();
                         Hashtable ht = (Hashtable) propHash.get(type);
 
                         //Have we ticked this before?
-                        if (!resultHash.containsKey(type)) {
-                            if (ht.containsKey(res)) {
+                        if (!resultHash.containsKey(type))
+                        {
+                            if (ht.containsKey(res))
+                            {
                                 resultHash.put(type, ht.get(res));
-                            } else {
+                            }
+                            else
+                            {
                                 resultHash.put(type, ht.get("-"));
                             }
-                        } else if (((Integer) resultHash.get(type)).equals(
-                                    (Integer) ht.get(res)) == false) {
+                        }
+                        else if (((Integer) resultHash.get(type)).equals(
+                                    (Integer) ht.get(res)) == false)
+                        {
                             resultHash.put(type, new Integer(-1));
                         }
                     }
@@ -171,40 +234,23 @@ public class Conservation {
         }
     }
 
-    public int countGaps(int j) {
-        int count = 0;
-
-        for (int i = 0; i < sequences.size(); i++) {
-            if ((j + 1) > ((Sequence) sequences.elementAt(i)).getSequence()
-                               .length()) {
-                count++;
-
-                continue;
-            }
-
-            char c = ((Sequence) sequences.elementAt(i)).getSequence().charAt(j);
-
-            if (jalview.util.Comparison.isGap((c))) {
-                count++;
-            }
-        }
-
-        return count;
-    }
 
     /***
      * countConsNGaps
      * returns gap count in int[0], and conserved residue count in int[1]
      */
-    public int[] countConsNGaps(int j) {
+    public int[] countConsNGaps(int j)
+    {
         int count = 0;
         int cons = 0;
         int nres = 0;
         int[] r = new int[2];
         char f = '$';
 
-        for (int i = 0; i < sequences.size(); i++) {
-            if (j >= ((Sequence) sequences.elementAt(i)).getSequence().length()) {
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            if (j >= ((Sequence) sequences.elementAt(i)).getSequence().length())
+            {
                 count++;
 
                 continue;
@@ -212,15 +258,21 @@ public class Conservation {
 
             char c = ((Sequence) sequences.elementAt(i)).getSequence().charAt(j);
 
-            if (jalview.util.Comparison.isGap((c))) {
+            if (jalview.util.Comparison.isGap((c)))
+            {
                 count++;
-            } else {
+            }
+            else
+            {
                 nres++;
 
-                if (nres == 1) {
+                if (nres == 1)
+                {
                     f = c;
                     cons++;
-                } else if (f == c) {
+                }
+                else if (f == c)
+                {
                     cons++;
                 }
             }
@@ -232,45 +284,64 @@ public class Conservation {
         return r;
     }
 
-    public void verdict(boolean consflag, float percentageGaps) {
+    /**
+     * Calculates the conservation sequence
+     *
+     * @param consflag if true, poitiveve conservation; false calculates negative conservation
+     * @param percentageGaps commonly used value is 25
+     */
+    public void verdict(boolean consflag, float percentageGaps)
+    {
         String consString = "";
 
-        for (int i = start; i <= end; i++) {
+        for (int i = start; i <= end; i++)
+        {
             int[] gapcons = countConsNGaps(i);
-            boolean cons = (gapcons[0] == 1) ? true : false;
             int totGaps = gapcons[1];
             float pgaps = ((float) totGaps * 100) / (float) sequences.size();
 
             //      System.out.println("percentage gaps = "+pgaps+"\n");
-            if (percentageGaps > pgaps) {
+            if (percentageGaps > pgaps)
+            {
                 Hashtable resultHash = (Hashtable) total.elementAt(i - start);
 
                 //Now find the verdict
                 int count = 0;
                 Enumeration e3 = resultHash.keys();
 
-                while (e3.hasMoreElements()) {
+                while (e3.hasMoreElements())
+                {
                     String type = (String) e3.nextElement();
                     Integer result = (Integer) resultHash.get(type);
 
                     //Do we want to count +ve conservation or +ve and -ve cons.?
-                    if (consflag) {
-                        if (result.intValue() == 1) {
+                    if (consflag)
+                    {
+                        if (result.intValue() == 1)
+                        {
                             count++;
                         }
-                    } else {
-                        if (result.intValue() != -1) {
+                    }
+                    else
+                    {
+                        if (result.intValue() != -1)
+                        {
                             count++;
                         }
                     }
                 }
 
-                if (count < 10) {
+                if (count < 10)
+                {
                     consString = consString + String.valueOf(count); // Conserved props!=Identity
-                } else {
+                }
+                else
+                {
                     consString = consString + ((gapcons[0] == 1) ? "*" : "+");
                 }
-            } else {
+            }
+            else
+            {
                 consString = consString + "-";
             }
         }
@@ -278,24 +349,38 @@ public class Conservation {
         consSequence = new Sequence(name, consString, start, end);
     }
 
-    public Sequence getConsSequence() {
+    /**
+     *
+     *
+     * @return Conservation sequence
+     */
+    public Sequence getConsSequence()
+    {
         return consSequence;
     }
 
     // From Alignment.java in jalview118
-    public void findQuality() {
+    public void findQuality()
+    {
         findQuality(0, maxLength - 1);
     }
 
-    private void percentIdentity2() {
+    /**
+     * DOCUMENT ME!
+     */
+    private void percentIdentity2()
+    {
         calcSeqNums(); // updates maxLength, too.
 
-        if ((cons2 == null) || seqNumsChanged) {
+        if ((cons2 == null) || seqNumsChanged)
+        {
             cons2 = new int[maxLength][24];
 
             // Initialize the array
-            for (int j = 0; j < 24; j++) {
-                for (int i = 0; i < maxLength; i++) {
+            for (int j = 0; j < 24; j++)
+            {
+                for (int i = 0; i < maxLength; i++)
+                {
                     cons2[i][j] = 0;
                 }
             }
@@ -303,14 +388,17 @@ public class Conservation {
             int[] sqnum;
             int j = 0;
 
-            while (j < sequences.size()) {
+            while (j < sequences.size())
+            {
                 sqnum = (int[]) seqNums.elementAt(j);
 
-                for (int i = 1; i < sqnum.length; i++) {
+                for (int i = 1; i < sqnum.length; i++)
+                {
                     cons2[i - 1][sqnum[i]]++;
                 }
 
-                for (int i = sqnum.length - 1; i < maxLength; i++) {
+                for (int i = sqnum.length - 1; i < maxLength; i++)
+                {
                     cons2[i][23]++; // gap count
                 }
 
@@ -336,7 +424,14 @@ public class Conservation {
         }
     }
 
-    public void findQuality(int start, int end) {
+    /**
+     * Calculates the quality of the set of sequences
+     *
+     * @param start Start residue
+     * @param end End residue
+     */
+    public void findQuality(int start, int end)
+    {
         quality = new Vector();
 
         double max = -10000;
@@ -354,21 +449,27 @@ public class Conservation {
         for (int l = 0; l < size; l++)
             lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
 
-        for (int j = start; j <= end; j++) {
+        for (int j = start; j <= end; j++)
+        {
             double bigtot = 0;
 
             // First Xr = depends on column only
             double[] x = new double[24];
 
-            for (int ii = 0; ii < 24; ii++) {
+            for (int ii = 0; ii < 24; ii++)
+            {
                 x[ii] = 0;
 
-                try {
-                    for (int i2 = 0; i2 < 24; i2++) {
+                try
+                {
+                    for (int i2 = 0; i2 < 24; i2++)
+                    {
                         x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) +
                         4);
                     }
-                } catch (Exception e) {
+                }
+                catch (Exception e)
+                {
                     System.err.println("Exception during quality calculation.");
                     e.printStackTrace();
                 }
@@ -380,19 +481,24 @@ public class Conservation {
             }
 
             // Now calculate D for each position and sum
-            for (int k = 0; k < size; k++) {
+            for (int k = 0; k < size; k++)
+            {
                 double tot = 0;
                 double[] xx = new double[24];
                 int seqNum = (j < lengths[k])
                     ? ((int[]) seqNums.elementAt(k))[j + 1] : 23; // Sequence, or gap at the end
 
                 // This is a loop over r
-                for (int i = 0; i < 23; i++) {
+                for (int i = 0; i < 23; i++)
+                {
                     double sr = 0;
 
-                    try {
+                    try
+                    {
                         sr = (double) BLOSUM62[i][seqNum] + 4;
-                    } catch (Exception e) {
+                    }
+                    catch (Exception e)
+                    {
                         System.out.println("Exception in sr: " + e);
                         e.printStackTrace();
                     }
@@ -408,7 +514,8 @@ public class Conservation {
             }
 
             // This is the quality for one column
-            if (max < bigtot) {
+            if (max < bigtot)
+            {
                 max = bigtot;
             }
 
@@ -422,14 +529,16 @@ public class Conservation {
 
         double newmax = -10000;
 
-        for (int j = start; j <= end; j++) {
+        for (int j = start; j <= end; j++)
+        {
             double tmp = ((Double) quality.elementAt(j)).doubleValue();
             tmp = ((max - tmp) * (size - cons2[j][23])) / size;
 
             //     System.out.println(tmp+ " " + j);
             quality.setElementAt(new Double(tmp), j);
 
-            if (tmp > newmax) {
+            if (tmp > newmax)
+            {
                 newmax = tmp;
             }
         }
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 6daee9b..71d6737 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -29,7 +29,14 @@ import jalview.util.*;
 import java.util.*;
 
 
-public class NJTree {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NJTree
+{
     Vector cluster;
     SequenceI[] sequence;
     int[] done;
@@ -54,12 +61,25 @@ public class NJTree {
     int start;
     int end;
 
-    public NJTree(SequenceNode node) {
+    /**
+     * Creates a new NJTree object.
+     *
+     * @param node DOCUMENT ME!
+     */
+    public NJTree(SequenceNode node)
+    {
         top = node;
         maxheight = findHeight(top);
     }
 
-    public NJTree(SequenceI[] seqs, NewickFile treefile) {
+    /**
+     * Creates a new NJTree object.
+     *
+     * @param seqs DOCUMENT ME!
+     * @param treefile DOCUMENT ME!
+     */
+    public NJTree(SequenceI[] seqs, NewickFile treefile)
+    {
         top = treefile.getTree();
         maxheight = findHeight(top);
 
@@ -75,31 +95,54 @@ public class NJTree {
         SequenceI nam;
         String realnam;
 
-        while (i < leaves.size()) {
+        while (i < leaves.size())
+        {
             j = (SequenceNode) leaves.elementAt(i++);
             realnam = j.getName();
             nam = null;
 
-            if (namesleft > -1) {
+            if (namesleft > -1)
+            {
                 nam = algnIds.findIdMatch(realnam);
             }
 
-            if (nam != null) {
+            if (nam != null)
+            {
                 j.setElement(nam);
                 namesleft--;
-            } else {
+            }
+            else
+            {
                 j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
                 j.setPlaceholder(true);
             }
         }
     }
 
-    public NJTree(SequenceI[] sequence, int start, int end) {
+    /**
+     * Creates a new NJTree object.
+     *
+     * @param sequence DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public NJTree(SequenceI[] sequence, int start, int end)
+    {
         this(sequence, "NJ", "BL", start, end);
     }
 
+    /**
+     * Creates a new NJTree object.
+     *
+     * @param sequence DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     * @param pwtype DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
     public NJTree(SequenceI[] sequence, String type, String pwtype, int start,
-        int end) {
+        int end)
+    {
         this.sequence = sequence;
         this.node = new Vector();
         this.type = type;
@@ -107,11 +150,13 @@ public class NJTree {
         this.start = start;
         this.end = end;
 
-        if (!(type.equals("NJ"))) {
+        if (!(type.equals("NJ")))
+        {
             type = "AV";
         }
 
-        if (!(pwtype.equals("PID"))) {
+        if (!(pwtype.equals("PID")))
+        {
             type = "BL";
         }
 
@@ -119,7 +164,8 @@ public class NJTree {
 
         done = new int[sequence.length];
 
-        while ((i < sequence.length) && (sequence[i] != null)) {
+        while ((i < sequence.length) && (sequence[i] != null))
+        {
             done[i] = 0;
             i++;
         }
@@ -135,7 +181,13 @@ public class NJTree {
         cluster();
     }
 
-    public String toString() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String toString()
+    {
         jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
 
         return fout.print(false, true); // distances only
@@ -147,7 +199,8 @@ public class NJTree {
      *
      * @param alignment Vector
      */
-    public void UpdatePlaceHolders(Vector alignment) {
+    public void UpdatePlaceHolders(Vector alignment)
+    {
         Vector leaves = new Vector();
         findLeaves(top, leaves);
 
@@ -155,13 +208,18 @@ public class NJTree {
         SequenceIdMatcher seqmatcher = null;
         int i = 0;
 
-        while (i < sz) {
+        while (i < sz)
+        {
             SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
 
-            if (alignment.contains(leaf.element())) {
+            if (alignment.contains(leaf.element()))
+            {
                 leaf.setPlaceholder(false);
-            } else {
-                if (seqmatcher == null) {
+            }
+            else
+            {
+                if (seqmatcher == null)
+                {
                     // Only create this the first time we need it
                     SequenceI[] seqs = new SequenceI[alignment.size()];
 
@@ -173,21 +231,32 @@ public class NJTree {
 
                 SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
 
-                if (nam != null) {
+                if (nam != null)
+                {
                     leaf.setPlaceholder(false);
                     leaf.setElement(nam);
-                } else {
+                }
+                else
+                {
                     leaf.setPlaceholder(true);
                 }
             }
         }
     }
 
-    public void cluster() {
-        while (noClus > 2) {
-            if (type.equals("NJ")) {
+    /**
+     * DOCUMENT ME!
+     */
+    public void cluster()
+    {
+        while (noClus > 2)
+        {
+            if (type.equals("NJ"))
+            {
                 float mind = findMinNJDistance();
-            } else {
+            }
+            else
+            {
                 float mind = findMinDistance();
             }
 
@@ -206,12 +275,17 @@ public class NJTree {
         int one = -1;
         int two = -1;
 
-        for (int i = 0; i < noseqs; i++) {
-            if (done[i] != 1) {
-                if (onefound == false) {
+        for (int i = 0; i < noseqs; i++)
+        {
+            if (done[i] != 1)
+            {
+                if (onefound == false)
+                {
                     two = i;
                     onefound = true;
-                } else {
+                }
+                else
+                {
                     one = i;
                 }
             }
@@ -225,7 +299,16 @@ public class NJTree {
         findMaxDist(top);
     }
 
-    public Cluster joinClusters(int i, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Cluster joinClusters(int i, int j)
+    {
         float dist = distance[i][j];
 
         int noi = ((Cluster) cluster.elementAt(i)).value.length;
@@ -233,11 +316,13 @@ public class NJTree {
 
         int[] value = new int[noi + noj];
 
-        for (int ii = 0; ii < noi; ii++) {
+        for (int ii = 0; ii < noi; ii++)
+        {
             value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
         }
 
-        for (int ii = noi; ii < (noi + noj); ii++) {
+        for (int ii = noi; ii < (noi + noj); ii++)
+        {
             value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
         }
 
@@ -246,9 +331,12 @@ public class NJTree {
         ri = findr(i, j);
         rj = findr(j, i);
 
-        if (type.equals("NJ")) {
+        if (type.equals("NJ"))
+        {
             findClusterNJDistance(i, j);
-        } else {
+        }
+        else
+        {
             findClusterDistance(i, j);
         }
 
@@ -260,9 +348,12 @@ public class NJTree {
         SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
         SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
 
-        if (type.equals("NJ")) {
+        if (type.equals("NJ"))
+        {
             findNewNJDistances(tmpi, tmpj, dist);
-        } else {
+        }
+        else
+        {
             findNewDistances(tmpi, tmpj, dist);
         }
 
@@ -274,8 +365,16 @@ public class NJTree {
         return c;
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tmpi DOCUMENT ME!
+     * @param tmpj DOCUMENT ME!
+     * @param dist DOCUMENT ME!
+     */
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
-        float dist) {
+        float dist)
+    {
         float ih = 0;
         float jh = 0;
 
@@ -285,29 +384,41 @@ public class NJTree {
         tmpi.dist = ((dist + ri) - rj) / 2;
         tmpj.dist = (dist - tmpi.dist);
 
-        if (tmpi.dist < 0) {
+        if (tmpi.dist < 0)
+        {
             tmpi.dist = 0;
         }
 
-        if (tmpj.dist < 0) {
+        if (tmpj.dist < 0)
+        {
             tmpj.dist = 0;
         }
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tmpi DOCUMENT ME!
+     * @param tmpj DOCUMENT ME!
+     * @param dist DOCUMENT ME!
+     */
     public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
-        float dist) {
+        float dist)
+    {
         float ih = 0;
         float jh = 0;
 
         SequenceNode sni = tmpi;
         SequenceNode snj = tmpj;
 
-        while (sni != null) {
+        while (sni != null)
+        {
             ih = ih + sni.dist;
             sni = (SequenceNode) sni.left();
         }
 
-        while (snj != null) {
+        while (snj != null)
+        {
             jh = jh + snj.dist;
             snj = (SequenceNode) snj.left();
         }
@@ -316,75 +427,121 @@ public class NJTree {
         tmpj.dist = ((dist / 2) - jh);
     }
 
-    public void findClusterDistance(int i, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void findClusterDistance(int i, int j)
+    {
         int noi = ((Cluster) cluster.elementAt(i)).value.length;
         int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
         // New distances from cluster to others
         float[] newdist = new float[noseqs];
 
-        for (int l = 0; l < noseqs; l++) {
-            if ((l != i) && (l != j)) {
+        for (int l = 0; l < noseqs; l++)
+        {
+            if ((l != i) && (l != j))
+            {
                 newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
                     noj);
-            } else {
+            }
+            else
+            {
                 newdist[l] = 0;
             }
         }
 
-        for (int ii = 0; ii < noseqs; ii++) {
+        for (int ii = 0; ii < noseqs; ii++)
+        {
             distance[i][ii] = newdist[ii];
             distance[ii][i] = newdist[ii];
         }
     }
 
-    public void findClusterNJDistance(int i, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void findClusterNJDistance(int i, int j)
+    {
         int noi = ((Cluster) cluster.elementAt(i)).value.length;
         int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
         // New distances from cluster to others
         float[] newdist = new float[noseqs];
 
-        for (int l = 0; l < noseqs; l++) {
-            if ((l != i) && (l != j)) {
+        for (int l = 0; l < noseqs; l++)
+        {
+            if ((l != i) && (l != j))
+            {
                 newdist[l] = ((distance[i][l] + distance[j][l]) -
                     distance[i][j]) / 2;
-            } else {
+            }
+            else
+            {
                 newdist[l] = 0;
             }
         }
 
-        for (int ii = 0; ii < noseqs; ii++) {
+        for (int ii = 0; ii < noseqs; ii++)
+        {
             distance[i][ii] = newdist[ii];
             distance[ii][i] = newdist[ii];
         }
     }
 
-    public float findr(int i, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float findr(int i, int j)
+    {
         float tmp = 1;
 
-        for (int k = 0; k < noseqs; k++) {
-            if ((k != i) && (k != j) && (done[k] != 1)) {
+        for (int k = 0; k < noseqs; k++)
+        {
+            if ((k != i) && (k != j) && (done[k] != 1))
+            {
                 tmp = tmp + distance[i][k];
             }
         }
 
-        if (noClus > 2) {
+        if (noClus > 2)
+        {
             tmp = tmp / (noClus - 2);
         }
 
         return tmp;
     }
 
-    public float findMinNJDistance() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float findMinNJDistance()
+    {
         float min = 100000;
 
-        for (int i = 0; i < (noseqs - 1); i++) {
-            for (int j = i + 1; j < noseqs; j++) {
-                if ((done[i] != 1) && (done[j] != 1)) {
+        for (int i = 0; i < (noseqs - 1); i++)
+        {
+            for (int j = i + 1; j < noseqs; j++)
+            {
+                if ((done[i] != 1) && (done[j] != 1))
+                {
                     float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
 
-                    if (tmp < min) {
+                    if (tmp < min)
+                    {
                         mini = i;
                         minj = j;
 
@@ -397,13 +554,23 @@ public class NJTree {
         return min;
     }
 
-    public float findMinDistance() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float findMinDistance()
+    {
         float min = 100000;
 
-        for (int i = 0; i < (noseqs - 1); i++) {
-            for (int j = i + 1; j < noseqs; j++) {
-                if ((done[i] != 1) && (done[j] != 1)) {
-                    if (distance[i][j] < min) {
+        for (int i = 0; i < (noseqs - 1); i++)
+        {
+            for (int j = i + 1; j < noseqs; j++)
+            {
+                if ((done[i] != 1) && (done[j] != 1))
+                {
+                    if (distance[i][j] < min)
+                    {
                         mini = i;
                         minj = j;
 
@@ -416,34 +583,54 @@ public class NJTree {
         return min;
     }
 
-    public float[][] findDistances() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float[][] findDistances()
+    {
         float[][] distance = new float[noseqs][noseqs];
 
-        if (pwtype.equals("PID")) {
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; j++) {
-                    if (j == i) {
+        if (pwtype.equals("PID"))
+        {
+            for (int i = 0; i < (noseqs - 1); i++)
+            {
+                for (int j = i; j < noseqs; j++)
+                {
+                    if (j == i)
+                    {
                         distance[i][i] = 0;
-                    } else {
+                    }
+                    else
+                    {
                         distance[i][j] = 100 -
                             Comparison.PID(sequence[i], sequence[j], start, end);
                         distance[j][i] = distance[i][j];
                     }
                 }
             }
-        } else if (pwtype.equals("BL")) {
+        }
+        else if (pwtype.equals("BL"))
+        {
             int maxscore = 0;
 
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; j++) {
+            for (int i = 0; i < (noseqs - 1); i++)
+            {
+                for (int j = i; j < noseqs; j++)
+                {
                     int score = 0;
 
-                    for (int k = start; k < end; k++) {
-                        try {
+                    for (int k = start; k < end; k++)
+                    {
+                        try
+                        {
                             score += ResidueProperties.getBLOSUM62(sequence[i].getSequence(
                                     k, k + 1), sequence[j].getSequence(k, k +
                                     1));
-                        } catch (Exception ex) {
+                        }
+                        catch (Exception ex)
+                        {
                             System.err.println("err creating BLOSUM62 tree");
                             ex.printStackTrace();
                         }
@@ -451,37 +638,47 @@ public class NJTree {
 
                     distance[i][j] = (float) score;
 
-                    if (score > maxscore) {
+                    if (score > maxscore)
+                    {
                         maxscore = score;
                     }
                 }
             }
 
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; j++) {
+            for (int i = 0; i < (noseqs - 1); i++)
+            {
+                for (int j = i; j < noseqs; j++)
+                {
                     distance[i][j] = (float) maxscore - distance[i][j];
                     distance[j][i] = distance[i][j];
                 }
             }
-        } else if (pwtype.equals("SW")) {
+        }
+        else if (pwtype.equals("SW"))
+        {
             float max = -1;
 
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; j++) {
+            for (int i = 0; i < (noseqs - 1); i++)
+            {
+                for (int j = i; j < noseqs; j++)
+                {
                     AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
                     as.calcScoreMatrix();
                     as.traceAlignment();
                     as.printAlignment();
                     distance[i][j] = (float) as.maxscore;
 
-                    if (max < distance[i][j]) {
+                    if (max < distance[i][j])
+                    {
                         max = distance[i][j];
                     }
                 }
             }
 
-            for (int i = 0; i < (noseqs - 1); i++) {
-                for (int j = i; j < noseqs; j++) {
+            for (int i = 0; i < (noseqs - 1); i++)
+            {
+                for (int j = i; j < noseqs; j++)
+                {
                     distance[i][j] = max - distance[i][j];
                     distance[j][i] = distance[i][j];
                 }
@@ -491,10 +688,15 @@ public class NJTree {
         return distance;
     }
 
-    public void makeLeaves() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void makeLeaves()
+    {
         cluster = new Vector();
 
-        for (int i = 0; i < noseqs; i++) {
+        for (int i = 0; i < noseqs; i++)
+        {
             SequenceNode sn = new SequenceNode();
 
             sn.setElement(sequence[i]);
@@ -509,16 +711,29 @@ public class NJTree {
         }
     }
 
-    public Vector findLeaves(SequenceNode node, Vector leaves) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param leaves DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector findLeaves(SequenceNode node, Vector leaves)
+    {
+        if (node == null)
+        {
             return leaves;
         }
 
-        if ((node.left() == null) && (node.right() == null)) {
+        if ((node.left() == null) && (node.right() == null))
+        {
             leaves.addElement(node);
 
             return leaves;
-        } else {
+        }
+        else
+        {
             findLeaves((SequenceNode) node.left(), leaves);
             findLeaves((SequenceNode) node.right(), leaves);
         }
@@ -526,22 +741,44 @@ public class NJTree {
         return leaves;
     }
 
-    public Object findLeaf(SequenceNode node, int count) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param count DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object findLeaf(SequenceNode node, int count)
+    {
         found = _findLeaf(node, count);
 
         return found;
     }
 
-    public Object _findLeaf(SequenceNode node, int count) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param count DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object _findLeaf(SequenceNode node, int count)
+    {
+        if (node == null)
+        {
             return null;
         }
 
-        if (node.ycount == count) {
+        if (node.ycount == count)
+        {
             found = node.element();
 
             return found;
-        } else {
+        }
+        else
+        {
             _findLeaf((SequenceNode) node.left(), count);
             _findLeaf((SequenceNode) node.right(), count);
         }
@@ -554,80 +791,137 @@ public class NJTree {
      *
      * @param node SequenceNode
      */
-    public void printNode(SequenceNode node) {
-        if (node == null) {
+    public void printNode(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.left() == null) && (node.right() == null)) {
+        if ((node.left() == null) && (node.right() == null))
+        {
             System.out.println("Leaf = " +
                 ((SequenceI) node.element()).getName());
             System.out.println("Dist " + ((SequenceNode) node).dist);
             System.out.println("Boot " + node.getBootstrap());
-        } else {
+        }
+        else
+        {
             System.out.println("Dist " + ((SequenceNode) node).dist);
             printNode((SequenceNode) node.left());
             printNode((SequenceNode) node.right());
         }
     }
 
-    public void findMaxDist(SequenceNode node) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void findMaxDist(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.left() == null) && (node.right() == null)) {
+        if ((node.left() == null) && (node.right() == null))
+        {
             float dist = ((SequenceNode) node).dist;
 
-            if (dist > maxDistValue) {
+            if (dist > maxDistValue)
+            {
                 maxdist = (SequenceNode) node;
                 maxDistValue = dist;
             }
-        } else {
+        }
+        else
+        {
             findMaxDist((SequenceNode) node.left());
             findMaxDist((SequenceNode) node.right());
         }
     }
 
-    public Vector getGroups() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getGroups()
+    {
         return groups;
     }
 
-    public float getMaxHeight() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float getMaxHeight()
+    {
         return maxheight;
     }
 
-    public void groupNodes(SequenceNode node, float threshold) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     */
+    public void groupNodes(SequenceNode node, float threshold)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.height / maxheight) > threshold) {
+        if ((node.height / maxheight) > threshold)
+        {
             groups.addElement(node);
-        } else {
+        }
+        else
+        {
             groupNodes((SequenceNode) node.left(), threshold);
             groupNodes((SequenceNode) node.right(), threshold);
         }
     }
 
-    public float findHeight(SequenceNode node) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float findHeight(SequenceNode node)
+    {
+        if (node == null)
+        {
             return maxheight;
         }
 
-        if ((node.left() == null) && (node.right() == null)) {
+        if ((node.left() == null) && (node.right() == null))
+        {
             node.height = ((SequenceNode) node.parent()).height + node.dist;
 
-            if (node.height > maxheight) {
+            if (node.height > maxheight)
+            {
                 return node.height;
-            } else {
+            }
+            else
+            {
                 return maxheight;
             }
-        } else {
-            if (node.parent() != null) {
+        }
+        else
+        {
+            if (node.parent() != null)
+            {
                 node.height = ((SequenceNode) node.parent()).height +
                     node.dist;
-            } else {
+            }
+            else
+            {
                 maxheight = 0;
                 node.height = (float) 0.0;
             }
@@ -639,8 +933,15 @@ public class NJTree {
         return maxheight;
     }
 
-    public SequenceNode reRoot() {
-        if (maxdist != null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceNode reRoot()
+    {
+        if (maxdist != null)
+        {
             ycount = 0;
 
             float tmpdist = maxdist.dist;
@@ -673,15 +974,25 @@ public class NJTree {
         return top;
     }
 
-    public static void printN(SequenceNode node) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public static void printN(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.left() != null) && (node.right() != null)) {
+        if ((node.left() != null) && (node.right() != null))
+        {
             printN((SequenceNode) node.left());
             printN((SequenceNode) node.right());
-        } else {
+        }
+        else
+        {
             System.out.println(" name = " +
                 ((SequenceI) node.element()).getName());
         }
@@ -690,17 +1001,31 @@ public class NJTree {
             ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
     }
 
-    public void reCount(SequenceNode node) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void reCount(SequenceNode node)
+    {
         ycount = 0;
         _reCount(node);
     }
 
-    public void _reCount(SequenceNode node) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void _reCount(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if ((node.left() != null) && (node.right() != null)) {
+        if ((node.left() != null) && (node.right() != null))
+        {
             _reCount((SequenceNode) node.left());
             _reCount((SequenceNode) node.right());
 
@@ -709,14 +1034,23 @@ public class NJTree {
 
             ((SequenceNode) node).count = l.count + r.count;
             ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
-        } else {
+        }
+        else
+        {
             ((SequenceNode) node).count = 1;
             ((SequenceNode) node).ycount = ycount++;
         }
     }
 
-    public void swapNodes(SequenceNode node) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void swapNodes(SequenceNode node)
+    {
+        if (node == null)
+        {
             return;
         }
 
@@ -726,62 +1060,116 @@ public class NJTree {
         node.setRight(tmp);
     }
 
-    public void changeDirection(SequenceNode node, SequenceNode dir) {
-        if (node == null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param dir DOCUMENT ME!
+     */
+    public void changeDirection(SequenceNode node, SequenceNode dir)
+    {
+        if (node == null)
+        {
             return;
         }
 
-        if (node.parent() != top) {
+        if (node.parent() != top)
+        {
             changeDirection((SequenceNode) node.parent(), node);
 
             SequenceNode tmp = (SequenceNode) node.parent();
 
-            if (dir == node.left()) {
+            if (dir == node.left())
+            {
                 node.setParent(dir);
                 node.setLeft(tmp);
-            } else if (dir == node.right()) {
+            }
+            else if (dir == node.right())
+            {
                 node.setParent(dir);
                 node.setRight(tmp);
             }
-        } else {
-            if (dir == node.left()) {
+        }
+        else
+        {
+            if (dir == node.left())
+            {
                 node.setParent(node.left());
 
-                if (top.left() == node) {
+                if (top.left() == node)
+                {
                     node.setRight(top.right());
-                } else {
+                }
+                else
+                {
                     node.setRight(top.left());
                 }
-            } else {
+            }
+            else
+            {
                 node.setParent(node.right());
 
-                if (top.left() == node) {
+                if (top.left() == node)
+                {
                     node.setLeft(top.right());
-                } else {
+                }
+                else
+                {
                     node.setLeft(top.left());
                 }
             }
         }
     }
 
-    public void setMaxDist(SequenceNode node) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void setMaxDist(SequenceNode node)
+    {
         this.maxdist = maxdist;
     }
 
-    public SequenceNode getMaxDist() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceNode getMaxDist()
+    {
         return maxdist;
     }
 
-    public SequenceNode getTopNode() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceNode getTopNode()
+    {
         return top;
     }
 }
 
 
-class Cluster {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+class Cluster
+{
     int[] value;
 
-    public Cluster(int[] value) {
+    /**
+     * Creates a new Cluster object.
+     *
+     * @param value DOCUMENT ME!
+     */
+    public Cluster(int[] value)
+    {
         this.value = value;
     }
 }
diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index ecbe4ab..2e37e6a 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -24,29 +24,37 @@ import jalview.math.*;
 
 import jalview.util.*;
 
-import java.awt.*;
-
 import java.io.*;
 
 
-public class PCA implements Runnable {
+/**
+ * Performs Principal Component Analysis on given sequences
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PCA implements Runnable
+{
     Matrix m;
     Matrix symm;
     Matrix m2;
     double[] eigenvalue;
     Matrix eigenvector;
 
-    public PCA(Matrix m) {
-        this.m = m;
-    }
 
-    public PCA(SequenceI[] s) {
-        Runtime rt = Runtime.getRuntime();
+    /**
+     * Creates a new PCA object.
+     *
+     * @param s Set of sequences to perform PCA on
+     */
+    public PCA(SequenceI[] s)
+    {
 
         BinarySequence[] bs = new BinarySequence[s.length];
         int ii = 0;
 
-        while ((ii < s.length) && (s[ii] != null)) {
+        while ((ii < s.length) && (s[ii] != null))
+        {
             bs[ii] = new BinarySequence(s[ii]);
             bs[ii].encode();
             ii++;
@@ -55,7 +63,8 @@ public class PCA implements Runnable {
         BinarySequence[] bs2 = new BinarySequence[s.length];
         ii = 0;
 
-        while ((ii < s.length) && (s[ii] != null)) {
+        while ((ii < s.length) && (s[ii] != null))
+        {
             bs2[ii] = new BinarySequence(s[ii]);
             bs2[ii].blosumEncode();
             ii++;
@@ -65,7 +74,8 @@ public class PCA implements Runnable {
         //printMemory(rt);
         int count = 0;
 
-        while ((count < bs.length) && (bs[count] != null)) {
+        while ((count < bs.length) && (bs[count] != null))
+        {
             count++;
         }
 
@@ -73,7 +83,8 @@ public class PCA implements Runnable {
         double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];
         int i = 0;
 
-        while (i < count) {
+        while (i < count)
+        {
             seqmat[i] = bs[i].getDBinary();
             seqmat2[i] = bs2[i].getDBinary();
             i++;
@@ -85,34 +96,47 @@ public class PCA implements Runnable {
         m = new Matrix(seqmat, count, bs[0].getDBinary().length);
         m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length);
 
-        //System.out.println("Created matrix");
-        printMemory(rt);
-    }
+      }
 
-    public static void printMemory(Runtime rt) {
-        System.out.println("PCA:Free memory = " + rt.freeMemory());
-    }
+      /**
+       * Returns the matrix used in PCA calculation
+       *
+       * @return java.math.Matrix object
+       */
 
-    public Matrix getM() {
+      public Matrix getM()
+      {
         return m;
-    }
-
-    public double[] getEigenvector(int i) {
-        return eigenvector.getColumn(i);
-    }
-
-    public double getEigenvalue(int i) {
+      }
+
+    /**
+     * Returns Eigenvalue
+     *
+     * @param i Index of diagonal within matrix
+     *
+     * @return Returns value of diagonal from matrix
+     */
+    public double getEigenvalue(int i)
+    {
         return eigenvector.d[i];
     }
 
-    public float[][] getComponents(int l, int n, int mm) {
-        return getComponents(l, n, mm, 1);
-    }
-
-    public float[][] getComponents(int l, int n, int mm, float factor) {
+     /**
+     * DOCUMENT ME!
+     *
+     * @param l DOCUMENT ME!
+     * @param n DOCUMENT ME!
+     * @param mm DOCUMENT ME!
+     * @param factor DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float[][] getComponents(int l, int n, int mm, float factor)
+    {
         float[][] out = new float[m.rows][3];
 
-        for (int i = 0; i < m.rows; i++) {
+        for (int i = 0; i < m.rows; i++)
+        {
             out[i][0] = (float) component(i, l) * factor;
             out[i][1] = (float) component(i, n) * factor;
             out[i][2] = (float) component(i, mm) * factor;
@@ -121,51 +145,52 @@ public class PCA implements Runnable {
         return out;
     }
 
-    public double[] component(int n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public double[] component(int n)
+    {
         // n = index of eigenvector
         double[] out = new double[m.rows];
 
-        for (int i = 0; i < m.rows; i++) {
+        for (int i = 0; i < m.rows; i++)
+        {
             out[i] = component(i, n);
         }
 
         return out;
     }
 
-    public double component(int row, int n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param row DOCUMENT ME!
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    double component(int row, int n)
+    {
         double out = 0.0;
 
-        for (int i = 0; i < symm.cols; i++) {
+        for (int i = 0; i < symm.cols; i++)
+        {
             out += (symm.value[row][i] * eigenvector.value[i][n]);
         }
 
         return out / eigenvector.d[n];
     }
 
-    public void checkEigenvector(int n, PrintStream ps) {
-        ps.println(" --- Eigenvector " + n + " --- ");
-
-        double[] eigenv = eigenvector.getColumn(n);
-
-        for (int i = 0; i < eigenv.length; i++) {
-            Format.print(ps, "%15.4f", eigenv[i]);
-        }
-
-        System.out.println();
-
-        double[] neigenv = symm.vectorPostMultiply(eigenv);
-        System.out.println(" --- symmat * eigenv / lambda --- ");
-
-        if (eigenvector.d[n] > 1e-4) {
-            for (int i = 0; i < neigenv.length; i++) {
-                Format.print(System.out, "%15.4f", neigenv[i] / eigenvector.d[n]);
-            }
-        }
-
-        System.out.println();
-    }
 
-    public void run() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
+    {
         Matrix mt = m.transpose();
 
         //    System.out.println(" --- OrigT * Orig ---- ");
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 8a8ae28..78f7278 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,138 +1,156 @@
-/*
-* 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
-*/
+/*
+ * 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.analysis;
 
-import jalview.datamodel.SequenceI;
-
-import java.util.Hashtable;
-
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class SeqsetUtils {
-    /**
- * Store essential properties of a sequence in a hashtable for later recovery
- *  Keys are Name, Start, End, SeqFeatures, PdbId
- * @param seq SequenceI
- * @return Hashtable
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
  */
-    public static Hashtable SeqCharacterHash(SequenceI seq) {
-        Hashtable sqinfo = new Hashtable();
-        sqinfo.put("Name", seq.getName());
-        sqinfo.put("Start", new Integer(seq.getStart()));
-        sqinfo.put("End", new Integer(seq.getEnd()));
-        sqinfo.put("SeqFeatures", seq.getSequenceFeatures());
-        sqinfo.put("PdbId",
-            (seq.getPDBId() != null) ? seq.getPDBId() : new String(""));
-
-        return sqinfo;
+public class SeqsetUtils
+{
+  /**
+   * Store essential properties of a sequence in a hashtable for later recovery
+   *  Keys are Name, Start, End, SeqFeatures, PdbId
+   * @param seq SequenceI
+   * @return Hashtable
+   */
+  public static Hashtable SeqCharacterHash(SequenceI seq)
+  {
+    Hashtable sqinfo = new Hashtable();
+    sqinfo.put("Name", seq.getName());
+    sqinfo.put("Start", new Integer(seq.getStart()));
+    sqinfo.put("End", new Integer(seq.getEnd()));
+    sqinfo.put("SeqFeatures", seq.getSequenceFeatures());
+    sqinfo.put("PdbId",
+               (seq.getPDBId() != null) ? seq.getPDBId() : new String(""));
+
+    return sqinfo;
+  }
+
+  /**
+   * Recover essential properties of a sequence from a hashtable
+   * TODO: replace these methods with something more elegant.
+   * @param sq SequenceI
+   * @param sqinfo Hashtable
+   * @return boolean
+   */
+  public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
+  {
+    boolean namePresent = true;
+    String oldname = (String) sqinfo.get("Name");
+    Integer start = (Integer) sqinfo.get("Start");
+    Integer end = (Integer) sqinfo.get("End");
+    java.util.Vector sfeatures = (java.util.Vector) sqinfo.get(
+        "SeqFeatures");
+    String pdbid = (String) sqinfo.get("PdbId");
+
+    if (oldname == null)
+    {
+      namePresent = false;
     }
-
-    /**
- * Recover essential properties of a sequence from a hashtable
- * TODO: replace these methods with something more elegant.
- * @param sq SequenceI
- * @param sqinfo Hashtable
- * @return boolean
- */
-    public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) {
-        boolean namePresent = true;
-        String oldname = (String) sqinfo.get("Name");
-        Integer start = (Integer) sqinfo.get("Start");
-        Integer end = (Integer) sqinfo.get("End");
-        java.util.Vector sfeatures = (java.util.Vector) sqinfo.get(
-                "SeqFeatures");
-        String pdbid = (String) sqinfo.get("PdbId");
-
-        if (oldname == null) {
-            namePresent = false;
-        } else {
-            sq.setName(oldname);
-        }
-
-        if (!pdbid.equals("")) {
-            sq.setPDBId(pdbid);
-        }
-
-        if ((start != null) && (end != null)) {
-            sq.setStart(start.intValue());
-            sq.setEnd(end.intValue());
-        }
-
-        if (sfeatures != null) {
-            sq.setSequenceFeatures(sfeatures);
-        }
-
-        return namePresent;
+    else
+    {
+      sq.setName(oldname);
     }
 
-    /**
- * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
- * @param i int
- * @return String
- */
-    public static String unique_name(int i) {
-        return new String("Sequence" + i);
+    if (!pdbid.equals(""))
+    {
+      sq.setPDBId(pdbid);
     }
 
-    public static Hashtable uniquify(SequenceI[] sequences, boolean write_names) {
-        // Generate a safely named sequence set and a hash to recover the sequence names
-        Hashtable map = new Hashtable();
-        String[] un_names = new String[sequences.length];
-
-        if (!write_names) {
-            for (int i = 0; i < sequences.length; i++) {
-                String safename = new String("Sequence" + i);
-                map.put(safename, SeqCharacterHash(sequences[i]));
-
-                if (write_names) {
-                    sequences[i].setName(safename);
-                }
-            }
-        }
+    if ( (start != null) && (end != null))
+    {
+      sq.setStart(start.intValue());
+      sq.setEnd(end.intValue());
+    }
 
-        return map;
+    if (sfeatures != null)
+    {
+      sq.setSequenceFeatures(sfeatures);
     }
 
-    public static boolean deuniquify(Hashtable map, SequenceI[] sequences) {
-        // recover unsafe sequence names for a sequence set
-        boolean allfound = true;
-
-        for (int i = 0; i < sequences.length; i++) {
-            if (map.containsKey(sequences[i].getName())) {
-                Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());
-                SeqCharacterUnhash(sequences[i], sqinfo);
-            } else {
-                allfound = false;
-            }
+    return namePresent;
+  }
+
+  /**
+   * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
+   * @param i int
+   * @return String
+   */
+  public static String unique_name(int i)
+  {
+    return new String("Sequence" + i);
+  }
+
+  public static Hashtable uniquify(SequenceI[] sequences, boolean write_names)
+  {
+    // Generate a safely named sequence set and a hash to recover the sequence names
+    Hashtable map = new Hashtable();
+    String[] un_names = new String[sequences.length];
+
+    if (!write_names)
+    {
+      for (int i = 0; i < sequences.length; i++)
+      {
+        String safename = new String("Sequence" + i);
+        map.put(safename, SeqCharacterHash(sequences[i]));
+
+        if (write_names)
+        {
+          sequences[i].setName(safename);
         }
+      }
+    }
 
-        return allfound;
+    return map;
+  }
+
+  public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
+  {
+    // recover unsafe sequence names for a sequence set
+    boolean allfound = true;
+
+    for (int i = 0; i < sequences.length; i++)
+    {
+      if (map.containsKey(sequences[i].getName()))
+      {
+        Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());
+        SeqCharacterUnhash(sequences[i], sqinfo);
+      }
+      else
+      {
+        allfound = false;
+      }
     }
+
+    return allfound;
+  }
 }
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index f786243..1efe498 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,139 +1,163 @@
-/*
-* 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
-*/
+/*
+ * 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.analysis;
 
-import jalview.datamodel.SequenceI;
-
-import java.util.Hashtable;
-import java.util.Vector;
-
-
-/**
- * <p>Title: </p>
- * SequenceIdMatcher
- * <p>Description: </p>
- * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * <p>Title: </p>
+ * SequenceIdMatcher
+ * <p>Description: </p>
+ * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
  */
-public class SequenceIdMatcher {
-    private Hashtable names;
+public class SequenceIdMatcher
+{
+  private Hashtable names;
 
-    public SequenceIdMatcher(SequenceI[] seqs) {
-        names = new Hashtable();
+  public SequenceIdMatcher(SequenceI[] seqs)
+  {
+    names = new Hashtable();
 
-        for (int i = 0; i < seqs.length; i++) {
-            names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
-        }
+    for (int i = 0; i < seqs.length; i++)
+    {
+      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
     }
+  }
 
-    SequenceI findIdMatch(SequenceI seq) {
-        SeqIdName nam = new SeqIdName(seq.getName());
+  SequenceI findIdMatch(SequenceI seq)
+  {
+    SeqIdName nam = new SeqIdName(seq.getName());
 
-        if (names.containsKey(nam)) {
-            return (SequenceI) names.get(nam);
-        }
-
-        return null;
+    if (names.containsKey(nam))
+    {
+      return (SequenceI) names.get(nam);
     }
 
-    SequenceI findIdMatch(String seqnam) {
-        SeqIdName nam = new SeqIdName(seqnam);
+    return null;
+  }
 
-        if (names.containsKey(nam)) {
-            return (SequenceI) names.get(nam);
-        }
+  SequenceI findIdMatch(String seqnam)
+  {
+    SeqIdName nam = new SeqIdName(seqnam);
 
-        return null;
+    if (names.containsKey(nam))
+    {
+      return (SequenceI) names.get(nam);
     }
 
-    /**
- * findIdMatch
- *
- * Return pointers to sequences (or sequence object containers)
- * which have same Id as a given set of different sequence objects
- *
- * @param seqs SequenceI[]
- * @return SequenceI[]
- */
-    SequenceI[] findIdMatch(SequenceI[] seqs) {
-        SequenceI[] namedseqs = new SequenceI[seqs.length];
-
-        int i = 0;
-        SeqIdName nam;
-
-        if (seqs.length > 0) {
-            do {
-                nam = new SeqIdName(seqs[i].getName());
-
-                if (names.containsKey(nam)) {
-                    namedseqs[i] = (SequenceI) names.get(nam);
-                } else {
-                    namedseqs[i] = null;
-                }
-            } while (i++ < seqs.length);
+    return null;
+  }
+
+  /**
+   * findIdMatch
+   *
+   * Return pointers to sequences (or sequence object containers)
+   * which have same Id as a given set of different sequence objects
+   *
+   * @param seqs SequenceI[]
+   * @return SequenceI[]
+   */
+  SequenceI[] findIdMatch(SequenceI[] seqs)
+  {
+    SequenceI[] namedseqs = new SequenceI[seqs.length];
+
+    int i = 0;
+    SeqIdName nam;
+
+    if (seqs.length > 0)
+    {
+      do
+      {
+        nam = new SeqIdName(seqs[i].getName());
+
+        if (names.containsKey(nam))
+        {
+          namedseqs[i] = (SequenceI) names.get(nam);
         }
-
-        return namedseqs;
+        else
+        {
+          namedseqs[i] = null;
+        }
+      }
+      while (i++ < seqs.length);
     }
 
-    private class SeqIdName {
-        String id;
+    return namedseqs;
+  }
 
-        SeqIdName(String s) {
-            id = new String(s);
-        }
+  private class SeqIdName
+  {
+    String id;
 
-        public int hashCode() {
-            return (id.substring(0, 4).hashCode());
-        }
+    SeqIdName(String s)
+    {
+      id = new String(s);
+    }
 
-        public boolean equals(Object s) {
-            if (s instanceof SeqIdName) {
-                return this.equals((SeqIdName) s);
-            } else {
-                if (s instanceof String) {
-                    return this.equals((String) s);
-                }
-            }
+    public int hashCode()
+    {
+      return (id.substring(0, 4).hashCode());
+    }
 
-            return false;
+    public boolean equals(Object s)
+    {
+      if (s instanceof SeqIdName)
+      {
+        return this.equals( (SeqIdName) s);
+      }
+      else
+      {
+        if (s instanceof String)
+        {
+          return this.equals( (String) s);
         }
+      }
 
-        public boolean equals(SeqIdName s) {
-            if (id.startsWith(s.id) || s.id.startsWith(id)) {
-                return true;
-            }
+      return false;
+    }
 
-            return false;
-        }
+    public boolean equals(SeqIdName s)
+    {
+      if (id.startsWith(s.id) || s.id.startsWith(id))
+      {
+        return true;
+      }
 
-        public boolean equals(String s) {
-            if (id.startsWith(s) || s.startsWith(id)) {
-                return true;
-            }
+      return false;
+    }
 
-            return false;
-        }
+    public boolean equals(String s)
+    {
+      if (id.startsWith(s) || s.startsWith(id))
+      {
+        return true;
+      }
+
+      return false;
     }
+  }
 }
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index cd6396f..ad4aeb8 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -352,7 +352,7 @@ public class AnnotationPanel
                     row.annotations[j - 1].secondaryStructure))
           {
 
-            g.drawString(row.annotations[j].displayCharacter, x,
+            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
                          y + iconOffset + 2);
           }
 
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 8b6939e..399506e 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -55,7 +55,7 @@ public class IdCanvas
     if (searchResults != null && searchResults.contains(s))
     {
       gg.setColor(Color.black);
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
@@ -63,14 +63,14 @@ public class IdCanvas
              av.getSelectionGroup().sequences.contains(s))
     {
       gg.setColor(Color.lightGray);
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
     else
     {
       gg.setColor(s.getColor());
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.black);
     }
@@ -82,7 +82,7 @@ public class IdCanvas
     }
 
     gg.drawString(string, 0,
-                  AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +
+                  ((i - starty) * charHeight) + ypos +
                   charHeight - (charHeight / 5));
 
   }
@@ -228,7 +228,7 @@ public class IdCanvas
         gg.setColor(currentColor);
 
         gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
+                    ((i - starty) * av.charHeight),
                     getSize().width,
                     av.charHeight);
 
@@ -239,7 +239,7 @@ public class IdCanvas
           string = av.alignment.getSequenceAt(i).getDisplayId();
         }
         gg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +
+                      ((i - starty) * av.charHeight) +
                       av.charHeight - (av.charHeight / 5));
       }
 
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5aa5d66..29616ef 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -374,7 +374,7 @@ public class SeqCanvas
       sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
                       (x1 - startx) * av.charWidth,
                       offset +
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
+                      (i-starty)*av.charHeight,
                       av.charWidth, av.charHeight);
 
       if (av.showSequenceFeatures)
@@ -382,7 +382,7 @@ public class SeqCanvas
         fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
                         (x1 - startx) * av.charWidth,
                         offset +
-                        AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
+                        (i-starty)*av.charHeight,
                         av.charWidth, av.charHeight);
       }
     }
@@ -413,7 +413,7 @@ public class SeqCanvas
         for (i = y1; i < y2; i++)
         {
           sx = (group.getStartRes() - startx) * av.charWidth;
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
+          sy = offset + (i-starty)*av.charHeight;
           ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;
 
           if (sx < getSize().width
@@ -484,7 +484,7 @@ public class SeqCanvas
             bottom = -1;
 
           }
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
+          sy = offset + (i-starty)*av.charHeight;
           g.drawLine(sx, oldY, sx, sy);
           g.drawLine(sx + ex, oldY, sx + ex, sy);
           inGroup = false;
@@ -531,9 +531,7 @@ public class SeqCanvas
                                   searchEnd,
                                   (searchStart - startx) * av.charWidth,
                                   offset +
-                                  AlignmentUtil.getPixelHeight(starty,
-              searchSeq,
-              av.charHeight),
+                                  (searchSeq-starty)*av.charHeight,
                                   av.charWidth,
                                   av.charHeight);
         }
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index e1978fe..57ae4ce 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,50 +1,71 @@
 /*
-* 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
-*/
+ * 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.bin;
 
 import java.io.*;
 
 import java.util.*;
-import java.util.jar.*;
 
 
-public class Cache {
-    public static String VERSION = "Release 2.0";
+/**
+ * Stores and retrieves Jalview Application Properties
+ * <br><br>Current properties include:
+ * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
+ * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
+ * <br>jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.
+ * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN
+ * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
+ * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
+ * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE
+
+ * @author $author$
+ * @version $Revision$
+ */
+public class Cache
+{
+    /** Current release tag */
+    public static String VERSION = "AW Test";
+
+    /** Date Jalview was last packaged, else compilation date of Cache.class */
     public static String BUILD_DATE = "";
+
+    /** Jalview Properties */
     public static Properties applicationProperties;
 
-    // Current properties include:
-    //
-    // LAST_DIRECTORY   , use this to cache record of where the user looked to find a file
-    // UNIPROT_CACHE
-    // USER_DEFINED_COLOUR - file describing last user set colours
-    // FONT_NAME
-    // FONT_STYLE
-    // FONT_SIZE
-    // logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
-    // logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
-    // jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.
-    public static void loadProperties() {
+    /** Default file is  ~/.jalview_properties */
+    static String propertiesFile;
+
+    /** Called when Jalview is started */
+    public static void loadProperties(String propsFile)
+    {
+      propertiesFile = propsFile;
+      if (propsFile == null)
+      {
+        propertiesFile = System.getProperty("user.home") + "/.jalview_properties";
+      }
+
+
         // get last build time.
         long date = 0;
 
-        try {
+        try
+        {
             String localFile = Cache.class.getProtectionDomain().getCodeSource()
                                           .getLocation().toString();
             localFile = localFile.concat("!/");
@@ -54,11 +75,14 @@ public class Cache {
             java.net.URL localJarFileURL = new java.net.URL(localJarFileString);
             java.net.JarURLConnection localJarFile = (java.net.JarURLConnection) localJarFileURL.openConnection();
             date = localJarFile.getLastModified();
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             ex.printStackTrace();
         }
 
-        if (date == 0) {
+        if (date == 0)
+        {
             // this is called for unpackaged class files, ie not in a Jar file
             // InstallAnywhere version will find build date this way
             // not entirely accurate as it only tells you when Cache.class was last compiled
@@ -67,36 +91,59 @@ public class Cache {
             date = f.lastModified();
         }
 
-        if (date != 0) {
+        if (date != 0)
+        {
             BUILD_DATE = new Date(date).toString();
         }
 
         applicationProperties = new Properties();
 
-        try {
-            FileInputStream in = new FileInputStream(System.getProperty(
-                        "user.home") + "/.jalview_properties");
+        try
+        {
+            FileInputStream in = new FileInputStream(propertiesFile);
             applicationProperties = new Properties();
             applicationProperties.load(in);
             in.close();
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
         }
     }
 
-    public static String getProperty(String key) {
+    /**
+     * Gets Jalview application property of given key. Returns null
+     * if key not found
+     *
+     * @param key Name of property
+     *
+     * @return Property value
+     */
+    public static String getProperty(String key)
+    {
         return applicationProperties.getProperty(key);
     }
 
-    public static String setProperty(String key, String obj) {
-        try {
-            FileOutputStream out = new FileOutputStream(System.getProperty(
-                        "user.home") + "/.jalview_properties");
+    /**
+     * Stores property in the file "HOME_DIR/.jalview_properties"
+     *
+     * @param key Name of object
+     * @param obj String value of property
+     *
+     * @return String value of property
+     */
+    public static String setProperty(String key, String obj)
+    {
+        try
+        {
+            FileOutputStream out = new FileOutputStream(propertiesFile);
 
             applicationProperties.setProperty(key, obj);
 
             applicationProperties.store(out, "---JalviewX Properties File---");
             out.close();
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
         }
 
         return obj;
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index c11d051..f05b394 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,88 +1,57 @@
 /*
-* 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
-*/
+ * 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.bin;
 
 import jalview.gui.*;
 
-import jalview.io.*;
-
 import org.apache.log4j.*;
 
-import java.awt.event.*;
-
 import javax.swing.*;
 
-
-public class Jalview extends JApplet {
-    public static JApplet applet;
-    Desktop frame;
-
-    public void init() {
-        applet = this;
-        Cache.loadProperties();
-        jalview.gui.Preferences.initPreferences();
-
-        frame = new Desktop();
-        frame.setResizable(true);
-        frame.setVisible(true);
-        frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
-        frame.addWindowListener(new WindowAdapter() {
-                public void windowClosing(WindowEvent e) {
-                    applet.stop();
-                    applet.destroy();
-                }
-            });
-
-        String file = getParameter("alignment");
-
-        if (file != null) {
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);
-
-            String protocol = "File";
-
-            if (file.indexOf("http:") > -1) {
-                protocol = "URL";
-            }
-
-            String format = jalview.io.IdentifyFile.Identify(file, protocol);
-
-            frame.LoadFile(file, protocol, format);
-        }
-    }
-
-    public void destroy() {
-        if (applet != null) {
-            applet.stop();
-        } else {
-            System.exit(0);
-        }
-
-        frame.setVisible(false);
-    }
-
-    private static void initLogger() {
+import java.util.Vector;
+
+
+/**
+ * Main class for Jalview Application
+ * <br>
+ * <br>start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview
+{
+    /**
+     * Initialises the Apache Axis logger
+     */
+    private static void initLogger()
+    {
         Logger laxis = Logger.getLogger("org.apache.axis");
         Logger lcastor = Logger.getLogger("org.exolab.castor");
-        if (Cache.getProperty("logs.Axis.Level") == null) {
+
+        if (Cache.getProperty("logs.Axis.Level") == null)
+        {
             Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
         }
-        if (Cache.getProperty("logs.Castor.Level") == null) {
+
+        if (Cache.getProperty("logs.Castor.Level") == null)
+        {
             Cache.setProperty("logs.Castor.Level", Level.INFO.toString());
         }
 
@@ -96,64 +65,231 @@ public class Jalview extends JApplet {
         lcastor.addAppender(ap);
     }
 
-    public static void main(String[] args) {
-        Cache.loadProperties();
-        jalview.gui.Preferences.initPreferences();
-
-        try {
-            initLogger();
-        } catch (Exception e) {
-            System.err.println("Problems initializing the log4j system\n");
-            e.printStackTrace();
-        }
-
-        try {
+    /**
+     * main class for Jalview application
+     *
+     * @param args open <em>filename</em>
+     */
+    public static void main(String[] args)
+    {
+      ArgsParser aparser = new ArgsParser(args);
+
+      try
+        {
             UIManager.setLookAndFeel(
-            //   "javax.swing.plaf.metal.MetalLookAndFeel"
+            //  "javax.swing.plaf.metal.MetalLookAndFeel"
             //  "javax.swing.plaf.multi.MultiLookAndFeel"
             UIManager.getSystemLookAndFeelClassName());
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
         }
 
-        Desktop frame = new Desktop();
-        frame.setResizable(true);
-        frame.setVisible(true);
+        Cache.loadProperties(aparser.getValue("props"));
+        jalview.gui.Preferences.initPreferences();
+        try
+        {
+          initLogger();
+        }
+        catch (Exception e)
+        {
+          System.err.println("Problems initializing the log4j system\n");
+        }
+
+
+        String file = null, protocol = null, format = null, groups=null;
+        Desktop desktop = new Desktop();
+
+
+        if(args==null || args.length==0)
+        {
+          desktop.setVisible(true);
+        }
+        else
+        {
+          if( aparser.contains("help") || aparser.contains("h") )
+          {
+            System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+                               +"-nodisplay\tRun Jalview without User Interface.\n"
+                               +"-props FILE\tUse the given Jalview properties file instead of users default.\n"
+                               +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"
+                               +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\n"
+                               +"SequenceID is used in preference to SequenceIndex if both are provided.\n"
+                               +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"
+                               +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"
+                               +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+                               +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+                               +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+                               +"-msf FILE\tCreate alignment file FILE in MSF format.\n"
+                               +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+                               +"-pir FILE\tCreate alignment file FILE in PIR format.\n"
+                               +"-blc FILE\tCreate alignment file FILE in BLC format.\n"
+                               +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+                               +"-png FILE\tCreate PNG image FILE from alignment.\n"
+                               +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+                               +"-eps FILE\tCreate EPS file FILE from alignment.");
+            System.exit(0);
+
+          }
+
 
-        if ((args != null) && (args.length > 0)) {
-            String file = null;
+          file = aparser.getValue("open");
 
-            if (args[0].equals("-open")) {
-                file = args[1];
-            } else {
-                file = args[0];
+          if (file == null)
+          {
+            System.out.println("No files to open!");
+            System.exit(1);
+          }
+          else if(!file.startsWith("http://"))
+          {
+            if (!(new java.io.File(file)).exists())
+            {
+              System.out.println("Can't find " + file);
+              System.exit(1);
             }
+          }
+
+          if (!aparser.contains("nodisplay"))
+            desktop.setVisible(true);
+
+          protocol = "File";
+
+          if (file.indexOf("http:") > -1)
+          {
+            protocol = "URL";
+          }
 
-            String protocol = "File";
+          if(file.endsWith(".jar"))
+            format = "Jalview";
+          else
+            format = jalview.io.IdentifyFile.Identify(file, protocol);
 
-            if (file.indexOf("http:") > -1) {
-                protocol = "URL";
+          System.out.println("Opening: " + format + " file " + file);
+
+          AlignFrame af = desktop.LoadFileWaitTillLoaded(file, protocol, format);
+
+          groups = aparser.getValue("groups");
+          if(groups!=null)
+          {
+            af.parseGroupsFile(groups);
+          }
+
+          String imageName = "unnamed.png";
+          while (aparser.getSize() > 1)
+          {
+            format = aparser.nextValue();
+            file = aparser.nextValue();
+
+            if (format.equalsIgnoreCase("png"))
+            {
+              af.createPNG(new java.io.File(file));
+              imageName = (new java.io.File(file)).getName();
+              System.out.println("Creating PNG image: " + file);
+              continue;
             }
+            else if (format.equalsIgnoreCase("imgMap"))
+            {
+              af.createImageMap(new java.io.File(file), imageName);
+              System.out.println("Creating image map: " + file);
+              continue;
+            }
+            else if (format.equalsIgnoreCase("eps"))
+            {
+              System.out.println("Creating EPS file: " + file);
+              af.createEPS(new java.io.File(file));
+              continue;
+            }
+
+            if (af.saveAlignment(file, format))
+              System.out.println("Written alignment in " + format +
+                                 " format to " + file);
+            else
+              System.out.println("Error writing file " + file + " in " + format +
+                                 " format!!");
 
-            String format = jalview.io.IdentifyFile.Identify(file, protocol);
+          }
 
-            frame.LoadFile(file, protocol, format);
+          while (aparser.getSize() > 0)
+          {
+            System.out.println("Unknown arg: " + aparser.nextValue());
+          }
         }
 
-        if (jalview.gui.Preferences.showStartupFile &&
-                (jalview.gui.Preferences.startupFile != null)) {
-            String file = jalview.gui.Preferences.startupFile;
-            String protocol = "File";
+          if (jalview.gui.Preferences.showStartupFile &&
+              (jalview.gui.Preferences.startupFile != null))
+          {
 
-            if (file.indexOf("http:") > -1) {
-                protocol = "URL";
+            file = jalview.gui.Preferences.startupFile;
+            protocol = "File";
+
+            if (file.indexOf("http:") > -1)
+            {
+              protocol = "URL";
             }
 
-            if (file.endsWith(".jar")) {
-                Jalview2XML.LoadJalviewAlign(file);
-            } else {
-                String format = jalview.io.IdentifyFile.Identify(file, protocol);
-                frame.LoadFile(file, protocol, format);
+            if (file.endsWith(".jar"))
+            {
+              Jalview2XML.LoadJalviewAlign(file);
             }
-        }
+            else
+            {
+              format = jalview.io.IdentifyFile.Identify(file, protocol);
+              desktop.LoadFile(file, protocol, format);
+            }
+          }
+
+          if (!desktop.isVisible())
+            System.exit(0);
     }
 }
+
+ class ArgsParser
+ {
+   Vector vargs = null;
+   public ArgsParser(String [] args)
+   {
+     vargs = new Vector();
+     for (int i = 0; i < args.length; i++)
+     {
+       String arg = args[i].trim();
+       if (arg.charAt(0) == '-')
+         arg = arg.substring(1);
+       vargs.addElement(arg);
+     }
+   }
+
+   public String getValue(String arg)
+   {
+     int index = vargs.indexOf(arg);
+     String ret = null;
+     if (index != -1)
+     {
+       ret = vargs.elementAt(index + 1).toString();
+       vargs.removeElementAt(index);
+       vargs.removeElementAt(index);
+     }
+     return ret;
+   }
+
+   public boolean contains(String arg)
+   {
+     if(vargs.contains(arg))
+     {
+       vargs.removeElement(arg);
+       return true;
+     }
+     else
+       return false;
+   }
+
+   public String nextValue()
+   {
+     return  vargs.remove(0).toString();
+   }
+
+   public int getSize()
+   {
+     return vargs.size();
+   }
+
+ }
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 2a411f7..451c478 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -30,7 +30,14 @@ import java.awt.*;
 import java.awt.event.*;
 
 
-public class JalviewLite extends Applet {
+/**
+ * Jalview Applet. Runs in Java 1.18 runtime
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class JalviewLite extends Applet
+{
     static int lastFrameX = 200;
     static int lastFrameY = 200;
     static Applet applet;
@@ -38,73 +45,127 @@ public class JalviewLite extends Applet {
     String file = "No file";
     Button launcher = new Button("Start Jalview");
 
-    public void init() {
+    /**
+     * init method for Jalview Applet
+     */
+    public void init()
+    {
         applet = this;
 
-        int r=255,g=255,b=255;
+        int r = 255;
+        int g = 255;
+        int b = 255;
         String param = getParameter("RGB");
-        if(param!=null)
+
+        if (param != null)
         {
-          try
-          {
-            r = Integer.parseInt(param.substring(0,2),16);
-            g = Integer.parseInt(param.substring(2,4),16);
-            b = Integer.parseInt(param.substring(4,6),16);
-          }
-          catch (Exception ex)
-          { r=255;g=255;b=255; }
+            try
+            {
+                r = Integer.parseInt(param.substring(0, 2), 16);
+                g = Integer.parseInt(param.substring(2, 4), 16);
+                b = Integer.parseInt(param.substring(4, 6), 16);
+            }
+            catch (Exception ex)
+            {
+                r = 255;
+                g = 255;
+                b = 255;
+            }
         }
 
-        this.setBackground(new Color(r,g,b));
+        this.setBackground(new Color(r, g, b));
 
         file = getParameter("file");
 
-        if (file != null) {
+        if (file != null)
+        {
             add(launcher);
             file = applet.getCodeBase() + file;
-            launcher.addActionListener(new java.awt.event.ActionListener() {
-                    public void actionPerformed(ActionEvent e) {
+            launcher.addActionListener(new java.awt.event.ActionListener()
+                {
+                    public void actionPerformed(ActionEvent e)
+                    {
                         String format = jalview.io.IdentifyFile.Identify(file,
                                 "URL");
                         LoadFile(file, "URL", format);
                     }
                 });
-        } else {
+        }
+        else
+        {
             file = "NO FILE";
             fileFound = false;
         }
     }
 
-    public static void showURL(String url) {
-        try {
+    /**
+     * Displays the given URL in a new browser window
+     *
+     * @param url URL to display in browser window.
+     * <br>New window will be named "HELP_WINDOW"
+     */
+    public static void showURL(String url)
+    {
+        try
+        {
             applet.getAppletContext().showDocument(new java.net.URL(url),
                 "HELP_WINDOW");
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
         }
     }
 
-    public void LoadFile(String file, String protocol, String format) {
+    /**
+     * Starts a new LoadingThread for loading an alignment file
+     *
+     * @param file file name including full path to file
+     * @param protocol file or URL or paste
+     * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview
+     */
+    public void LoadFile(String file, String protocol, String format)
+    {
         LoadingThread loader = new LoadingThread(file, protocol, format, this);
         loader.start();
     }
 
+    /**
+     * Initialises and displays a new java.awt.Frame
+     *
+     * @param frame java.awt.Frame to be displayed
+     * @param title title of new frame
+     * @param width width if new frame
+     * @param height height of new frame
+     */
     public static void addFrame(final Frame frame, String title, int width,
-        int height) {
+        int height)
+    {
         frame.setLocation(lastFrameX, lastFrameY);
         lastFrameX += 40;
         lastFrameY += 40;
         frame.setSize(width, height);
         frame.setTitle(title);
-        frame.addWindowListener(new WindowAdapter() {
-                public void windowClosing(WindowEvent e) {
+        frame.addWindowListener(new WindowAdapter()
+            {
+                public void windowClosing(WindowEvent e)
+                {
                     frame.dispose();
                 }
             });
         frame.setVisible(true);
     }
 
-    public void paint(Graphics g) {
-        if (!fileFound) {
+    /**
+     * This paints the background surrounding the "Launch Jalview button"
+     * <br>
+     * <br>If file given in parameter not found, displays error message
+     *
+     * @param g graphics context
+     */
+    public void paint(Graphics g)
+    {
+        if (!fileFound)
+        {
             g.setColor(new Color(200, 200, 200));
             g.setColor(Color.cyan);
             g.fillRect(0, 0, getSize().width, getSize().height);
@@ -114,31 +175,37 @@ public class JalviewLite extends Applet {
         }
     }
 
-    class LoadingThread extends Thread {
+    class LoadingThread extends Thread
+    {
         String file;
         String protocol;
         String format;
         JalviewLite jlapplet;
 
         public LoadingThread(String file, String protocol, String format,
-            JalviewLite applet) {
+            JalviewLite applet)
+        {
             this.file = file;
             this.protocol = protocol;
             this.format = format;
             this.jlapplet = applet;
         }
 
-        public void run() {
+        public void run()
+        {
             SequenceI[] sequences = null;
             sequences = FormatAdapter.readFile(file, protocol, format);
 
-            if ((sequences != null) && (sequences.length > 0)) {
+            if ((sequences != null) && (sequences.length > 0))
+            {
                 AlignFrame af = new AlignFrame(new Alignment(sequences),
                         jlapplet);
                 addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
                     AlignFrame.NEW_WINDOW_HEIGHT);
                 af.statusBar.setText("Successfully loaded file " + file);
-            } else {
+            }
+            else
+            {
                 fileFound = false;
                 remove(launcher);
                 repaint();
diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 9a38f10..78fff89 100755
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,36 +1,36 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
+
 import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+
+
 /**
  * Class Alignment.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class Alignment implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class Alignment implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -43,131 +43,148 @@ public class Alignment implements java.io.Serializable {
      */
     private jalview.binding.SequenceSet _sequenceSet;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public Alignment() {
+    //- Constructors -/
+    //----------------/
+    public Alignment()
+    {
         super();
-    } //-- jalview.binding.Alignment()
+    }
 
-
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.Alignment()
     //-----------/
 
     /**
-     * Returns the value of field 'annotation'.
-     * 
-     * @return Annotation
-     * @return the value of field 'annotation'.
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
      */
     public jalview.binding.Annotation getAnnotation()
     {
         return this._annotation;
-    } //-- jalview.binding.Annotation getAnnotation() 
+    }
+
+    //-- jalview.binding.Annotation getAnnotation() 
 
     /**
      * Returns the value of field 'sequenceSet'.
-     * 
+     *
      * @return SequenceSet
      * @return the value of field 'sequenceSet'.
      */
     public jalview.binding.SequenceSet getSequenceSet()
     {
         return this._sequenceSet;
-    } //-- jalview.binding.SequenceSet getSequenceSet() 
+    }
+
+    //-- jalview.binding.SequenceSet getSequenceSet() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Sets the value of field 'annotation'.
-     * 
+     *
      * @param annotation the value of field 'annotation'.
      */
     public void setAnnotation(jalview.binding.Annotation annotation)
     {
         this._annotation = annotation;
-    } //-- void setAnnotation(jalview.binding.Annotation) 
+    }
+
+    //-- void setAnnotation(jalview.binding.Annotation) 
 
     /**
      * Sets the value of field 'sequenceSet'.
-     * 
+     *
      * @param sequenceSet the value of field 'sequenceSet'.
      */
     public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)
     {
         this._sequenceSet = sequenceSet;
-    } //-- void setSequenceSet(jalview.binding.SequenceSet) 
+    }
+
+    //-- void setSequenceSet(jalview.binding.SequenceSet) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java
index fefdd12..14b09c4 100755
--- a/src/jalview/binding/Annotation.java
+++ b/src/jalview/binding/Annotation.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,373 +7,385 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Annotation.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class Annotation implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _graph
-     */
-    private boolean _graph;
-
-    /**
-     * keeps track of state for field: _graph
-     */
-    private boolean _has_graph;
-
-    /**
-     * Field _annotationElementList
-     */
-    private java.util.Vector _annotationElementList;
-
-    /**
-     * Field _label
-     */
-    private java.lang.String _label;
-
-    /**
-     * Field _description
-     */
-    private java.lang.String _description;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Annotation() {
-        super();
-        _annotationElementList = new Vector();
-    } //-- jalview.binding.Annotation()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAnnotationElement
-     * 
-     * 
-     * 
-     * @param vAnnotationElement
-     */
-    public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _annotationElementList.addElement(vAnnotationElement);
-    } //-- void addAnnotationElement(jalview.binding.AnnotationElement) 
-
-    /**
-     * Method addAnnotationElement
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     */
-    public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _annotationElementList.insertElementAt(vAnnotationElement, index);
-    } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) 
-
-    /**
-     * Method deleteGraph
-     * 
-     */
-    public void deleteGraph()
-    {
-        this._has_graph= false;
-    } //-- void deleteGraph() 
-
-    /**
-     * Method enumerateAnnotationElement
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateAnnotationElement()
-    {
-        return _annotationElementList.elements();
-    } //-- java.util.Enumeration enumerateAnnotationElement() 
-
-    /**
-     * Method getAnnotationElement
-     * 
-     * 
-     * 
-     * @param index
-     * @return AnnotationElement
-     */
-    public jalview.binding.AnnotationElement getAnnotationElement(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _annotationElementList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);
-    } //-- jalview.binding.AnnotationElement getAnnotationElement(int) 
-
-    /**
-     * Method getAnnotationElement
-     * 
-     * 
-     * 
-     * @return AnnotationElement
-     */
-    public jalview.binding.AnnotationElement[] getAnnotationElement()
-    {
-        int size = _annotationElementList.size();
-        jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.AnnotationElement[] getAnnotationElement() 
-
-    /**
-     * Method getAnnotationElementCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getAnnotationElementCount()
-    {
-        return _annotationElementList.size();
-    } //-- int getAnnotationElementCount() 
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return String
-     * @return the value of field 'description'.
-     */
-    public java.lang.String getDescription()
-    {
-        return this._description;
-    } //-- java.lang.String getDescription() 
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return boolean
-     * @return the value of field 'graph'.
-     */
-    public boolean getGraph()
-    {
-        return this._graph;
-    } //-- boolean getGraph() 
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return String
-     * @return the value of field 'label'.
-     */
-    public java.lang.String getLabel()
-    {
-        return this._label;
-    } //-- java.lang.String getLabel() 
-
-    /**
-     * Method hasGraph
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasGraph()
-    {
-        return this._has_graph;
-    } //-- boolean hasGraph() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllAnnotationElement
-     * 
-     */
-    public void removeAllAnnotationElement()
-    {
-        _annotationElementList.removeAllElements();
-    } //-- void removeAllAnnotationElement() 
-
-    /**
-     * Method removeAnnotationElement
-     * 
-     * 
-     * 
-     * @param index
-     * @return AnnotationElement
-     */
-    public jalview.binding.AnnotationElement removeAnnotationElement(int index)
-    {
-        java.lang.Object obj = _annotationElementList.elementAt(index);
-        _annotationElementList.removeElementAt(index);
-        return (jalview.binding.AnnotationElement) obj;
-    } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) 
-
-    /**
-     * Method setAnnotationElement
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     */
-    public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _annotationElementList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _annotationElementList.setElementAt(vAnnotationElement, index);
-    } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) 
-
-    /**
-     * Method setAnnotationElement
-     * 
-     * 
-     * 
-     * @param annotationElementArray
-     */
-    public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)
+public class Annotation
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _graph
+   */
+  private boolean _graph;
+
+  /**
+   * keeps track of state for field: _graph
+   */
+  private boolean _has_graph;
+
+  /**
+   * Field _annotationElementList
+   */
+  private java.util.Vector _annotationElementList;
+
+  /**
+   * Field _label
+   */
+  private java.lang.String _label;
+
+  /**
+   * Field _description
+   */
+  private java.lang.String _description;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public Annotation()
+  {
+    super();
+    _annotationElementList = new Vector();
+  } //-- jalview.binding.Annotation()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addAnnotationElement
+   *
+   *
+   *
+   * @param vAnnotationElement
+   */
+  public void addAnnotationElement(jalview.binding.AnnotationElement
+                                   vAnnotationElement)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _annotationElementList.addElement(vAnnotationElement);
+  } //-- void addAnnotationElement(jalview.binding.AnnotationElement)
+
+  /**
+   * Method addAnnotationElement
+   *
+   *
+   *
+   * @param index
+   * @param vAnnotationElement
+   */
+  public void addAnnotationElement(int index,
+                                   jalview.binding.AnnotationElement
+                                   vAnnotationElement)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _annotationElementList.insertElementAt(vAnnotationElement, index);
+  } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)
+
+  /**
+   * Method deleteGraph
+   *
+   */
+  public void deleteGraph()
+  {
+    this._has_graph = false;
+  } //-- void deleteGraph()
+
+  /**
+   * Method enumerateAnnotationElement
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateAnnotationElement()
+  {
+    return _annotationElementList.elements();
+  } //-- java.util.Enumeration enumerateAnnotationElement()
+
+  /**
+   * Method getAnnotationElement
+   *
+   *
+   *
+   * @param index
+   * @return AnnotationElement
+   */
+  public jalview.binding.AnnotationElement getAnnotationElement(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _annotationElementList.size()))
     {
-        //-- copy array
-        _annotationElementList.removeAllElements();
-        for (int i = 0; i < annotationElementArray.length; i++) {
-            _annotationElementList.addElement(annotationElementArray[i]);
-        }
-    } //-- void setAnnotationElement(jalview.binding.AnnotationElement) 
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(java.lang.String description)
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(
+        index);
+  } //-- jalview.binding.AnnotationElement getAnnotationElement(int)
+
+  /**
+   * Method getAnnotationElement
+   *
+   *
+   *
+   * @return AnnotationElement
+   */
+  public jalview.binding.AnnotationElement[] getAnnotationElement()
+  {
+    int size = _annotationElementList.size();
+    jalview.binding.AnnotationElement[] mArray = new jalview.binding.
+        AnnotationElement[size];
+    for (int index = 0; index < size; index++)
     {
-        this._description = description;
-    } //-- void setDescription(java.lang.String) 
-
-    /**
-     * Sets the value of field 'graph'.
-     * 
-     * @param graph the value of field 'graph'.
-     */
-    public void setGraph(boolean graph)
+      mArray[index] = (jalview.binding.AnnotationElement)
+          _annotationElementList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.binding.AnnotationElement[] getAnnotationElement()
+
+  /**
+   * Method getAnnotationElementCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getAnnotationElementCount()
+  {
+    return _annotationElementList.size();
+  } //-- int getAnnotationElementCount()
+
+  /**
+   * Returns the value of field 'description'.
+   *
+   * @return String
+   * @return the value of field 'description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  } //-- java.lang.String getDescription()
+
+  /**
+   * Returns the value of field 'graph'.
+   *
+   * @return boolean
+   * @return the value of field 'graph'.
+   */
+  public boolean getGraph()
+  {
+    return this._graph;
+  } //-- boolean getGraph()
+
+  /**
+   * Returns the value of field 'label'.
+   *
+   * @return String
+   * @return the value of field 'label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  } //-- java.lang.String getLabel()
+
+  /**
+   * Method hasGraph
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasGraph()
+  {
+    return this._has_graph;
+  } //-- boolean hasGraph()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        this._graph = graph;
-        this._has_graph = true;
-    } //-- void setGraph(boolean) 
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(java.lang.String label)
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        this._label = label;
-    } //-- void setLabel(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllAnnotationElement
+   *
+   */
+  public void removeAllAnnotationElement()
+  {
+    _annotationElementList.removeAllElements();
+  } //-- void removeAllAnnotationElement()
+
+  /**
+   * Method removeAnnotationElement
+   *
+   *
+   *
+   * @param index
+   * @return AnnotationElement
+   */
+  public jalview.binding.AnnotationElement removeAnnotationElement(int index)
+  {
+    java.lang.Object obj = _annotationElementList.elementAt(index);
+    _annotationElementList.removeElementAt(index);
+    return (jalview.binding.AnnotationElement) obj;
+  } //-- jalview.binding.AnnotationElement removeAnnotationElement(int)
+
+  /**
+   * Method setAnnotationElement
+   *
+   *
+   *
+   * @param index
+   * @param vAnnotationElement
+   */
+  public void setAnnotationElement(int index,
+                                   jalview.binding.AnnotationElement
+                                   vAnnotationElement)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _annotationElementList.size()))
     {
-        return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      throw new IndexOutOfBoundsException();
+    }
+    _annotationElementList.setElementAt(vAnnotationElement, index);
+  } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)
+
+  /**
+   * Method setAnnotationElement
+   *
+   *
+   *
+   * @param annotationElementArray
+   */
+  public void setAnnotationElement(jalview.binding.AnnotationElement[]
+                                   annotationElementArray)
+  {
+    //-- copy array
+    _annotationElementList.removeAllElements();
+    for (int i = 0; i < annotationElementArray.length; i++)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      _annotationElementList.addElement(annotationElementArray[i]);
+    }
+  } //-- void setAnnotationElement(jalview.binding.AnnotationElement)
+
+  /**
+   * Sets the value of field 'description'.
+   *
+   * @param description the value of field 'description'.
+   */
+  public void setDescription(java.lang.String description)
+  {
+    this._description = description;
+  } //-- void setDescription(java.lang.String)
+
+  /**
+   * Sets the value of field 'graph'.
+   *
+   * @param graph the value of field 'graph'.
+   */
+  public void setGraph(boolean graph)
+  {
+    this._graph = graph;
+    this._has_graph = true;
+  } //-- void setGraph(boolean)
+
+  /**
+   * Sets the value of field 'label'.
+   *
+   * @param label the value of field 'label'.
+   */
+  public void setLabel(java.lang.String label)
+  {
+    this._label = label;
+  } //-- void setLabel(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.
+        Annotation.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java
index e4aec31..16c3dab 100755
--- a/src/jalview/binding/AnnotationElement.java
+++ b/src/jalview/binding/AnnotationElement.java
@@ -1,36 +1,36 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
+
 import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+
+
 /**
  * Class AnnotationElement.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class AnnotationElement implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class AnnotationElement implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -68,239 +68,276 @@ public class AnnotationElement implements java.io.Serializable {
      */
     private boolean _has_value;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public AnnotationElement() {
+    //- Constructors -/
+    //----------------/
+    public AnnotationElement()
+    {
         super();
-    } //-- jalview.binding.AnnotationElement()
-
+    }
 
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.AnnotationElement()
     //-----------/
 
     /**
-     * Method deletePosition
-     * 
+     * DOCUMENT ME!
      */
     public void deletePosition()
     {
-        this._has_position= false;
-    } //-- void deletePosition() 
+        this._has_position = false;
+    }
+
+    //-- void deletePosition() 
 
     /**
      * Method deleteValue
-     * 
+     *
      */
     public void deleteValue()
     {
-        this._has_value= false;
-    } //-- void deleteValue() 
+        this._has_value = false;
+    }
+
+    //-- void deleteValue() 
 
     /**
      * Returns the value of field 'description'.
-     * 
+     *
      * @return String
      * @return the value of field 'description'.
      */
     public java.lang.String getDescription()
     {
         return this._description;
-    } //-- java.lang.String getDescription() 
+    }
+
+    //-- java.lang.String getDescription() 
 
     /**
      * Returns the value of field 'displayCharacter'.
-     * 
+     *
      * @return String
      * @return the value of field 'displayCharacter'.
      */
     public java.lang.String getDisplayCharacter()
     {
         return this._displayCharacter;
-    } //-- java.lang.String getDisplayCharacter() 
+    }
+
+    //-- java.lang.String getDisplayCharacter() 
 
     /**
      * Returns the value of field 'position'.
-     * 
+     *
      * @return int
      * @return the value of field 'position'.
      */
     public int getPosition()
     {
         return this._position;
-    } //-- int getPosition() 
+    }
+
+    //-- int getPosition() 
 
     /**
      * Returns the value of field 'secondaryStructure'.
-     * 
+     *
      * @return String
      * @return the value of field 'secondaryStructure'.
      */
     public java.lang.String getSecondaryStructure()
     {
         return this._secondaryStructure;
-    } //-- java.lang.String getSecondaryStructure() 
+    }
+
+    //-- java.lang.String getSecondaryStructure() 
 
     /**
      * Returns the value of field 'value'.
-     * 
+     *
      * @return float
      * @return the value of field 'value'.
      */
     public float getValue()
     {
         return this._value;
-    } //-- float getValue() 
+    }
+
+    //-- float getValue() 
 
     /**
      * Method hasPosition
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasPosition()
     {
         return this._has_position;
-    } //-- boolean hasPosition() 
+    }
+
+    //-- boolean hasPosition() 
 
     /**
      * Method hasValue
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasValue()
     {
         return this._has_value;
-    } //-- boolean hasValue() 
+    }
+
+    //-- boolean hasValue() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Sets the value of field 'description'.
-     * 
+     *
      * @param description the value of field 'description'.
      */
     public void setDescription(java.lang.String description)
     {
         this._description = description;
-    } //-- void setDescription(java.lang.String) 
+    }
+
+    //-- void setDescription(java.lang.String) 
 
     /**
      * Sets the value of field 'displayCharacter'.
-     * 
+     *
      * @param displayCharacter the value of field 'displayCharacter'
      */
     public void setDisplayCharacter(java.lang.String displayCharacter)
     {
         this._displayCharacter = displayCharacter;
-    } //-- void setDisplayCharacter(java.lang.String) 
+    }
+
+    //-- void setDisplayCharacter(java.lang.String) 
 
     /**
      * Sets the value of field 'position'.
-     * 
+     *
      * @param position the value of field 'position'.
      */
     public void setPosition(int position)
     {
         this._position = position;
         this._has_position = true;
-    } //-- void setPosition(int) 
+    }
+
+    //-- void setPosition(int) 
 
     /**
      * Sets the value of field 'secondaryStructure'.
-     * 
+     *
      * @param secondaryStructure the value of field
      * 'secondaryStructure'.
      */
     public void setSecondaryStructure(java.lang.String secondaryStructure)
     {
         this._secondaryStructure = secondaryStructure;
-    } //-- void setSecondaryStructure(java.lang.String) 
+    }
+
+    //-- void setSecondaryStructure(java.lang.String) 
 
     /**
      * Sets the value of field 'value'.
-     * 
+     *
      * @param value the value of field 'value'.
      */
     public void setValue(float value)
     {
         this._value = value;
         this._has_value = true;
-    } //-- void setValue(float) 
+    }
+
+    //-- void setValue(float) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
index a51102b..4e57c3f 100755
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -1,36 +1,36 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
+
 import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+
+
 /**
  * Class Colour.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class Colour implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class Colour implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -43,131 +43,148 @@ public class Colour implements java.io.Serializable {
      */
     private java.lang.String _RGB;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public Colour() {
+    //- Constructors -/
+    //----------------/
+    public Colour()
+    {
         super();
-    } //-- jalview.binding.Colour()
-
+    }
 
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.Colour()
     //-----------/
 
     /**
-     * Returns the value of field 'name'.
-     * 
-     * @return String
-     * @return the value of field 'name'.
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
      */
     public java.lang.String getName()
     {
         return this._name;
-    } //-- java.lang.String getName() 
+    }
+
+    //-- java.lang.String getName() 
 
     /**
      * Returns the value of field 'RGB'.
-     * 
+     *
      * @return String
      * @return the value of field 'RGB'.
      */
     public java.lang.String getRGB()
     {
         return this._RGB;
-    } //-- java.lang.String getRGB() 
+    }
+
+    //-- java.lang.String getRGB() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Sets the value of field 'name'.
-     * 
+     *
      * @param name the value of field 'name'.
      */
     public void setName(java.lang.String name)
     {
         this._name = name;
-    } //-- void setName(java.lang.String) 
+    }
+
+    //-- void setName(java.lang.String) 
 
     /**
      * Sets the value of field 'RGB'.
-     * 
+     *
      * @param RGB the value of field 'RGB'.
      */
     public void setRGB(java.lang.String RGB)
     {
         this._RGB = RGB;
-    } //-- void setRGB(java.lang.String) 
+    }
+
+    //-- void setRGB(java.lang.String) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java
index 6473149..5b6d74e 100755
--- a/src/jalview/binding/JGroup.java
+++ b/src/jalview/binding/JGroup.java
@@ -1,38 +1,39 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
 
+import org.xml.sax.ContentHandler;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
 import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+
 import java.util.Enumeration;
 import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+
 
 /**
  * Class JGroup.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JGroup implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class JGroup implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -130,39 +131,37 @@ public class JGroup implements java.io.Serializable {
      */
     private java.util.Vector _seqList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public JGroup() {
+    //- Constructors -/
+    //----------------/
+    public JGroup()
+    {
         super();
         _seqList = new Vector();
-    } //-- jalview.binding.JGroup()
-
+    }
 
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.JGroup()
     //-----------/
 
     /**
-     * Method addSeq
-     * 
-     * 
-     * 
-     * @param vSeq
+     * DOCUMENT ME!
+     *
+     * @param vSeq DOCUMENT ME!
+     *
+     * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!
      */
-    public void addSeq(int vSeq)
-        throws java.lang.IndexOutOfBoundsException
+    public void addSeq(int vSeq) throws java.lang.IndexOutOfBoundsException
     {
         _seqList.addElement(new java.lang.Integer(vSeq));
-    } //-- void addSeq(int) 
+    }
+
+    //-- void addSeq(int) 
 
     /**
      * Method addSeq
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vSeq
      */
@@ -170,406 +169,482 @@ public class JGroup implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
-    } //-- void addSeq(int, int) 
+    }
+
+    //-- void addSeq(int, int) 
 
     /**
      * Method deleteColourText
-     * 
+     *
      */
     public void deleteColourText()
     {
-        this._has_colourText= false;
-    } //-- void deleteColourText() 
+        this._has_colourText = false;
+    }
+
+    //-- void deleteColourText() 
 
     /**
      * Method deleteConsThreshold
-     * 
+     *
      */
     public void deleteConsThreshold()
     {
-        this._has_consThreshold= false;
-    } //-- void deleteConsThreshold() 
+        this._has_consThreshold = false;
+    }
+
+    //-- void deleteConsThreshold() 
 
     /**
      * Method deleteDisplayBoxes
-     * 
+     *
      */
     public void deleteDisplayBoxes()
     {
-        this._has_displayBoxes= false;
-    } //-- void deleteDisplayBoxes() 
+        this._has_displayBoxes = false;
+    }
+
+    //-- void deleteDisplayBoxes() 
 
     /**
      * Method deleteDisplayText
-     * 
+     *
      */
     public void deleteDisplayText()
     {
-        this._has_displayText= false;
-    } //-- void deleteDisplayText() 
+        this._has_displayText = false;
+    }
+
+    //-- void deleteDisplayText() 
 
     /**
      * Method deleteEnd
-     * 
+     *
      */
     public void deleteEnd()
     {
-        this._has_end= false;
-    } //-- void deleteEnd() 
+        this._has_end = false;
+    }
+
+    //-- void deleteEnd() 
 
     /**
      * Method deleteOutlineColour
-     * 
+     *
      */
     public void deleteOutlineColour()
     {
-        this._has_outlineColour= false;
-    } //-- void deleteOutlineColour() 
+        this._has_outlineColour = false;
+    }
+
+    //-- void deleteOutlineColour() 
 
     /**
      * Method deletePidThreshold
-     * 
+     *
      */
     public void deletePidThreshold()
     {
-        this._has_pidThreshold= false;
-    } //-- void deletePidThreshold() 
+        this._has_pidThreshold = false;
+    }
+
+    //-- void deletePidThreshold() 
 
     /**
      * Method deleteStart
-     * 
+     *
      */
     public void deleteStart()
     {
-        this._has_start= false;
-    } //-- void deleteStart() 
+        this._has_start = false;
+    }
+
+    //-- void deleteStart() 
 
     /**
      * Method enumerateSeq
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Enumeration
      */
     public java.util.Enumeration enumerateSeq()
     {
         return _seqList.elements();
-    } //-- java.util.Enumeration enumerateSeq() 
+    }
+
+    //-- java.util.Enumeration enumerateSeq() 
 
     /**
      * Returns the value of field 'colour'.
-     * 
+     *
      * @return String
      * @return the value of field 'colour'.
      */
     public java.lang.String getColour()
     {
         return this._colour;
-    } //-- java.lang.String getColour() 
+    }
+
+    //-- java.lang.String getColour() 
 
     /**
      * Returns the value of field 'colourText'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'colourText'.
      */
     public boolean getColourText()
     {
         return this._colourText;
-    } //-- boolean getColourText() 
+    }
+
+    //-- boolean getColourText() 
 
     /**
      * Returns the value of field 'consThreshold'.
-     * 
+     *
      * @return int
      * @return the value of field 'consThreshold'.
      */
     public int getConsThreshold()
     {
         return this._consThreshold;
-    } //-- int getConsThreshold() 
+    }
+
+    //-- int getConsThreshold() 
 
     /**
      * Returns the value of field 'displayBoxes'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'displayBoxes'.
      */
     public boolean getDisplayBoxes()
     {
         return this._displayBoxes;
-    } //-- boolean getDisplayBoxes() 
+    }
+
+    //-- boolean getDisplayBoxes() 
 
     /**
      * Returns the value of field 'displayText'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'displayText'.
      */
     public boolean getDisplayText()
     {
         return this._displayText;
-    } //-- boolean getDisplayText() 
+    }
+
+    //-- boolean getDisplayText() 
 
     /**
      * Returns the value of field 'end'.
-     * 
+     *
      * @return int
      * @return the value of field 'end'.
      */
     public int getEnd()
     {
         return this._end;
-    } //-- int getEnd() 
+    }
+
+    //-- int getEnd() 
 
     /**
      * Returns the value of field 'name'.
-     * 
+     *
      * @return String
      * @return the value of field 'name'.
      */
     public java.lang.String getName()
     {
         return this._name;
-    } //-- java.lang.String getName() 
+    }
+
+    //-- java.lang.String getName() 
 
     /**
      * Returns the value of field 'outlineColour'.
-     * 
+     *
      * @return int
      * @return the value of field 'outlineColour'.
      */
     public int getOutlineColour()
     {
         return this._outlineColour;
-    } //-- int getOutlineColour() 
+    }
+
+    //-- int getOutlineColour() 
 
     /**
      * Returns the value of field 'pidThreshold'.
-     * 
+     *
      * @return int
      * @return the value of field 'pidThreshold'.
      */
     public int getPidThreshold()
     {
         return this._pidThreshold;
-    } //-- int getPidThreshold() 
+    }
+
+    //-- int getPidThreshold() 
 
     /**
      * Method getSeq
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return int
      */
-    public int getSeq(int index)
-        throws java.lang.IndexOutOfBoundsException
+    public int getSeq(int index) throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _seqList.size())) {
+        if ((index < 0) || (index > _seqList.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
-        
-        return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
-    } //-- int getSeq(int) 
+
+        return ((java.lang.Integer) _seqList.elementAt(index)).intValue();
+    }
+
+    //-- int getSeq(int) 
 
     /**
      * Method getSeq
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return int
      */
     public int[] getSeq()
     {
         int size = _seqList.size();
         int[] mArray = new int[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
+
+        for (int index = 0; index < size; index++)
+        {
+            mArray[index] = ((java.lang.Integer) _seqList.elementAt(index)).intValue();
         }
+
         return mArray;
-    } //-- int[] getSeq() 
+    }
+
+    //-- int[] getSeq() 
 
     /**
      * Method getSeqCount
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return int
      */
     public int getSeqCount()
     {
         return _seqList.size();
-    } //-- int getSeqCount() 
+    }
+
+    //-- int getSeqCount() 
 
     /**
      * Returns the value of field 'start'.
-     * 
+     *
      * @return int
      * @return the value of field 'start'.
      */
     public int getStart()
     {
         return this._start;
-    } //-- int getStart() 
+    }
+
+    //-- int getStart() 
 
     /**
      * Method hasColourText
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasColourText()
     {
         return this._has_colourText;
-    } //-- boolean hasColourText() 
+    }
+
+    //-- boolean hasColourText() 
 
     /**
      * Method hasConsThreshold
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasConsThreshold()
     {
         return this._has_consThreshold;
-    } //-- boolean hasConsThreshold() 
+    }
+
+    //-- boolean hasConsThreshold() 
 
     /**
      * Method hasDisplayBoxes
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasDisplayBoxes()
     {
         return this._has_displayBoxes;
-    } //-- boolean hasDisplayBoxes() 
+    }
+
+    //-- boolean hasDisplayBoxes() 
 
     /**
      * Method hasDisplayText
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasDisplayText()
     {
         return this._has_displayText;
-    } //-- boolean hasDisplayText() 
+    }
+
+    //-- boolean hasDisplayText() 
 
     /**
      * Method hasEnd
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasEnd()
     {
         return this._has_end;
-    } //-- boolean hasEnd() 
+    }
+
+    //-- boolean hasEnd() 
 
     /**
      * Method hasOutlineColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasOutlineColour()
     {
         return this._has_outlineColour;
-    } //-- boolean hasOutlineColour() 
+    }
+
+    //-- boolean hasOutlineColour() 
 
     /**
      * Method hasPidThreshold
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasPidThreshold()
     {
         return this._has_pidThreshold;
-    } //-- boolean hasPidThreshold() 
+    }
+
+    //-- boolean hasPidThreshold() 
 
     /**
      * Method hasStart
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasStart()
     {
         return this._has_start;
-    } //-- boolean hasStart() 
+    }
+
+    //-- boolean hasStart() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Method removeAllSeq
-     * 
+     *
      */
     public void removeAllSeq()
     {
         _seqList.removeAllElements();
-    } //-- void removeAllSeq() 
+    }
+
+    //-- void removeAllSeq() 
 
     /**
      * Method removeSeq
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return int
      */
@@ -577,111 +652,132 @@ public class JGroup implements java.io.Serializable {
     {
         java.lang.Object obj = _seqList.elementAt(index);
         _seqList.removeElementAt(index);
-        return ((java.lang.Integer)obj).intValue();
-    } //-- int removeSeq(int) 
+
+        return ((java.lang.Integer) obj).intValue();
+    }
+
+    //-- int removeSeq(int) 
 
     /**
      * Sets the value of field 'colour'.
-     * 
+     *
      * @param colour the value of field 'colour'.
      */
     public void setColour(java.lang.String colour)
     {
         this._colour = colour;
-    } //-- void setColour(java.lang.String) 
+    }
+
+    //-- void setColour(java.lang.String) 
 
     /**
      * Sets the value of field 'colourText'.
-     * 
+     *
      * @param colourText the value of field 'colourText'.
      */
     public void setColourText(boolean colourText)
     {
         this._colourText = colourText;
         this._has_colourText = true;
-    } //-- void setColourText(boolean) 
+    }
+
+    //-- void setColourText(boolean) 
 
     /**
      * Sets the value of field 'consThreshold'.
-     * 
+     *
      * @param consThreshold the value of field 'consThreshold'.
      */
     public void setConsThreshold(int consThreshold)
     {
         this._consThreshold = consThreshold;
         this._has_consThreshold = true;
-    } //-- void setConsThreshold(int) 
+    }
+
+    //-- void setConsThreshold(int) 
 
     /**
      * Sets the value of field 'displayBoxes'.
-     * 
+     *
      * @param displayBoxes the value of field 'displayBoxes'.
      */
     public void setDisplayBoxes(boolean displayBoxes)
     {
         this._displayBoxes = displayBoxes;
         this._has_displayBoxes = true;
-    } //-- void setDisplayBoxes(boolean) 
+    }
+
+    //-- void setDisplayBoxes(boolean) 
 
     /**
      * Sets the value of field 'displayText'.
-     * 
+     *
      * @param displayText the value of field 'displayText'.
      */
     public void setDisplayText(boolean displayText)
     {
         this._displayText = displayText;
         this._has_displayText = true;
-    } //-- void setDisplayText(boolean) 
+    }
+
+    //-- void setDisplayText(boolean) 
 
     /**
      * Sets the value of field 'end'.
-     * 
+     *
      * @param end the value of field 'end'.
      */
     public void setEnd(int end)
     {
         this._end = end;
         this._has_end = true;
-    } //-- void setEnd(int) 
+    }
+
+    //-- void setEnd(int) 
 
     /**
      * Sets the value of field 'name'.
-     * 
+     *
      * @param name the value of field 'name'.
      */
     public void setName(java.lang.String name)
     {
         this._name = name;
-    } //-- void setName(java.lang.String) 
+    }
+
+    //-- void setName(java.lang.String) 
 
     /**
      * Sets the value of field 'outlineColour'.
-     * 
+     *
      * @param outlineColour the value of field 'outlineColour'.
      */
     public void setOutlineColour(int outlineColour)
     {
         this._outlineColour = outlineColour;
         this._has_outlineColour = true;
-    } //-- void setOutlineColour(int) 
+    }
+
+    //-- void setOutlineColour(int) 
 
     /**
      * Sets the value of field 'pidThreshold'.
-     * 
+     *
      * @param pidThreshold the value of field 'pidThreshold'.
      */
     public void setPidThreshold(int pidThreshold)
     {
         this._pidThreshold = pidThreshold;
         this._has_pidThreshold = true;
-    } //-- void setPidThreshold(int) 
+    }
+
+    //-- void setPidThreshold(int) 
 
     /**
      * Method setSeq
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vSeq
      */
@@ -689,62 +785,76 @@ public class JGroup implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _seqList.size())) {
+        if ((index < 0) || (index > _seqList.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
+
         _seqList.setElementAt(new java.lang.Integer(vSeq), index);
-    } //-- void setSeq(int, int) 
+    }
+
+    //-- void setSeq(int, int) 
 
     /**
      * Method setSeq
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param seqArray
      */
     public void setSeq(int[] seqArray)
     {
         //-- copy array
         _seqList.removeAllElements();
-        for (int i = 0; i < seqArray.length; i++) {
+
+        for (int i = 0; i < seqArray.length; i++)
+        {
             _seqList.addElement(new java.lang.Integer(seqArray[i]));
         }
-    } //-- void setSeq(int) 
+    }
+
+    //-- void setSeq(int) 
 
     /**
      * Sets the value of field 'start'.
-     * 
+     *
      * @param start the value of field 'start'.
      */
     public void setStart(int start)
     {
         this._start = start;
         this._has_start = true;
-    } //-- void setStart(int) 
+    }
+
+    //-- void setStart(int) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
index 751409f..9b8ddcb 100755
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -1,36 +1,36 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
+
 import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+
+
 /**
  * Class JSeq.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JSeq implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class JSeq implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -73,261 +73,302 @@ public class JSeq implements java.io.Serializable {
      */
     private boolean _has_id;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public JSeq() {
+    //- Constructors -/
+    //----------------/
+    public JSeq()
+    {
         super();
-    } //-- jalview.binding.JSeq()
+    }
 
-
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.JSeq()
     //-----------/
 
     /**
-     * Method deleteColour
-     * 
+     * DOCUMENT ME!
      */
     public void deleteColour()
     {
-        this._has_colour= false;
-    } //-- void deleteColour() 
+        this._has_colour = false;
+    }
+
+    //-- void deleteColour() 
 
     /**
      * Method deleteEnd
-     * 
+     *
      */
     public void deleteEnd()
     {
-        this._has_end= false;
-    } //-- void deleteEnd() 
+        this._has_end = false;
+    }
+
+    //-- void deleteEnd() 
 
     /**
      * Method deleteId
-     * 
+     *
      */
     public void deleteId()
     {
-        this._has_id= false;
-    } //-- void deleteId() 
+        this._has_id = false;
+    }
+
+    //-- void deleteId() 
 
     /**
      * Method deleteStart
-     * 
+     *
      */
     public void deleteStart()
     {
-        this._has_start= false;
-    } //-- void deleteStart() 
+        this._has_start = false;
+    }
+
+    //-- void deleteStart() 
 
     /**
      * Returns the value of field 'colour'.
-     * 
+     *
      * @return int
      * @return the value of field 'colour'.
      */
     public int getColour()
     {
         return this._colour;
-    } //-- int getColour() 
+    }
+
+    //-- int getColour() 
 
     /**
      * Returns the value of field 'end'.
-     * 
+     *
      * @return int
      * @return the value of field 'end'.
      */
     public int getEnd()
     {
         return this._end;
-    } //-- int getEnd() 
+    }
+
+    //-- int getEnd() 
 
     /**
      * Returns the value of field 'id'.
-     * 
+     *
      * @return int
      * @return the value of field 'id'.
      */
     public int getId()
     {
         return this._id;
-    } //-- int getId() 
+    }
+
+    //-- int getId() 
 
     /**
      * Returns the value of field 'start'.
-     * 
+     *
      * @return int
      * @return the value of field 'start'.
      */
     public int getStart()
     {
         return this._start;
-    } //-- int getStart() 
+    }
+
+    //-- int getStart() 
 
     /**
      * Method hasColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasColour()
     {
         return this._has_colour;
-    } //-- boolean hasColour() 
+    }
+
+    //-- boolean hasColour() 
 
     /**
      * Method hasEnd
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasEnd()
     {
         return this._has_end;
-    } //-- boolean hasEnd() 
+    }
+
+    //-- boolean hasEnd() 
 
     /**
      * Method hasId
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasId()
     {
         return this._has_id;
-    } //-- boolean hasId() 
+    }
+
+    //-- boolean hasId() 
 
     /**
      * Method hasStart
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasStart()
     {
         return this._has_start;
-    } //-- boolean hasStart() 
+    }
+
+    //-- boolean hasStart() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Sets the value of field 'colour'.
-     * 
+     *
      * @param colour the value of field 'colour'.
      */
     public void setColour(int colour)
     {
         this._colour = colour;
         this._has_colour = true;
-    } //-- void setColour(int) 
+    }
+
+    //-- void setColour(int) 
 
     /**
      * Sets the value of field 'end'.
-     * 
+     *
      * @param end the value of field 'end'.
      */
     public void setEnd(int end)
     {
         this._end = end;
         this._has_end = true;
-    } //-- void setEnd(int) 
+    }
+
+    //-- void setEnd(int) 
 
     /**
      * Sets the value of field 'id'.
-     * 
+     *
      * @param id the value of field 'id'.
      */
     public void setId(int id)
     {
         this._id = id;
         this._has_id = true;
-    } //-- void setId(int) 
+    }
+
+    //-- void setId(int) 
 
     /**
      * Sets the value of field 'start'.
-     * 
+     *
      * @param start the value of field 'start'.
      */
     public void setStart(int start)
     {
         this._start = start;
         this._has_start = true;
-    } //-- void setStart(int) 
+    }
+
+    //-- void setStart(int) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java
index 8edd012..bfdbddc 100755
--- a/src/jalview/binding/JalviewModel.java
+++ b/src/jalview/binding/JalviewModel.java
@@ -1,37 +1,38 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+
+import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
 import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+
 import java.util.Date;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+
 
 /**
  * Class JalviewModel.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewModel implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class JalviewModel implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -54,174 +55,200 @@ public class JalviewModel implements java.io.Serializable {
      */
     private jalview.binding.JalviewModelSequence _jalviewModelSequence;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public JalviewModel() {
+    //- Constructors -/
+    //----------------/
+    public JalviewModel()
+    {
         super();
-    } //-- jalview.binding.JalviewModel()
+    }
 
-
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.JalviewModel()
     //-----------/
 
     /**
-     * Returns the value of field 'creationDate'.
-     * 
-     * @return Date
-     * @return the value of field 'creationDate'.
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
      */
     public java.util.Date getCreationDate()
     {
         return this._creationDate;
-    } //-- java.util.Date getCreationDate() 
+    }
+
+    //-- java.util.Date getCreationDate() 
 
     /**
      * Returns the value of field 'jalviewModelSequence'.
-     * 
+     *
      * @return JalviewModelSequence
      * @return the value of field 'jalviewModelSequence'.
      */
     public jalview.binding.JalviewModelSequence getJalviewModelSequence()
     {
         return this._jalviewModelSequence;
-    } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() 
+    }
+
+    //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() 
 
     /**
      * Returns the value of field 'vamsasModel'.
-     * 
+     *
      * @return VamsasModel
      * @return the value of field 'vamsasModel'.
      */
     public jalview.binding.VamsasModel getVamsasModel()
     {
         return this._vamsasModel;
-    } //-- jalview.binding.VamsasModel getVamsasModel() 
+    }
+
+    //-- jalview.binding.VamsasModel getVamsasModel() 
 
     /**
      * Returns the value of field 'version'.
-     * 
+     *
      * @return String
      * @return the value of field 'version'.
      */
     public java.lang.String getVersion()
     {
         return this._version;
-    } //-- java.lang.String getVersion() 
+    }
+
+    //-- java.lang.String getVersion() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Sets the value of field 'creationDate'.
-     * 
+     *
      * @param creationDate the value of field 'creationDate'.
      */
     public void setCreationDate(java.util.Date creationDate)
     {
         this._creationDate = creationDate;
-    } //-- void setCreationDate(java.util.Date) 
+    }
+
+    //-- void setCreationDate(java.util.Date) 
 
     /**
      * Sets the value of field 'jalviewModelSequence'.
-     * 
+     *
      * @param jalviewModelSequence the value of field
      * 'jalviewModelSequence'.
      */
-    public void setJalviewModelSequence(jalview.binding.JalviewModelSequence jalviewModelSequence)
+    public void setJalviewModelSequence(
+        jalview.binding.JalviewModelSequence jalviewModelSequence)
     {
         this._jalviewModelSequence = jalviewModelSequence;
-    } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) 
+    }
+
+    //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) 
 
     /**
      * Sets the value of field 'vamsasModel'.
-     * 
+     *
      * @param vamsasModel the value of field 'vamsasModel'.
      */
     public void setVamsasModel(jalview.binding.VamsasModel vamsasModel)
     {
         this._vamsasModel = vamsasModel;
-    } //-- void setVamsasModel(jalview.binding.VamsasModel) 
+    }
+
+    //-- void setVamsasModel(jalview.binding.VamsasModel) 
 
     /**
      * Sets the value of field 'version'.
-     * 
+     *
      * @param version the value of field 'version'.
      */
     public void setVersion(java.lang.String version)
     {
         this._version = version;
-    } //-- void setVersion(java.lang.String) 
+    }
+
+    //-- void setVersion(java.lang.String) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 4ac40d5..2c2abff 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,872 +7,894 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class JalviewModelSequence.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _JSeqList
-     */
-    private java.util.Vector _JSeqList;
-
-    /**
-     * Field _JGroupList
-     */
-    private java.util.Vector _JGroupList;
-
-    /**
-     * Field _viewportList
-     */
-    private java.util.Vector _viewportList;
-
-    /**
-     * Field _userColoursList
-     */
-    private java.util.Vector _userColoursList;
-
-    /**
-     * Field _treeList
-     */
-    private java.util.Vector _treeList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequence() {
-        super();
-        _JSeqList = new Vector();
-        _JGroupList = new Vector();
-        _viewportList = new Vector();
-        _userColoursList = new Vector();
-        _treeList = new Vector();
-    } //-- jalview.binding.JalviewModelSequence()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addJGroup
-     * 
-     * 
-     * 
-     * @param vJGroup
-     */
-    public void addJGroup(jalview.binding.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JGroupList.addElement(vJGroup);
-    } //-- void addJGroup(jalview.binding.JGroup) 
-
-    /**
-     * Method addJGroup
-     * 
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     */
-    public void addJGroup(int index, jalview.binding.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JGroupList.insertElementAt(vJGroup, index);
-    } //-- void addJGroup(int, jalview.binding.JGroup) 
-
-    /**
-     * Method addJSeq
-     * 
-     * 
-     * 
-     * @param vJSeq
-     */
-    public void addJSeq(jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JSeqList.addElement(vJSeq);
-    } //-- void addJSeq(jalview.binding.JSeq) 
-
-    /**
-     * Method addJSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     */
-    public void addJSeq(int index, jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JSeqList.insertElementAt(vJSeq, index);
-    } //-- void addJSeq(int, jalview.binding.JSeq) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param vTree
-     */
-    public void addTree(jalview.binding.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.addElement(vTree);
-    } //-- void addTree(jalview.binding.Tree) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void addTree(int index, jalview.binding.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.insertElementAt(vTree, index);
-    } //-- void addTree(int, jalview.binding.Tree) 
-
-    /**
-     * Method addUserColours
-     * 
-     * 
-     * 
-     * @param vUserColours
-     */
-    public void addUserColours(jalview.binding.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _userColoursList.addElement(vUserColours);
-    } //-- void addUserColours(jalview.binding.UserColours) 
-
-    /**
-     * Method addUserColours
-     * 
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     */
-    public void addUserColours(int index, jalview.binding.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _userColoursList.insertElementAt(vUserColours, index);
-    } //-- void addUserColours(int, jalview.binding.UserColours) 
-
-    /**
-     * Method addViewport
-     * 
-     * 
-     * 
-     * @param vViewport
-     */
-    public void addViewport(jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _viewportList.addElement(vViewport);
-    } //-- void addViewport(jalview.binding.Viewport) 
-
-    /**
-     * Method addViewport
-     * 
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     */
-    public void addViewport(int index, jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _viewportList.insertElementAt(vViewport, index);
-    } //-- void addViewport(int, jalview.binding.Viewport) 
-
-    /**
-     * Method enumerateJGroup
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateJGroup()
-    {
-        return _JGroupList.elements();
-    } //-- java.util.Enumeration enumerateJGroup() 
-
-    /**
-     * Method enumerateJSeq
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateJSeq()
-    {
-        return _JSeqList.elements();
-    } //-- java.util.Enumeration enumerateJSeq() 
-
-    /**
-     * Method enumerateTree
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateTree()
-    {
-        return _treeList.elements();
-    } //-- java.util.Enumeration enumerateTree() 
-
-    /**
-     * Method enumerateUserColours
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateUserColours()
-    {
-        return _userColoursList.elements();
-    } //-- java.util.Enumeration enumerateUserColours() 
-
-    /**
-     * Method enumerateViewport
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateViewport()
-    {
-        return _viewportList.elements();
-    } //-- java.util.Enumeration enumerateViewport() 
-
-    /**
-     * Method getJGroup
-     * 
-     * 
-     * 
-     * @param index
-     * @return JGroup
-     */
-    public jalview.binding.JGroup getJGroup(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JGroupList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.JGroup) _JGroupList.elementAt(index);
-    } //-- jalview.binding.JGroup getJGroup(int) 
-
-    /**
-     * Method getJGroup
-     * 
-     * 
-     * 
-     * @return JGroup
-     */
-    public jalview.binding.JGroup[] getJGroup()
-    {
-        int size = _JGroupList.size();
-        jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.JGroup[] getJGroup() 
-
-    /**
-     * Method getJGroupCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getJGroupCount()
-    {
-        return _JGroupList.size();
-    } //-- int getJGroupCount() 
-
-    /**
-     * Method getJSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @return JSeq
-     */
-    public jalview.binding.JSeq getJSeq(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JSeqList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.JSeq) _JSeqList.elementAt(index);
-    } //-- jalview.binding.JSeq getJSeq(int) 
-
-    /**
-     * Method getJSeq
-     * 
-     * 
-     * 
-     * @return JSeq
-     */
-    public jalview.binding.JSeq[] getJSeq()
-    {
-        int size = _JSeqList.size();
-        jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.JSeq[] getJSeq() 
-
-    /**
-     * Method getJSeqCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getJSeqCount()
-    {
-        return _JSeqList.size();
-    } //-- int getJSeqCount() 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return Tree
-     */
-    public jalview.binding.Tree getTree(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.Tree) _treeList.elementAt(index);
-    } //-- jalview.binding.Tree getTree(int) 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @return Tree
-     */
-    public jalview.binding.Tree[] getTree()
-    {
-        int size = _treeList.size();
-        jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.Tree[] getTree() 
-
-    /**
-     * Method getTreeCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getTreeCount()
-    {
-        return _treeList.size();
-    } //-- int getTreeCount() 
-
-    /**
-     * Method getUserColours
-     * 
-     * 
-     * 
-     * @param index
-     * @return UserColours
-     */
-    public jalview.binding.UserColours getUserColours(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _userColoursList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.UserColours) _userColoursList.elementAt(index);
-    } //-- jalview.binding.UserColours getUserColours(int) 
-
-    /**
-     * Method getUserColours
-     * 
-     * 
-     * 
-     * @return UserColours
-     */
-    public jalview.binding.UserColours[] getUserColours()
-    {
-        int size = _userColoursList.size();
-        jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.UserColours[] getUserColours() 
-
-    /**
-     * Method getUserColoursCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getUserColoursCount()
-    {
-        return _userColoursList.size();
-    } //-- int getUserColoursCount() 
-
-    /**
-     * Method getViewport
-     * 
-     * 
-     * 
-     * @param index
-     * @return Viewport
-     */
-    public jalview.binding.Viewport getViewport(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _viewportList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.Viewport) _viewportList.elementAt(index);
-    } //-- jalview.binding.Viewport getViewport(int) 
-
-    /**
-     * Method getViewport
-     * 
-     * 
-     * 
-     * @return Viewport
-     */
-    public jalview.binding.Viewport[] getViewport()
-    {
-        int size = _viewportList.size();
-        jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.Viewport[] getViewport() 
-
-    /**
-     * Method getViewportCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getViewportCount()
-    {
-        return _viewportList.size();
-    } //-- int getViewportCount() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllJGroup
-     * 
-     */
-    public void removeAllJGroup()
-    {
-        _JGroupList.removeAllElements();
-    } //-- void removeAllJGroup() 
-
-    /**
-     * Method removeAllJSeq
-     * 
-     */
-    public void removeAllJSeq()
-    {
-        _JSeqList.removeAllElements();
-    } //-- void removeAllJSeq() 
-
-    /**
-     * Method removeAllTree
-     * 
-     */
-    public void removeAllTree()
-    {
-        _treeList.removeAllElements();
-    } //-- void removeAllTree() 
-
-    /**
-     * Method removeAllUserColours
-     * 
-     */
-    public void removeAllUserColours()
-    {
-        _userColoursList.removeAllElements();
-    } //-- void removeAllUserColours() 
-
-    /**
-     * Method removeAllViewport
-     * 
-     */
-    public void removeAllViewport()
-    {
-        _viewportList.removeAllElements();
-    } //-- void removeAllViewport() 
-
-    /**
-     * Method removeJGroup
-     * 
-     * 
-     * 
-     * @param index
-     * @return JGroup
-     */
-    public jalview.binding.JGroup removeJGroup(int index)
-    {
-        java.lang.Object obj = _JGroupList.elementAt(index);
-        _JGroupList.removeElementAt(index);
-        return (jalview.binding.JGroup) obj;
-    } //-- jalview.binding.JGroup removeJGroup(int) 
-
-    /**
-     * Method removeJSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @return JSeq
-     */
-    public jalview.binding.JSeq removeJSeq(int index)
-    {
-        java.lang.Object obj = _JSeqList.elementAt(index);
-        _JSeqList.removeElementAt(index);
-        return (jalview.binding.JSeq) obj;
-    } //-- jalview.binding.JSeq removeJSeq(int) 
-
-    /**
-     * Method removeTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return Tree
-     */
-    public jalview.binding.Tree removeTree(int index)
-    {
-        java.lang.Object obj = _treeList.elementAt(index);
-        _treeList.removeElementAt(index);
-        return (jalview.binding.Tree) obj;
-    } //-- jalview.binding.Tree removeTree(int) 
-
-    /**
-     * Method removeUserColours
-     * 
-     * 
-     * 
-     * @param index
-     * @return UserColours
-     */
-    public jalview.binding.UserColours removeUserColours(int index)
-    {
-        java.lang.Object obj = _userColoursList.elementAt(index);
-        _userColoursList.removeElementAt(index);
-        return (jalview.binding.UserColours) obj;
-    } //-- jalview.binding.UserColours removeUserColours(int) 
-
-    /**
-     * Method removeViewport
-     * 
-     * 
-     * 
-     * @param index
-     * @return Viewport
-     */
-    public jalview.binding.Viewport removeViewport(int index)
-    {
-        java.lang.Object obj = _viewportList.elementAt(index);
-        _viewportList.removeElementAt(index);
-        return (jalview.binding.Viewport) obj;
-    } //-- jalview.binding.Viewport removeViewport(int) 
-
-    /**
-     * Method setJGroup
-     * 
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     */
-    public void setJGroup(int index, jalview.binding.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JGroupList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _JGroupList.setElementAt(vJGroup, index);
-    } //-- void setJGroup(int, jalview.binding.JGroup) 
-
-    /**
-     * Method setJGroup
-     * 
-     * 
-     * 
-     * @param JGroupArray
-     */
-    public void setJGroup(jalview.binding.JGroup[] JGroupArray)
-    {
-        //-- copy array
-        _JGroupList.removeAllElements();
-        for (int i = 0; i < JGroupArray.length; i++) {
-            _JGroupList.addElement(JGroupArray[i]);
-        }
-    } //-- void setJGroup(jalview.binding.JGroup) 
-
-    /**
-     * Method setJSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     */
-    public void setJSeq(int index, jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JSeqList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _JSeqList.setElementAt(vJSeq, index);
-    } //-- void setJSeq(int, jalview.binding.JSeq) 
-
-    /**
-     * Method setJSeq
-     * 
-     * 
-     * 
-     * @param JSeqArray
-     */
-    public void setJSeq(jalview.binding.JSeq[] JSeqArray)
-    {
-        //-- copy array
-        _JSeqList.removeAllElements();
-        for (int i = 0; i < JSeqArray.length; i++) {
-            _JSeqList.addElement(JSeqArray[i]);
-        }
-    } //-- void setJSeq(jalview.binding.JSeq) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void setTree(int index, jalview.binding.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _treeList.setElementAt(vTree, index);
-    } //-- void setTree(int, jalview.binding.Tree) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param treeArray
-     */
-    public void setTree(jalview.binding.Tree[] treeArray)
-    {
-        //-- copy array
-        _treeList.removeAllElements();
-        for (int i = 0; i < treeArray.length; i++) {
-            _treeList.addElement(treeArray[i]);
-        }
-    } //-- void setTree(jalview.binding.Tree) 
-
-    /**
-     * Method setUserColours
-     * 
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     */
-    public void setUserColours(int index, jalview.binding.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _userColoursList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _userColoursList.setElementAt(vUserColours, index);
-    } //-- void setUserColours(int, jalview.binding.UserColours) 
-
-    /**
-     * Method setUserColours
-     * 
-     * 
-     * 
-     * @param userColoursArray
-     */
-    public void setUserColours(jalview.binding.UserColours[] userColoursArray)
-    {
-        //-- copy array
-        _userColoursList.removeAllElements();
-        for (int i = 0; i < userColoursArray.length; i++) {
-            _userColoursList.addElement(userColoursArray[i]);
-        }
-    } //-- void setUserColours(jalview.binding.UserColours) 
-
-    /**
-     * Method setViewport
-     * 
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     */
-    public void setViewport(int index, jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _viewportList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _viewportList.setElementAt(vViewport, index);
-    } //-- void setViewport(int, jalview.binding.Viewport) 
-
-    /**
-     * Method setViewport
-     * 
-     * 
-     * 
-     * @param viewportArray
-     */
-    public void setViewport(jalview.binding.Viewport[] viewportArray)
-    {
-        //-- copy array
-        _viewportList.removeAllElements();
-        for (int i = 0; i < viewportArray.length; i++) {
-            _viewportList.addElement(viewportArray[i]);
-        }
-    } //-- void setViewport(jalview.binding.Viewport) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+public class JalviewModelSequence
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _JSeqList
+   */
+  private java.util.Vector _JSeqList;
+
+  /**
+   * Field _JGroupList
+   */
+  private java.util.Vector _JGroupList;
+
+  /**
+   * Field _viewportList
+   */
+  private java.util.Vector _viewportList;
+
+  /**
+   * Field _userColoursList
+   */
+  private java.util.Vector _userColoursList;
+
+  /**
+   * Field _treeList
+   */
+  private java.util.Vector _treeList;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public JalviewModelSequence()
+  {
+    super();
+    _JSeqList = new Vector();
+    _JGroupList = new Vector();
+    _viewportList = new Vector();
+    _userColoursList = new Vector();
+    _treeList = new Vector();
+  } //-- jalview.binding.JalviewModelSequence()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addJGroup
+   *
+   *
+   *
+   * @param vJGroup
+   */
+  public void addJGroup(jalview.binding.JGroup vJGroup)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _JGroupList.addElement(vJGroup);
+  } //-- void addJGroup(jalview.binding.JGroup)
+
+  /**
+   * Method addJGroup
+   *
+   *
+   *
+   * @param index
+   * @param vJGroup
+   */
+  public void addJGroup(int index, jalview.binding.JGroup vJGroup)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _JGroupList.insertElementAt(vJGroup, index);
+  } //-- void addJGroup(int, jalview.binding.JGroup)
+
+  /**
+   * Method addJSeq
+   *
+   *
+   *
+   * @param vJSeq
+   */
+  public void addJSeq(jalview.binding.JSeq vJSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _JSeqList.addElement(vJSeq);
+  } //-- void addJSeq(jalview.binding.JSeq)
+
+  /**
+   * Method addJSeq
+   *
+   *
+   *
+   * @param index
+   * @param vJSeq
+   */
+  public void addJSeq(int index, jalview.binding.JSeq vJSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _JSeqList.insertElementAt(vJSeq, index);
+  } //-- void addJSeq(int, jalview.binding.JSeq)
+
+  /**
+   * Method addTree
+   *
+   *
+   *
+   * @param vTree
+   */
+  public void addTree(jalview.binding.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _treeList.addElement(vTree);
+  } //-- void addTree(jalview.binding.Tree)
+
+  /**
+   * Method addTree
+   *
+   *
+   *
+   * @param index
+   * @param vTree
+   */
+  public void addTree(int index, jalview.binding.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _treeList.insertElementAt(vTree, index);
+  } //-- void addTree(int, jalview.binding.Tree)
+
+  /**
+   * Method addUserColours
+   *
+   *
+   *
+   * @param vUserColours
+   */
+  public void addUserColours(jalview.binding.UserColours vUserColours)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _userColoursList.addElement(vUserColours);
+  } //-- void addUserColours(jalview.binding.UserColours)
+
+  /**
+   * Method addUserColours
+   *
+   *
+   *
+   * @param index
+   * @param vUserColours
+   */
+  public void addUserColours(int index,
+                             jalview.binding.UserColours vUserColours)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _userColoursList.insertElementAt(vUserColours, index);
+  } //-- void addUserColours(int, jalview.binding.UserColours)
+
+  /**
+   * Method addViewport
+   *
+   *
+   *
+   * @param vViewport
+   */
+  public void addViewport(jalview.binding.Viewport vViewport)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _viewportList.addElement(vViewport);
+  } //-- void addViewport(jalview.binding.Viewport)
+
+  /**
+   * Method addViewport
+   *
+   *
+   *
+   * @param index
+   * @param vViewport
+   */
+  public void addViewport(int index, jalview.binding.Viewport vViewport)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _viewportList.insertElementAt(vViewport, index);
+  } //-- void addViewport(int, jalview.binding.Viewport)
+
+  /**
+   * Method enumerateJGroup
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateJGroup()
+  {
+    return _JGroupList.elements();
+  } //-- java.util.Enumeration enumerateJGroup()
+
+  /**
+   * Method enumerateJSeq
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateJSeq()
+  {
+    return _JSeqList.elements();
+  } //-- java.util.Enumeration enumerateJSeq()
+
+  /**
+   * Method enumerateTree
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return _treeList.elements();
+  } //-- java.util.Enumeration enumerateTree()
+
+  /**
+   * Method enumerateUserColours
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateUserColours()
+  {
+    return _userColoursList.elements();
+  } //-- java.util.Enumeration enumerateUserColours()
+
+  /**
+   * Method enumerateViewport
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateViewport()
+  {
+    return _viewportList.elements();
+  } //-- java.util.Enumeration enumerateViewport()
+
+  /**
+   * Method getJGroup
+   *
+   *
+   *
+   * @param index
+   * @return JGroup
+   */
+  public jalview.binding.JGroup getJGroup(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _JGroupList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.JGroup) _JGroupList.elementAt(index);
+  } //-- jalview.binding.JGroup getJGroup(int)
+
+  /**
+   * Method getJGroup
+   *
+   *
+   *
+   * @return JGroup
+   */
+  public jalview.binding.JGroup[] getJGroup()
+  {
+    int size = _JGroupList.size();
+    jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.binding.JGroup[] getJGroup()
+
+  /**
+   * Method getJGroupCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getJGroupCount()
+  {
+    return _JGroupList.size();
+  } //-- int getJGroupCount()
+
+  /**
+   * Method getJSeq
+   *
+   *
+   *
+   * @param index
+   * @return JSeq
+   */
+  public jalview.binding.JSeq getJSeq(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _JSeqList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.JSeq) _JSeqList.elementAt(index);
+  } //-- jalview.binding.JSeq getJSeq(int)
+
+  /**
+   * Method getJSeq
+   *
+   *
+   *
+   * @return JSeq
+   */
+  public jalview.binding.JSeq[] getJSeq()
+  {
+    int size = _JSeqList.size();
+    jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.binding.JSeq[] getJSeq()
+
+  /**
+   * Method getJSeqCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getJSeqCount()
+  {
+    return _JSeqList.size();
+  } //-- int getJSeqCount()
+
+  /**
+   * Method getTree
+   *
+   *
+   *
+   * @param index
+   * @return Tree
+   */
+  public jalview.binding.Tree getTree(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _treeList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.Tree) _treeList.elementAt(index);
+  } //-- jalview.binding.Tree getTree(int)
+
+  /**
+   * Method getTree
+   *
+   *
+   *
+   * @return Tree
+   */
+  public jalview.binding.Tree[] getTree()
+  {
+    int size = _treeList.size();
+    jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.binding.Tree[] getTree()
+
+  /**
+   * Method getTreeCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getTreeCount()
+  {
+    return _treeList.size();
+  } //-- int getTreeCount()
+
+  /**
+   * Method getUserColours
+   *
+   *
+   *
+   * @param index
+   * @return UserColours
+   */
+  public jalview.binding.UserColours getUserColours(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _userColoursList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.UserColours) _userColoursList.elementAt(index);
+  } //-- jalview.binding.UserColours getUserColours(int)
+
+  /**
+   * Method getUserColours
+   *
+   *
+   *
+   * @return UserColours
+   */
+  public jalview.binding.UserColours[] getUserColours()
+  {
+    int size = _userColoursList.size();
+    jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(
+          index);
+    }
+    return mArray;
+  } //-- jalview.binding.UserColours[] getUserColours()
+
+  /**
+   * Method getUserColoursCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getUserColoursCount()
+  {
+    return _userColoursList.size();
+  } //-- int getUserColoursCount()
+
+  /**
+   * Method getViewport
+   *
+   *
+   *
+   * @param index
+   * @return Viewport
+   */
+  public jalview.binding.Viewport getViewport(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _viewportList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.Viewport) _viewportList.elementAt(index);
+  } //-- jalview.binding.Viewport getViewport(int)
+
+  /**
+   * Method getViewport
+   *
+   *
+   *
+   * @return Viewport
+   */
+  public jalview.binding.Viewport[] getViewport()
+  {
+    int size = _viewportList.size();
+    jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.binding.Viewport[] getViewport()
+
+  /**
+   * Method getViewportCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getViewportCount()
+  {
+    return _viewportList.size();
+  } //-- int getViewportCount()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllJGroup
+   *
+   */
+  public void removeAllJGroup()
+  {
+    _JGroupList.removeAllElements();
+  } //-- void removeAllJGroup()
+
+  /**
+   * Method removeAllJSeq
+   *
+   */
+  public void removeAllJSeq()
+  {
+    _JSeqList.removeAllElements();
+  } //-- void removeAllJSeq()
+
+  /**
+   * Method removeAllTree
+   *
+   */
+  public void removeAllTree()
+  {
+    _treeList.removeAllElements();
+  } //-- void removeAllTree()
+
+  /**
+   * Method removeAllUserColours
+   *
+   */
+  public void removeAllUserColours()
+  {
+    _userColoursList.removeAllElements();
+  } //-- void removeAllUserColours()
+
+  /**
+   * Method removeAllViewport
+   *
+   */
+  public void removeAllViewport()
+  {
+    _viewportList.removeAllElements();
+  } //-- void removeAllViewport()
+
+  /**
+   * Method removeJGroup
+   *
+   *
+   *
+   * @param index
+   * @return JGroup
+   */
+  public jalview.binding.JGroup removeJGroup(int index)
+  {
+    java.lang.Object obj = _JGroupList.elementAt(index);
+    _JGroupList.removeElementAt(index);
+    return (jalview.binding.JGroup) obj;
+  } //-- jalview.binding.JGroup removeJGroup(int)
+
+  /**
+   * Method removeJSeq
+   *
+   *
+   *
+   * @param index
+   * @return JSeq
+   */
+  public jalview.binding.JSeq removeJSeq(int index)
+  {
+    java.lang.Object obj = _JSeqList.elementAt(index);
+    _JSeqList.removeElementAt(index);
+    return (jalview.binding.JSeq) obj;
+  } //-- jalview.binding.JSeq removeJSeq(int)
+
+  /**
+   * Method removeTree
+   *
+   *
+   *
+   * @param index
+   * @return Tree
+   */
+  public jalview.binding.Tree removeTree(int index)
+  {
+    java.lang.Object obj = _treeList.elementAt(index);
+    _treeList.removeElementAt(index);
+    return (jalview.binding.Tree) obj;
+  } //-- jalview.binding.Tree removeTree(int)
+
+  /**
+   * Method removeUserColours
+   *
+   *
+   *
+   * @param index
+   * @return UserColours
+   */
+  public jalview.binding.UserColours removeUserColours(int index)
+  {
+    java.lang.Object obj = _userColoursList.elementAt(index);
+    _userColoursList.removeElementAt(index);
+    return (jalview.binding.UserColours) obj;
+  } //-- jalview.binding.UserColours removeUserColours(int)
+
+  /**
+   * Method removeViewport
+   *
+   *
+   *
+   * @param index
+   * @return Viewport
+   */
+  public jalview.binding.Viewport removeViewport(int index)
+  {
+    java.lang.Object obj = _viewportList.elementAt(index);
+    _viewportList.removeElementAt(index);
+    return (jalview.binding.Viewport) obj;
+  } //-- jalview.binding.Viewport removeViewport(int)
+
+  /**
+   * Method setJGroup
+   *
+   *
+   *
+   * @param index
+   * @param vJGroup
+   */
+  public void setJGroup(int index, jalview.binding.JGroup vJGroup)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _JGroupList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _JGroupList.setElementAt(vJGroup, index);
+  } //-- void setJGroup(int, jalview.binding.JGroup)
+
+  /**
+   * Method setJGroup
+   *
+   *
+   *
+   * @param JGroupArray
+   */
+  public void setJGroup(jalview.binding.JGroup[] JGroupArray)
+  {
+    //-- copy array
+    _JGroupList.removeAllElements();
+    for (int i = 0; i < JGroupArray.length; i++)
+    {
+      _JGroupList.addElement(JGroupArray[i]);
+    }
+  } //-- void setJGroup(jalview.binding.JGroup)
+
+  /**
+   * Method setJSeq
+   *
+   *
+   *
+   * @param index
+   * @param vJSeq
+   */
+  public void setJSeq(int index, jalview.binding.JSeq vJSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _JSeqList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _JSeqList.setElementAt(vJSeq, index);
+  } //-- void setJSeq(int, jalview.binding.JSeq)
+
+  /**
+   * Method setJSeq
+   *
+   *
+   *
+   * @param JSeqArray
+   */
+  public void setJSeq(jalview.binding.JSeq[] JSeqArray)
+  {
+    //-- copy array
+    _JSeqList.removeAllElements();
+    for (int i = 0; i < JSeqArray.length; i++)
+    {
+      _JSeqList.addElement(JSeqArray[i]);
+    }
+  } //-- void setJSeq(jalview.binding.JSeq)
+
+  /**
+   * Method setTree
+   *
+   *
+   *
+   * @param index
+   * @param vTree
+   */
+  public void setTree(int index, jalview.binding.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _treeList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _treeList.setElementAt(vTree, index);
+  } //-- void setTree(int, jalview.binding.Tree)
+
+  /**
+   * Method setTree
+   *
+   *
+   *
+   * @param treeArray
+   */
+  public void setTree(jalview.binding.Tree[] treeArray)
+  {
+    //-- copy array
+    _treeList.removeAllElements();
+    for (int i = 0; i < treeArray.length; i++)
+    {
+      _treeList.addElement(treeArray[i]);
+    }
+  } //-- void setTree(jalview.binding.Tree)
+
+  /**
+   * Method setUserColours
+   *
+   *
+   *
+   * @param index
+   * @param vUserColours
+   */
+  public void setUserColours(int index,
+                             jalview.binding.UserColours vUserColours)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _userColoursList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _userColoursList.setElementAt(vUserColours, index);
+  } //-- void setUserColours(int, jalview.binding.UserColours)
+
+  /**
+   * Method setUserColours
+   *
+   *
+   *
+   * @param userColoursArray
+   */
+  public void setUserColours(jalview.binding.UserColours[] userColoursArray)
+  {
+    //-- copy array
+    _userColoursList.removeAllElements();
+    for (int i = 0; i < userColoursArray.length; i++)
+    {
+      _userColoursList.addElement(userColoursArray[i]);
+    }
+  } //-- void setUserColours(jalview.binding.UserColours)
+
+  /**
+   * Method setViewport
+   *
+   *
+   *
+   * @param index
+   * @param vViewport
+   */
+  public void setViewport(int index, jalview.binding.Viewport vViewport)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _viewportList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _viewportList.setElementAt(vViewport, index);
+  } //-- void setViewport(int, jalview.binding.Viewport)
+
+  /**
+   * Method setViewport
+   *
+   *
+   *
+   * @param viewportArray
+   */
+  public void setViewport(jalview.binding.Viewport[] viewportArray)
+  {
+    //-- copy array
+    _viewportList.removeAllElements();
+    for (int i = 0; i < viewportArray.length; i++)
+    {
+      _viewportList.addElement(viewportArray[i]);
+    }
+  } //-- void setViewport(jalview.binding.Viewport)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(
+        jalview.binding.JalviewModelSequence.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/JalviewModelSequence2.java b/src/jalview/binding/JalviewModelSequence2.java
index 36e5579..2cfd72c 100755
--- a/src/jalview/binding/JalviewModelSequence2.java
+++ b/src/jalview/binding/JalviewModelSequence2.java
@@ -1,38 +1,39 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
 
+import org.xml.sax.ContentHandler;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
 import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+
 import java.util.Enumeration;
 import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+
 
 /**
  * Class JalviewModelSequence2.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence2 implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class JalviewModelSequence2 implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -40,235 +41,279 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      */
     private java.util.Vector _items;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public JalviewModelSequence2() {
+    //- Constructors -/
+    //----------------/
+    public JalviewModelSequence2()
+    {
         super();
         _items = new Vector();
-    } //-- jalview.binding.JalviewModelSequence2()
-
+    }
 
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.JalviewModelSequence2()
     //-----------/
 
     /**
-     * Method addJalviewModelSequence2Item
-     * 
-     * 
-     * 
-     * @param vJalviewModelSequence2Item
+     * DOCUMENT ME!
+     *
+     * @param vJalviewModelSequence2Item DOCUMENT ME!
+     *
+     * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!
      */
-    public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
+    public void addJalviewModelSequence2Item(
+        jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
         throws java.lang.IndexOutOfBoundsException
     {
         _items.addElement(vJalviewModelSequence2Item);
-    } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) 
+    }
+
+    //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) 
 
     /**
      * Method addJalviewModelSequence2Item
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vJalviewModelSequence2Item
      */
-    public void addJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
+    public void addJalviewModelSequence2Item(int index,
+        jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
         throws java.lang.IndexOutOfBoundsException
     {
         _items.insertElementAt(vJalviewModelSequence2Item, index);
-    } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) 
+    }
+
+    //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) 
 
     /**
      * Method enumerateJalviewModelSequence2Item
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Enumeration
      */
     public java.util.Enumeration enumerateJalviewModelSequence2Item()
     {
         return _items.elements();
-    } //-- java.util.Enumeration enumerateJalviewModelSequence2Item() 
+    }
+
+    //-- java.util.Enumeration enumerateJalviewModelSequence2Item() 
 
     /**
      * Method getJalviewModelSequence2Item
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return JalviewModelSequence2Item
      */
-    public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int index)
-        throws java.lang.IndexOutOfBoundsException
+    public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(
+        int index) throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _items.size())) {
+        if ((index < 0) || (index > _items.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
-        
+
         return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);
-    } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) 
+    }
+
+    //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) 
 
     /**
      * Method getJalviewModelSequence2Item
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return JalviewModelSequence2Item
      */
     public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()
     {
         int size = _items.size();
         jalview.binding.JalviewModelSequence2Item[] mArray = new jalview.binding.JalviewModelSequence2Item[size];
-        for (int index = 0; index < size; index++) {
+
+        for (int index = 0; index < size; index++)
+        {
             mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() 
+    }
+
+    //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() 
 
     /**
      * Method getJalviewModelSequence2ItemCount
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return int
      */
     public int getJalviewModelSequence2ItemCount()
     {
         return _items.size();
-    } //-- int getJalviewModelSequence2ItemCount() 
+    }
+
+    //-- int getJalviewModelSequence2ItemCount() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Method removeAllJalviewModelSequence2Item
-     * 
+     *
      */
     public void removeAllJalviewModelSequence2Item()
     {
         _items.removeAllElements();
-    } //-- void removeAllJalviewModelSequence2Item() 
+    }
+
+    //-- void removeAllJalviewModelSequence2Item() 
 
     /**
      * Method removeJalviewModelSequence2Item
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return JalviewModelSequence2Item
      */
-    public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int index)
+    public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(
+        int index)
     {
         java.lang.Object obj = _items.elementAt(index);
         _items.removeElementAt(index);
+
         return (jalview.binding.JalviewModelSequence2Item) obj;
-    } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) 
+    }
+
+    //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) 
 
     /**
      * Method setJalviewModelSequence2Item
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vJalviewModelSequence2Item
      */
-    public void setJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
+    public void setJalviewModelSequence2Item(int index,
+        jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _items.size())) {
+        if ((index < 0) || (index > _items.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
+
         _items.setElementAt(vJalviewModelSequence2Item, index);
-    } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) 
+    }
+
+    //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) 
 
     /**
      * Method setJalviewModelSequence2Item
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param jalviewModelSequence2ItemArray
      */
-    public void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray)
+    public void setJalviewModelSequence2Item(
+        jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray)
     {
         //-- copy array
         _items.removeAllElements();
-        for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) {
+
+        for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++)
+        {
             _items.addElement(jalviewModelSequence2ItemArray[i]);
         }
-    } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) 
+    }
+
+    //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/JalviewModelSequence2Item.java b/src/jalview/binding/JalviewModelSequence2Item.java
index 8678b09..6e54565 100755
--- a/src/jalview/binding/JalviewModelSequence2Item.java
+++ b/src/jalview/binding/JalviewModelSequence2Item.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,191 +7,200 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.Serializable;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
+import java.util.*;
 
 /**
  * Class JalviewModelSequence2Item.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence2Item implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _userColourSchemeList
-     */
-    private java.util.Vector _userColourSchemeList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequence2Item() {
-        super();
-        _userColourSchemeList = new Vector();
-    } //-- jalview.binding.JalviewModelSequence2Item()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addUserColourScheme
-     * 
-     * 
-     * 
-     * @param vUserColourScheme
-     */
-    public void addUserColourScheme(jalview.binding.UserColourScheme vUserColourScheme)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _userColourSchemeList.addElement(vUserColourScheme);
-    } //-- void addUserColourScheme(jalview.binding.UserColourScheme) 
-
-    /**
-     * Method addUserColourScheme
-     * 
-     * 
-     * 
-     * @param index
-     * @param vUserColourScheme
-     */
-    public void addUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _userColourSchemeList.insertElementAt(vUserColourScheme, index);
-    } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme) 
-
-    /**
-     * Method enumerateUserColourScheme
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateUserColourScheme()
-    {
-        return _userColourSchemeList.elements();
-    } //-- java.util.Enumeration enumerateUserColourScheme() 
-
-    /**
-     * Method getUserColourScheme
-     * 
-     * 
-     * 
-     * @param index
-     * @return UserColourScheme
-     */
-    public jalview.binding.UserColourScheme getUserColourScheme(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _userColourSchemeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);
-    } //-- jalview.binding.UserColourScheme getUserColourScheme(int) 
-
-    /**
-     * Method getUserColourScheme
-     * 
-     * 
-     * 
-     * @return UserColourScheme
-     */
-    public jalview.binding.UserColourScheme[] getUserColourScheme()
-    {
-        int size = _userColourSchemeList.size();
-        jalview.binding.UserColourScheme[] mArray = new jalview.binding.UserColourScheme[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.UserColourScheme[] getUserColourScheme() 
-
-    /**
-     * Method getUserColourSchemeCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getUserColourSchemeCount()
-    {
-        return _userColourSchemeList.size();
-    } //-- int getUserColourSchemeCount() 
-
-    /**
-     * Method removeAllUserColourScheme
-     * 
-     */
-    public void removeAllUserColourScheme()
+public class JalviewModelSequence2Item
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _userColourSchemeList
+   */
+  private java.util.Vector _userColourSchemeList;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public JalviewModelSequence2Item()
+  {
+    super();
+    _userColourSchemeList = new Vector();
+  } //-- jalview.binding.JalviewModelSequence2Item()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addUserColourScheme
+   *
+   *
+   *
+   * @param vUserColourScheme
+   */
+  public void addUserColourScheme(jalview.binding.UserColourScheme
+                                  vUserColourScheme)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _userColourSchemeList.addElement(vUserColourScheme);
+  } //-- void addUserColourScheme(jalview.binding.UserColourScheme)
+
+  /**
+   * Method addUserColourScheme
+   *
+   *
+   *
+   * @param index
+   * @param vUserColourScheme
+   */
+  public void addUserColourScheme(int index,
+                                  jalview.binding.UserColourScheme
+                                  vUserColourScheme)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _userColourSchemeList.insertElementAt(vUserColourScheme, index);
+  } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme)
+
+  /**
+   * Method enumerateUserColourScheme
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateUserColourScheme()
+  {
+    return _userColourSchemeList.elements();
+  } //-- java.util.Enumeration enumerateUserColourScheme()
+
+  /**
+   * Method getUserColourScheme
+   *
+   *
+   *
+   * @param index
+   * @return UserColourScheme
+   */
+  public jalview.binding.UserColourScheme getUserColourScheme(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _userColourSchemeList.size()))
     {
-        _userColourSchemeList.removeAllElements();
-    } //-- void removeAllUserColourScheme() 
-
-    /**
-     * Method removeUserColourScheme
-     * 
-     * 
-     * 
-     * @param index
-     * @return UserColourScheme
-     */
-    public jalview.binding.UserColourScheme removeUserColourScheme(int index)
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(
+        index);
+  } //-- jalview.binding.UserColourScheme getUserColourScheme(int)
+
+  /**
+   * Method getUserColourScheme
+   *
+   *
+   *
+   * @return UserColourScheme
+   */
+  public jalview.binding.UserColourScheme[] getUserColourScheme()
+  {
+    int size = _userColourSchemeList.size();
+    jalview.binding.UserColourScheme[] mArray = new jalview.binding.
+        UserColourScheme[size];
+    for (int index = 0; index < size; index++)
     {
-        java.lang.Object obj = _userColourSchemeList.elementAt(index);
-        _userColourSchemeList.removeElementAt(index);
-        return (jalview.binding.UserColourScheme) obj;
-    } //-- jalview.binding.UserColourScheme removeUserColourScheme(int) 
-
-    /**
-     * Method setUserColourScheme
-     * 
-     * 
-     * 
-     * @param index
-     * @param vUserColourScheme
-     */
-    public void setUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)
-        throws java.lang.IndexOutOfBoundsException
+      mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.binding.UserColourScheme[] getUserColourScheme()
+
+  /**
+   * Method getUserColourSchemeCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getUserColourSchemeCount()
+  {
+    return _userColourSchemeList.size();
+  } //-- int getUserColourSchemeCount()
+
+  /**
+   * Method removeAllUserColourScheme
+   *
+   */
+  public void removeAllUserColourScheme()
+  {
+    _userColourSchemeList.removeAllElements();
+  } //-- void removeAllUserColourScheme()
+
+  /**
+   * Method removeUserColourScheme
+   *
+   *
+   *
+   * @param index
+   * @return UserColourScheme
+   */
+  public jalview.binding.UserColourScheme removeUserColourScheme(int index)
+  {
+    java.lang.Object obj = _userColourSchemeList.elementAt(index);
+    _userColourSchemeList.removeElementAt(index);
+    return (jalview.binding.UserColourScheme) obj;
+  } //-- jalview.binding.UserColourScheme removeUserColourScheme(int)
+
+  /**
+   * Method setUserColourScheme
+   *
+   *
+   *
+   * @param index
+   * @param vUserColourScheme
+   */
+  public void setUserColourScheme(int index,
+                                  jalview.binding.UserColourScheme
+                                  vUserColourScheme)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _userColourSchemeList.size()))
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _userColourSchemeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _userColourSchemeList.setElementAt(vUserColourScheme, index);
-    } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme) 
-
-    /**
-     * Method setUserColourScheme
-     * 
-     * 
-     * 
-     * @param userColourSchemeArray
-     */
-    public void setUserColourScheme(jalview.binding.UserColourScheme[] userColourSchemeArray)
+      throw new IndexOutOfBoundsException();
+    }
+    _userColourSchemeList.setElementAt(vUserColourScheme, index);
+  } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme)
+
+  /**
+   * Method setUserColourScheme
+   *
+   *
+   *
+   * @param userColourSchemeArray
+   */
+  public void setUserColourScheme(jalview.binding.UserColourScheme[]
+                                  userColourSchemeArray)
+  {
+    //-- copy array
+    _userColourSchemeList.removeAllElements();
+    for (int i = 0; i < userColourSchemeArray.length; i++)
     {
-        //-- copy array
-        _userColourSchemeList.removeAllElements();
-        for (int i = 0; i < userColourSchemeArray.length; i++) {
-            _userColourSchemeList.addElement(userColourSchemeArray[i]);
-        }
-    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) 
+      _userColourSchemeList.addElement(userColourSchemeArray[i]);
+    }
+  } //-- void setUserColourScheme(jalview.binding.UserColourScheme)
 
 }
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
index 676a623..8df0d44 100755
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -1,38 +1,39 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
 
+import org.xml.sax.ContentHandler;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
 import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+
 import java.util.Enumeration;
 import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+
 
 /**
  * Class JalviewUserColours.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewUserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class JalviewUserColours implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -40,39 +41,38 @@ public class JalviewUserColours implements java.io.Serializable {
      */
     private java.util.Vector _colourList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public JalviewUserColours() {
+    //- Constructors -/
+    //----------------/
+    public JalviewUserColours()
+    {
         super();
         _colourList = new Vector();
-    } //-- jalview.binding.JalviewUserColours()
+    }
 
-
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.JalviewUserColours()
     //-----------/
 
     /**
-     * Method addColour
-     * 
-     * 
-     * 
-     * @param vColour
+     * DOCUMENT ME!
+     *
+     * @param vColour DOCUMENT ME!
+     *
+     * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!
      */
     public void addColour(jalview.binding.Colour vColour)
         throws java.lang.IndexOutOfBoundsException
     {
         _colourList.addElement(vColour);
-    } //-- void addColour(jalview.binding.Colour) 
+    }
+
+    //-- void addColour(jalview.binding.Colour) 
 
     /**
      * Method addColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vColour
      */
@@ -80,25 +80,29 @@ public class JalviewUserColours implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         _colourList.insertElementAt(vColour, index);
-    } //-- void addColour(int, jalview.binding.Colour) 
+    }
+
+    //-- void addColour(int, jalview.binding.Colour) 
 
     /**
      * Method enumerateColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Enumeration
      */
     public java.util.Enumeration enumerateColour()
     {
         return _colourList.elements();
-    } //-- java.util.Enumeration enumerateColour() 
+    }
+
+    //-- java.util.Enumeration enumerateColour() 
 
     /**
      * Method getColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Colour
      */
@@ -106,102 +110,123 @@ public class JalviewUserColours implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _colourList.size())) {
+        if ((index < 0) || (index > _colourList.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
-        
+
         return (jalview.binding.Colour) _colourList.elementAt(index);
-    } //-- jalview.binding.Colour getColour(int) 
+    }
+
+    //-- jalview.binding.Colour getColour(int) 
 
     /**
      * Method getColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Colour
      */
     public jalview.binding.Colour[] getColour()
     {
         int size = _colourList.size();
         jalview.binding.Colour[] mArray = new jalview.binding.Colour[size];
-        for (int index = 0; index < size; index++) {
+
+        for (int index = 0; index < size; index++)
+        {
             mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.Colour[] getColour() 
+    }
+
+    //-- jalview.binding.Colour[] getColour() 
 
     /**
      * Method getColourCount
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return int
      */
     public int getColourCount()
     {
         return _colourList.size();
-    } //-- int getColourCount() 
+    }
+
+    //-- int getColourCount() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Method removeAllColour
-     * 
+     *
      */
     public void removeAllColour()
     {
         _colourList.removeAllElements();
-    } //-- void removeAllColour() 
+    }
+
+    //-- void removeAllColour() 
 
     /**
      * Method removeColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Colour
      */
@@ -209,14 +234,17 @@ public class JalviewUserColours implements java.io.Serializable {
     {
         java.lang.Object obj = _colourList.elementAt(index);
         _colourList.removeElementAt(index);
+
         return (jalview.binding.Colour) obj;
-    } //-- jalview.binding.Colour removeColour(int) 
+    }
+
+    //-- jalview.binding.Colour removeColour(int) 
 
     /**
      * Method setColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vColour
      */
@@ -224,51 +252,63 @@ public class JalviewUserColours implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _colourList.size())) {
+        if ((index < 0) || (index > _colourList.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
+
         _colourList.setElementAt(vColour, index);
-    } //-- void setColour(int, jalview.binding.Colour) 
+    }
+
+    //-- void setColour(int, jalview.binding.Colour) 
 
     /**
      * Method setColour
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param colourArray
      */
     public void setColour(jalview.binding.Colour[] colourArray)
     {
         //-- copy array
         _colourList.removeAllElements();
-        for (int i = 0; i < colourArray.length; i++) {
+
+        for (int i = 0; i < colourArray.length; i++)
+        {
             _colourList.addElement(colourArray[i]);
         }
-    } //-- void setColour(jalview.binding.Colour) 
+    }
+
+    //-- void setColour(jalview.binding.Colour) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/JalviewUserColoursItem.java b/src/jalview/binding/JalviewUserColoursItem.java
index ce6919c..9c88831 100755
--- a/src/jalview/binding/JalviewUserColoursItem.java
+++ b/src/jalview/binding/JalviewUserColoursItem.java
@@ -1,30 +1,29 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.Serializable;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.Serializable;
+
+
 /**
  * Class JalviewUserColoursItem.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewUserColoursItem implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class JalviewUserColoursItem implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -32,39 +31,38 @@ public class JalviewUserColoursItem implements java.io.Serializable {
      */
     private jalview.binding.Colour _colour;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public JalviewUserColoursItem() {
+    //- Constructors -/
+    //----------------/
+    public JalviewUserColoursItem()
+    {
         super();
-    } //-- jalview.binding.JalviewUserColoursItem()
+    }
 
-
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.JalviewUserColoursItem()
     //-----------/
 
     /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return Colour
-     * @return the value of field 'colour'.
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
      */
     public jalview.binding.Colour getColour()
     {
         return this._colour;
-    } //-- jalview.binding.Colour getColour() 
+    }
+
+    //-- jalview.binding.Colour getColour() 
 
     /**
      * Sets the value of field 'colour'.
-     * 
+     *
      * @param colour the value of field 'colour'.
      */
     public void setColour(jalview.binding.Colour colour)
     {
         this._colour = colour;
-    } //-- void setColour(jalview.binding.Colour) 
+    }
 
+    //-- void setColour(jalview.binding.Colour) 
 }
diff --git a/src/jalview/binding/Residue.java b/src/jalview/binding/Residue.java
index 69e4312..2588f38 100755
--- a/src/jalview/binding/Residue.java
+++ b/src/jalview/binding/Residue.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,194 +7,193 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Residue.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class Residue implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _RGB
-     */
-    private int _RGB;
-
-    /**
-     * keeps track of state for field: _RGB
-     */
-    private boolean _has_RGB;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Residue() {
-        super();
-    } //-- jalview.binding.Residue()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteRGB
-     * 
-     */
-    public void deleteRGB()
-    {
-        this._has_RGB= false;
-    } //-- void deleteRGB() 
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return String
-     * @return the value of field 'name'.
-     */
-    public java.lang.String getName()
-    {
-        return this._name;
-    } //-- java.lang.String getName() 
-
-    /**
-     * Returns the value of field 'RGB'.
-     * 
-     * @return int
-     * @return the value of field 'RGB'.
-     */
-    public int getRGB()
-    {
-        return this._RGB;
-    } //-- int getRGB() 
-
-    /**
-     * Method hasRGB
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasRGB()
-    {
-        return this._has_RGB;
-    } //-- boolean hasRGB() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(java.lang.String name)
-    {
-        this._name = name;
-    } //-- void setName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'RGB'.
-     * 
-     * @param RGB the value of field 'RGB'.
-     */
-    public void setRGB(int RGB)
-    {
-        this._RGB = RGB;
-        this._has_RGB = true;
-    } //-- void setRGB(int) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+public class Residue
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _name
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _RGB
+   */
+  private int _RGB;
+
+  /**
+   * keeps track of state for field: _RGB
+   */
+  private boolean _has_RGB;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public Residue()
+  {
+    super();
+  } //-- jalview.binding.Residue()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteRGB
+   *
+   */
+  public void deleteRGB()
+  {
+    this._has_RGB = false;
+  } //-- void deleteRGB()
+
+  /**
+   * Returns the value of field 'name'.
+   *
+   * @return String
+   * @return the value of field 'name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  } //-- java.lang.String getName()
+
+  /**
+   * Returns the value of field 'RGB'.
+   *
+   * @return int
+   * @return the value of field 'RGB'.
+   */
+  public int getRGB()
+  {
+    return this._RGB;
+  } //-- int getRGB()
+
+  /**
+   * Method hasRGB
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasRGB()
+  {
+    return this._has_RGB;
+  } //-- boolean hasRGB()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'name'.
+   *
+   * @param name the value of field 'name'.
+   */
+  public void setName(java.lang.String name)
+  {
+    this._name = name;
+  } //-- void setName(java.lang.String)
+
+  /**
+   * Sets the value of field 'RGB'.
+   *
+   * @param RGB the value of field 'RGB'.
+   */
+  public void setRGB(int RGB)
+  {
+    this._RGB = RGB;
+    this._has_RGB = true;
+  } //-- void setRGB(int)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.
+        Residue.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java
index f3fd4e4..b583b4e 100755
--- a/src/jalview/binding/Sequence.java
+++ b/src/jalview/binding/Sequence.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,112 +7,110 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Sequence.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class Sequence extends SequenceType 
-implements java.io.Serializable
+public class Sequence
+    extends SequenceType implements java.io.Serializable
 {
 
+  //----------------/
+  //- Constructors -/
+  //----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  public Sequence()
+  {
+    super();
+  } //-- jalview.binding.Sequence()
 
-    public Sequence() {
-        super();
-    } //-- jalview.binding.Sequence()
+  //-----------/
+  //- Methods -/
+  //-----------/
 
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
 
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.
+        Sequence.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
 
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index 7ed3b52..a0d116e 100755
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -1,38 +1,39 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+
+import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
 import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+
 import java.util.Enumeration;
 import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+
 
 /**
  * Class SequenceSet.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class SequenceSet implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -60,40 +61,39 @@ public class SequenceSet implements java.io.Serializable {
      */
     private java.util.Vector _annotationList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public SequenceSet() {
+    //- Constructors -/
+    //----------------/
+    public SequenceSet()
+    {
         super();
         _sequenceList = new Vector();
         _annotationList = new Vector();
-    } //-- jalview.binding.SequenceSet()
-
+    }
 
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.SequenceSet()
     //-----------/
 
     /**
-     * Method addAnnotation
-     * 
-     * 
-     * 
-     * @param vAnnotation
+     * DOCUMENT ME!
+     *
+     * @param vAnnotation DOCUMENT ME!
+     *
+     * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!
      */
     public void addAnnotation(jalview.binding.Annotation vAnnotation)
         throws java.lang.IndexOutOfBoundsException
     {
         _annotationList.addElement(vAnnotation);
-    } //-- void addAnnotation(jalview.binding.Annotation) 
+    }
+
+    //-- void addAnnotation(jalview.binding.Annotation) 
 
     /**
      * Method addAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vAnnotation
      */
@@ -101,26 +101,30 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         _annotationList.insertElementAt(vAnnotation, index);
-    } //-- void addAnnotation(int, jalview.binding.Annotation) 
+    }
+
+    //-- void addAnnotation(int, jalview.binding.Annotation) 
 
     /**
      * Method addSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param vSequence
      */
     public void addSequence(jalview.binding.Sequence vSequence)
         throws java.lang.IndexOutOfBoundsException
     {
         _sequenceList.addElement(vSequence);
-    } //-- void addSequence(jalview.binding.Sequence) 
+    }
+
+    //-- void addSequence(jalview.binding.Sequence) 
 
     /**
      * Method addSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vSequence
      */
@@ -128,57 +132,67 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         _sequenceList.insertElementAt(vSequence, index);
-    } //-- void addSequence(int, jalview.binding.Sequence) 
+    }
+
+    //-- void addSequence(int, jalview.binding.Sequence) 
 
     /**
      * Method deleteAligned
-     * 
+     *
      */
     public void deleteAligned()
     {
-        this._has_aligned= false;
-    } //-- void deleteAligned() 
+        this._has_aligned = false;
+    }
+
+    //-- void deleteAligned() 
 
     /**
      * Method enumerateAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Enumeration
      */
     public java.util.Enumeration enumerateAnnotation()
     {
         return _annotationList.elements();
-    } //-- java.util.Enumeration enumerateAnnotation() 
+    }
+
+    //-- java.util.Enumeration enumerateAnnotation() 
 
     /**
      * Method enumerateSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Enumeration
      */
     public java.util.Enumeration enumerateSequence()
     {
         return _sequenceList.elements();
-    } //-- java.util.Enumeration enumerateSequence() 
+    }
+
+    //-- java.util.Enumeration enumerateSequence() 
 
     /**
      * Returns the value of field 'aligned'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'aligned'.
      */
     public boolean getAligned()
     {
         return this._aligned;
-    } //-- boolean getAligned() 
+    }
+
+    //-- boolean getAligned() 
 
     /**
      * Method getAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Annotation
      */
@@ -186,58 +200,70 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _annotationList.size())) {
+        if ((index < 0) || (index > _annotationList.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
-        
+
         return (jalview.binding.Annotation) _annotationList.elementAt(index);
-    } //-- jalview.binding.Annotation getAnnotation(int) 
+    }
+
+    //-- jalview.binding.Annotation getAnnotation(int) 
 
     /**
      * Method getAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Annotation
      */
     public jalview.binding.Annotation[] getAnnotation()
     {
         int size = _annotationList.size();
         jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];
-        for (int index = 0; index < size; index++) {
+
+        for (int index = 0; index < size; index++)
+        {
             mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.Annotation[] getAnnotation() 
+    }
+
+    //-- jalview.binding.Annotation[] getAnnotation() 
 
     /**
      * Method getAnnotationCount
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return int
      */
     public int getAnnotationCount()
     {
         return _annotationList.size();
-    } //-- int getAnnotationCount() 
+    }
+
+    //-- int getAnnotationCount() 
 
     /**
      * Returns the value of field 'gapChar'.
-     * 
+     *
      * @return String
      * @return the value of field 'gapChar'.
      */
     public java.lang.String getGapChar()
     {
         return this._gapChar;
-    } //-- java.lang.String getGapChar() 
+    }
+
+    //-- java.lang.String getGapChar() 
 
     /**
      * Method getSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Sequence
      */
@@ -245,123 +271,148 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _sequenceList.size())) {
+        if ((index < 0) || (index > _sequenceList.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
-        
+
         return (jalview.binding.Sequence) _sequenceList.elementAt(index);
-    } //-- jalview.binding.Sequence getSequence(int) 
+    }
+
+    //-- jalview.binding.Sequence getSequence(int) 
 
     /**
      * Method getSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Sequence
      */
     public jalview.binding.Sequence[] getSequence()
     {
         int size = _sequenceList.size();
         jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];
-        for (int index = 0; index < size; index++) {
+
+        for (int index = 0; index < size; index++)
+        {
             mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.Sequence[] getSequence() 
+    }
+
+    //-- jalview.binding.Sequence[] getSequence() 
 
     /**
      * Method getSequenceCount
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return int
      */
     public int getSequenceCount()
     {
         return _sequenceList.size();
-    } //-- int getSequenceCount() 
+    }
+
+    //-- int getSequenceCount() 
 
     /**
      * Method hasAligned
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasAligned()
     {
         return this._has_aligned;
-    } //-- boolean hasAligned() 
+    }
+
+    //-- boolean hasAligned() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Method removeAllAnnotation
-     * 
+     *
      */
     public void removeAllAnnotation()
     {
         _annotationList.removeAllElements();
-    } //-- void removeAllAnnotation() 
+    }
+
+    //-- void removeAllAnnotation() 
 
     /**
      * Method removeAllSequence
-     * 
+     *
      */
     public void removeAllSequence()
     {
         _sequenceList.removeAllElements();
-    } //-- void removeAllSequence() 
+    }
+
+    //-- void removeAllSequence() 
 
     /**
      * Method removeAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Annotation
      */
@@ -369,14 +420,17 @@ public class SequenceSet implements java.io.Serializable {
     {
         java.lang.Object obj = _annotationList.elementAt(index);
         _annotationList.removeElementAt(index);
+
         return (jalview.binding.Annotation) obj;
-    } //-- jalview.binding.Annotation removeAnnotation(int) 
+    }
+
+    //-- jalview.binding.Annotation removeAnnotation(int) 
 
     /**
      * Method removeSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Sequence
      */
@@ -384,25 +438,30 @@ public class SequenceSet implements java.io.Serializable {
     {
         java.lang.Object obj = _sequenceList.elementAt(index);
         _sequenceList.removeElementAt(index);
+
         return (jalview.binding.Sequence) obj;
-    } //-- jalview.binding.Sequence removeSequence(int) 
+    }
+
+    //-- jalview.binding.Sequence removeSequence(int) 
 
     /**
      * Sets the value of field 'aligned'.
-     * 
+     *
      * @param aligned the value of field 'aligned'.
      */
     public void setAligned(boolean aligned)
     {
         this._aligned = aligned;
         this._has_aligned = true;
-    } //-- void setAligned(boolean) 
+    }
+
+    //-- void setAligned(boolean) 
 
     /**
      * Method setAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vAnnotation
      */
@@ -410,43 +469,53 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _annotationList.size())) {
+        if ((index < 0) || (index > _annotationList.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
+
         _annotationList.setElementAt(vAnnotation, index);
-    } //-- void setAnnotation(int, jalview.binding.Annotation) 
+    }
+
+    //-- void setAnnotation(int, jalview.binding.Annotation) 
 
     /**
      * Method setAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param annotationArray
      */
     public void setAnnotation(jalview.binding.Annotation[] annotationArray)
     {
         //-- copy array
         _annotationList.removeAllElements();
-        for (int i = 0; i < annotationArray.length; i++) {
+
+        for (int i = 0; i < annotationArray.length; i++)
+        {
             _annotationList.addElement(annotationArray[i]);
         }
-    } //-- void setAnnotation(jalview.binding.Annotation) 
+    }
+
+    //-- void setAnnotation(jalview.binding.Annotation) 
 
     /**
      * Sets the value of field 'gapChar'.
-     * 
+     *
      * @param gapChar the value of field 'gapChar'.
      */
     public void setGapChar(java.lang.String gapChar)
     {
         this._gapChar = gapChar;
-    } //-- void setGapChar(java.lang.String) 
+    }
+
+    //-- void setGapChar(java.lang.String) 
 
     /**
      * Method setSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vSequence
      */
@@ -454,51 +523,63 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _sequenceList.size())) {
+        if ((index < 0) || (index > _sequenceList.size()))
+        {
             throw new IndexOutOfBoundsException();
         }
+
         _sequenceList.setElementAt(vSequence, index);
-    } //-- void setSequence(int, jalview.binding.Sequence) 
+    }
+
+    //-- void setSequence(int, jalview.binding.Sequence) 
 
     /**
      * Method setSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param sequenceArray
      */
     public void setSequence(jalview.binding.Sequence[] sequenceArray)
     {
         //-- copy array
         _sequenceList.removeAllElements();
-        for (int i = 0; i < sequenceArray.length; i++) {
+
+        for (int i = 0; i < sequenceArray.length; i++)
+        {
             _sequenceList.addElement(sequenceArray[i]);
         }
-    } //-- void setSequence(jalview.binding.Sequence) 
+    }
+
+    //-- void setSequence(jalview.binding.Sequence) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java
index 3a935e4..780c8ba 100755
--- a/src/jalview/binding/SequenceType.java
+++ b/src/jalview/binding/SequenceType.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,193 +7,192 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class SequenceType.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class SequenceType implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _sequence
-     */
-    private java.lang.String _sequence;
-
-    /**
-     * Field _name
-     */
-    private java.lang.String _name;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceType() {
-        super();
-    } //-- jalview.binding.SequenceType()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return String
-     * @return the value of field 'name'.
-     */
-    public java.lang.String getName()
-    {
-        return this._name;
-    } //-- java.lang.String getName() 
-
-    /**
-     * Returns the value of field 'sequence'.
-     * 
-     * @return String
-     * @return the value of field 'sequence'.
-     */
-    public java.lang.String getSequence()
-    {
-        return this._sequence;
-    } //-- java.lang.String getSequence() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(java.lang.String name)
-    {
-        this._name = name;
-    } //-- void setName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'sequence'.
-     * 
-     * @param sequence the value of field 'sequence'.
-     */
-    public void setSequence(java.lang.String sequence)
-    {
-        this._sequence = sequence;
-    } //-- void setSequence(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+public class SequenceType
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _id
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _sequence
+   */
+  private java.lang.String _sequence;
+
+  /**
+   * Field _name
+   */
+  private java.lang.String _name;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public SequenceType()
+  {
+    super();
+  } //-- jalview.binding.SequenceType()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'id'.
+   *
+   * @return String
+   * @return the value of field 'id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  } //-- java.lang.String getId()
+
+  /**
+   * Returns the value of field 'name'.
+   *
+   * @return String
+   * @return the value of field 'name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  } //-- java.lang.String getName()
+
+  /**
+   * Returns the value of field 'sequence'.
+   *
+   * @return String
+   * @return the value of field 'sequence'.
+   */
+  public java.lang.String getSequence()
+  {
+    return this._sequence;
+  } //-- java.lang.String getSequence()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'id'.
+   *
+   * @param id the value of field 'id'.
+   */
+  public void setId(java.lang.String id)
+  {
+    this._id = id;
+  } //-- void setId(java.lang.String)
+
+  /**
+   * Sets the value of field 'name'.
+   *
+   * @param name the value of field 'name'.
+   */
+  public void setName(java.lang.String name)
+  {
+    this._name = name;
+  } //-- void setName(java.lang.String)
+
+  /**
+   * Sets the value of field 'sequence'.
+   *
+   * @param sequence the value of field 'sequence'.
+   */
+  public void setSequence(java.lang.String sequence)
+  {
+    this._sequence = sequence;
+  } //-- void setSequence(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.
+        binding.SequenceType.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java
index 2821029..9fc63d2 100755
--- a/src/jalview/binding/Tree.java
+++ b/src/jalview/binding/Tree.java
@@ -1,36 +1,36 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
+
 import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+
+
 /**
  * Class Tree.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class Tree implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class Tree implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -153,604 +153,709 @@ public class Tree implements java.io.Serializable {
      */
     private java.lang.String _newick;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public Tree() {
+    //- Constructors -/
+    //----------------/
+    public Tree()
+    {
         super();
-    } //-- jalview.binding.Tree()
+    }
 
-
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.Tree()
     //-----------/
 
     /**
-     * Method deleteCurrentTree
-     * 
+     * DOCUMENT ME!
      */
     public void deleteCurrentTree()
     {
-        this._has_currentTree= false;
-    } //-- void deleteCurrentTree() 
+        this._has_currentTree = false;
+    }
+
+    //-- void deleteCurrentTree() 
 
     /**
      * Method deleteFitToWindow
-     * 
+     *
      */
     public void deleteFitToWindow()
     {
-        this._has_fitToWindow= false;
-    } //-- void deleteFitToWindow() 
+        this._has_fitToWindow = false;
+    }
+
+    //-- void deleteFitToWindow() 
 
     /**
      * Method deleteFontSize
-     * 
+     *
      */
     public void deleteFontSize()
     {
-        this._has_fontSize= false;
-    } //-- void deleteFontSize() 
+        this._has_fontSize = false;
+    }
+
+    //-- void deleteFontSize() 
 
     /**
      * Method deleteHeight
-     * 
+     *
      */
     public void deleteHeight()
     {
-        this._has_height= false;
-    } //-- void deleteHeight() 
+        this._has_height = false;
+    }
+
+    //-- void deleteHeight() 
 
     /**
      * Method deleteMarkUnlinked
-     * 
+     *
      */
     public void deleteMarkUnlinked()
     {
-        this._has_markUnlinked= false;
-    } //-- void deleteMarkUnlinked() 
+        this._has_markUnlinked = false;
+    }
+
+    //-- void deleteMarkUnlinked() 
 
     /**
      * Method deleteShowBootstrap
-     * 
+     *
      */
     public void deleteShowBootstrap()
     {
-        this._has_showBootstrap= false;
-    } //-- void deleteShowBootstrap() 
+        this._has_showBootstrap = false;
+    }
+
+    //-- void deleteShowBootstrap() 
 
     /**
      * Method deleteShowDistances
-     * 
+     *
      */
     public void deleteShowDistances()
     {
-        this._has_showDistances= false;
-    } //-- void deleteShowDistances() 
+        this._has_showDistances = false;
+    }
+
+    //-- void deleteShowDistances() 
 
     /**
      * Method deleteThreshold
-     * 
+     *
      */
     public void deleteThreshold()
     {
-        this._has_threshold= false;
-    } //-- void deleteThreshold() 
+        this._has_threshold = false;
+    }
+
+    //-- void deleteThreshold() 
 
     /**
      * Method deleteWidth
-     * 
+     *
      */
     public void deleteWidth()
     {
-        this._has_width= false;
-    } //-- void deleteWidth() 
+        this._has_width = false;
+    }
+
+    //-- void deleteWidth() 
 
     /**
      * Method deleteXpos
-     * 
+     *
      */
     public void deleteXpos()
     {
-        this._has_xpos= false;
-    } //-- void deleteXpos() 
+        this._has_xpos = false;
+    }
+
+    //-- void deleteXpos() 
 
     /**
      * Method deleteYpos
-     * 
+     *
      */
     public void deleteYpos()
     {
-        this._has_ypos= false;
-    } //-- void deleteYpos() 
+        this._has_ypos = false;
+    }
+
+    //-- void deleteYpos() 
 
     /**
      * Returns the value of field 'currentTree'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'currentTree'.
      */
     public boolean getCurrentTree()
     {
         return this._currentTree;
-    } //-- boolean getCurrentTree() 
+    }
+
+    //-- boolean getCurrentTree() 
 
     /**
      * Returns the value of field 'fitToWindow'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'fitToWindow'.
      */
     public boolean getFitToWindow()
     {
         return this._fitToWindow;
-    } //-- boolean getFitToWindow() 
+    }
+
+    //-- boolean getFitToWindow() 
 
     /**
      * Returns the value of field 'fontSize'.
-     * 
+     *
      * @return int
      * @return the value of field 'fontSize'.
      */
     public int getFontSize()
     {
         return this._fontSize;
-    } //-- int getFontSize() 
+    }
+
+    //-- int getFontSize() 
 
     /**
      * Returns the value of field 'height'.
-     * 
+     *
      * @return int
      * @return the value of field 'height'.
      */
     public int getHeight()
     {
         return this._height;
-    } //-- int getHeight() 
+    }
+
+    //-- int getHeight() 
 
     /**
      * Returns the value of field 'markUnlinked'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'markUnlinked'.
      */
     public boolean getMarkUnlinked()
     {
         return this._markUnlinked;
-    } //-- boolean getMarkUnlinked() 
+    }
+
+    //-- boolean getMarkUnlinked() 
 
     /**
      * Returns the value of field 'newick'.
-     * 
+     *
      * @return String
      * @return the value of field 'newick'.
      */
     public java.lang.String getNewick()
     {
         return this._newick;
-    } //-- java.lang.String getNewick() 
+    }
+
+    //-- java.lang.String getNewick() 
 
     /**
      * Returns the value of field 'showBootstrap'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'showBootstrap'.
      */
     public boolean getShowBootstrap()
     {
         return this._showBootstrap;
-    } //-- boolean getShowBootstrap() 
+    }
+
+    //-- boolean getShowBootstrap() 
 
     /**
      * Returns the value of field 'showDistances'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'showDistances'.
      */
     public boolean getShowDistances()
     {
         return this._showDistances;
-    } //-- boolean getShowDistances() 
+    }
+
+    //-- boolean getShowDistances() 
 
     /**
      * Returns the value of field 'threshold'.
-     * 
+     *
      * @return float
      * @return the value of field 'threshold'.
      */
     public float getThreshold()
     {
         return this._threshold;
-    } //-- float getThreshold() 
+    }
+
+    //-- float getThreshold() 
 
     /**
      * Returns the value of field 'title'.
-     * 
+     *
      * @return String
      * @return the value of field 'title'.
      */
     public java.lang.String getTitle()
     {
         return this._title;
-    } //-- java.lang.String getTitle() 
+    }
+
+    //-- java.lang.String getTitle() 
 
     /**
      * Returns the value of field 'width'.
-     * 
+     *
      * @return int
      * @return the value of field 'width'.
      */
     public int getWidth()
     {
         return this._width;
-    } //-- int getWidth() 
+    }
+
+    //-- int getWidth() 
 
     /**
      * Returns the value of field 'xpos'.
-     * 
+     *
      * @return int
      * @return the value of field 'xpos'.
      */
     public int getXpos()
     {
         return this._xpos;
-    } //-- int getXpos() 
+    }
+
+    //-- int getXpos() 
 
     /**
      * Returns the value of field 'ypos'.
-     * 
+     *
      * @return int
      * @return the value of field 'ypos'.
      */
     public int getYpos()
     {
         return this._ypos;
-    } //-- int getYpos() 
+    }
+
+    //-- int getYpos() 
 
     /**
      * Method hasCurrentTree
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasCurrentTree()
     {
         return this._has_currentTree;
-    } //-- boolean hasCurrentTree() 
+    }
+
+    //-- boolean hasCurrentTree() 
 
     /**
      * Method hasFitToWindow
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasFitToWindow()
     {
         return this._has_fitToWindow;
-    } //-- boolean hasFitToWindow() 
+    }
+
+    //-- boolean hasFitToWindow() 
 
     /**
      * Method hasFontSize
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasFontSize()
     {
         return this._has_fontSize;
-    } //-- boolean hasFontSize() 
+    }
+
+    //-- boolean hasFontSize() 
 
     /**
      * Method hasHeight
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasHeight()
     {
         return this._has_height;
-    } //-- boolean hasHeight() 
+    }
+
+    //-- boolean hasHeight() 
 
     /**
      * Method hasMarkUnlinked
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasMarkUnlinked()
     {
         return this._has_markUnlinked;
-    } //-- boolean hasMarkUnlinked() 
+    }
+
+    //-- boolean hasMarkUnlinked() 
 
     /**
      * Method hasShowBootstrap
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasShowBootstrap()
     {
         return this._has_showBootstrap;
-    } //-- boolean hasShowBootstrap() 
+    }
+
+    //-- boolean hasShowBootstrap() 
 
     /**
      * Method hasShowDistances
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasShowDistances()
     {
         return this._has_showDistances;
-    } //-- boolean hasShowDistances() 
+    }
+
+    //-- boolean hasShowDistances() 
 
     /**
      * Method hasThreshold
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasThreshold()
     {
         return this._has_threshold;
-    } //-- boolean hasThreshold() 
+    }
+
+    //-- boolean hasThreshold() 
 
     /**
      * Method hasWidth
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasWidth()
     {
         return this._has_width;
-    } //-- boolean hasWidth() 
+    }
+
+    //-- boolean hasWidth() 
 
     /**
      * Method hasXpos
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasXpos()
     {
         return this._has_xpos;
-    } //-- boolean hasXpos() 
+    }
+
+    //-- boolean hasXpos() 
 
     /**
      * Method hasYpos
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasYpos()
     {
         return this._has_ypos;
-    } //-- boolean hasYpos() 
+    }
+
+    //-- boolean hasYpos() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Sets the value of field 'currentTree'.
-     * 
+     *
      * @param currentTree the value of field 'currentTree'.
      */
     public void setCurrentTree(boolean currentTree)
     {
         this._currentTree = currentTree;
         this._has_currentTree = true;
-    } //-- void setCurrentTree(boolean) 
+    }
+
+    //-- void setCurrentTree(boolean) 
 
     /**
      * Sets the value of field 'fitToWindow'.
-     * 
+     *
      * @param fitToWindow the value of field 'fitToWindow'.
      */
     public void setFitToWindow(boolean fitToWindow)
     {
         this._fitToWindow = fitToWindow;
         this._has_fitToWindow = true;
-    } //-- void setFitToWindow(boolean) 
+    }
+
+    //-- void setFitToWindow(boolean) 
 
     /**
      * Sets the value of field 'fontSize'.
-     * 
+     *
      * @param fontSize the value of field 'fontSize'.
      */
     public void setFontSize(int fontSize)
     {
         this._fontSize = fontSize;
         this._has_fontSize = true;
-    } //-- void setFontSize(int) 
+    }
+
+    //-- void setFontSize(int) 
 
     /**
      * Sets the value of field 'height'.
-     * 
+     *
      * @param height the value of field 'height'.
      */
     public void setHeight(int height)
     {
         this._height = height;
         this._has_height = true;
-    } //-- void setHeight(int) 
+    }
+
+    //-- void setHeight(int) 
 
     /**
      * Sets the value of field 'markUnlinked'.
-     * 
+     *
      * @param markUnlinked the value of field 'markUnlinked'.
      */
     public void setMarkUnlinked(boolean markUnlinked)
     {
         this._markUnlinked = markUnlinked;
         this._has_markUnlinked = true;
-    } //-- void setMarkUnlinked(boolean) 
+    }
+
+    //-- void setMarkUnlinked(boolean) 
 
     /**
      * Sets the value of field 'newick'.
-     * 
+     *
      * @param newick the value of field 'newick'.
      */
     public void setNewick(java.lang.String newick)
     {
         this._newick = newick;
-    } //-- void setNewick(java.lang.String) 
+    }
+
+    //-- void setNewick(java.lang.String) 
 
     /**
      * Sets the value of field 'showBootstrap'.
-     * 
+     *
      * @param showBootstrap the value of field 'showBootstrap'.
      */
     public void setShowBootstrap(boolean showBootstrap)
     {
         this._showBootstrap = showBootstrap;
         this._has_showBootstrap = true;
-    } //-- void setShowBootstrap(boolean) 
+    }
+
+    //-- void setShowBootstrap(boolean) 
 
     /**
      * Sets the value of field 'showDistances'.
-     * 
+     *
      * @param showDistances the value of field 'showDistances'.
      */
     public void setShowDistances(boolean showDistances)
     {
         this._showDistances = showDistances;
         this._has_showDistances = true;
-    } //-- void setShowDistances(boolean) 
+    }
+
+    //-- void setShowDistances(boolean) 
 
     /**
      * Sets the value of field 'threshold'.
-     * 
+     *
      * @param threshold the value of field 'threshold'.
      */
     public void setThreshold(float threshold)
     {
         this._threshold = threshold;
         this._has_threshold = true;
-    } //-- void setThreshold(float) 
+    }
+
+    //-- void setThreshold(float) 
 
     /**
      * Sets the value of field 'title'.
-     * 
+     *
      * @param title the value of field 'title'.
      */
     public void setTitle(java.lang.String title)
     {
         this._title = title;
-    } //-- void setTitle(java.lang.String) 
+    }
+
+    //-- void setTitle(java.lang.String) 
 
     /**
      * Sets the value of field 'width'.
-     * 
+     *
      * @param width the value of field 'width'.
      */
     public void setWidth(int width)
     {
         this._width = width;
         this._has_width = true;
-    } //-- void setWidth(int) 
+    }
+
+    //-- void setWidth(int) 
 
     /**
      * Sets the value of field 'xpos'.
-     * 
+     *
      * @param xpos the value of field 'xpos'.
      */
     public void setXpos(int xpos)
     {
         this._xpos = xpos;
         this._has_xpos = true;
-    } //-- void setXpos(int) 
+    }
+
+    //-- void setXpos(int) 
 
     /**
      * Sets the value of field 'ypos'.
-     * 
+     *
      * @param ypos the value of field 'ypos'.
      */
     public void setYpos(int ypos)
     {
         this._ypos = ypos;
         this._has_ypos = true;
-    } //-- void setYpos(int) 
+    }
+
+    //-- void setYpos(int) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/UserColour.java b/src/jalview/binding/UserColour.java
index 837d9af..1d27451 100755
--- a/src/jalview/binding/UserColour.java
+++ b/src/jalview/binding/UserColour.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,194 +7,194 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class UserColour.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class UserColour implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id
-     */
-    private int _id;
-
-    /**
-     * keeps track of state for field: _id
-     */
-    private boolean _has_id;
-
-    /**
-     * Field _userColourScheme
-     */
-    private jalview.binding.UserColourScheme _userColourScheme;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColour() {
-        super();
-    } //-- jalview.binding.UserColour()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteId
-     * 
-     */
-    public void deleteId()
-    {
-        this._has_id= false;
-    } //-- void deleteId() 
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return int
-     * @return the value of field 'id'.
-     */
-    public int getId()
-    {
-        return this._id;
-    } //-- int getId() 
-
-    /**
-     * Returns the value of field 'userColourScheme'.
-     * 
-     * @return UserColourScheme
-     * @return the value of field 'userColourScheme'.
-     */
-    public jalview.binding.UserColourScheme getUserColourScheme()
-    {
-        return this._userColourScheme;
-    } //-- jalview.binding.UserColourScheme getUserColourScheme() 
-
-    /**
-     * Method hasId
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasId()
-    {
-        return this._has_id;
-    } //-- boolean hasId() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(int id)
-    {
-        this._id = id;
-        this._has_id = true;
-    } //-- void setId(int) 
-
-    /**
-     * Sets the value of field 'userColourScheme'.
-     * 
-     * @param userColourScheme the value of field 'userColourScheme'
-     */
-    public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)
-    {
-        this._userColourScheme = userColourScheme;
-    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+public class UserColour
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _id
+   */
+  private int _id;
+
+  /**
+   * keeps track of state for field: _id
+   */
+  private boolean _has_id;
+
+  /**
+   * Field _userColourScheme
+   */
+  private jalview.binding.UserColourScheme _userColourScheme;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public UserColour()
+  {
+    super();
+  } //-- jalview.binding.UserColour()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteId
+   *
+   */
+  public void deleteId()
+  {
+    this._has_id = false;
+  } //-- void deleteId()
+
+  /**
+   * Returns the value of field 'id'.
+   *
+   * @return int
+   * @return the value of field 'id'.
+   */
+  public int getId()
+  {
+    return this._id;
+  } //-- int getId()
+
+  /**
+   * Returns the value of field 'userColourScheme'.
+   *
+   * @return UserColourScheme
+   * @return the value of field 'userColourScheme'.
+   */
+  public jalview.binding.UserColourScheme getUserColourScheme()
+  {
+    return this._userColourScheme;
+  } //-- jalview.binding.UserColourScheme getUserColourScheme()
+
+  /**
+   * Method hasId
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasId()
+  {
+    return this._has_id;
+  } //-- boolean hasId()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'id'.
+   *
+   * @param id the value of field 'id'.
+   */
+  public void setId(int id)
+  {
+    this._id = id;
+    this._has_id = true;
+  } //-- void setId(int)
+
+  /**
+   * Sets the value of field 'userColourScheme'.
+   *
+   * @param userColourScheme the value of field 'userColourScheme'
+   */
+  public void setUserColourScheme(jalview.binding.UserColourScheme
+                                  userColourScheme)
+  {
+    this._userColourScheme = userColourScheme;
+  } //-- void setUserColourScheme(jalview.binding.UserColourScheme)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.
+        UserColour.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java
index 79ea637..6d6c265 100755
--- a/src/jalview/binding/UserColourScheme.java
+++ b/src/jalview/binding/UserColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,112 +7,110 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class UserColourScheme.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class UserColourScheme extends JalviewUserColours 
-implements java.io.Serializable
+public class UserColourScheme
+    extends JalviewUserColours implements java.io.Serializable
 {
 
+  //----------------/
+  //- Constructors -/
+  //----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  public UserColourScheme()
+  {
+    super();
+  } //-- jalview.binding.UserColourScheme()
 
-    public UserColourScheme() {
-        super();
-    } //-- jalview.binding.UserColourScheme()
+  //-----------/
+  //- Methods -/
+  //-----------/
 
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
 
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.
+        binding.UserColourScheme.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
 
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java
index 241aaab..f00e341 100755
--- a/src/jalview/binding/UserColours.java
+++ b/src/jalview/binding/UserColours.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,167 +7,167 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class UserColours.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class UserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _userColourScheme
-     */
-    private jalview.binding.UserColourScheme _userColourScheme;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColours() {
-        super();
-    } //-- jalview.binding.UserColours()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Returns the value of field 'userColourScheme'.
-     * 
-     * @return UserColourScheme
-     * @return the value of field 'userColourScheme'.
-     */
-    public jalview.binding.UserColourScheme getUserColourScheme()
-    {
-        return this._userColourScheme;
-    } //-- jalview.binding.UserColourScheme getUserColourScheme() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'userColourScheme'.
-     * 
-     * @param userColourScheme the value of field 'userColourScheme'
-     */
-    public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)
-    {
-        this._userColourScheme = userColourScheme;
-    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+public class UserColours
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _id
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _userColourScheme
+   */
+  private jalview.binding.UserColourScheme _userColourScheme;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public UserColours()
+  {
+    super();
+  } //-- jalview.binding.UserColours()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'id'.
+   *
+   * @return String
+   * @return the value of field 'id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  } //-- java.lang.String getId()
+
+  /**
+   * Returns the value of field 'userColourScheme'.
+   *
+   * @return UserColourScheme
+   * @return the value of field 'userColourScheme'.
+   */
+  public jalview.binding.UserColourScheme getUserColourScheme()
+  {
+    return this._userColourScheme;
+  } //-- jalview.binding.UserColourScheme getUserColourScheme()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'id'.
+   *
+   * @param id the value of field 'id'.
+   */
+  public void setId(java.lang.String id)
+  {
+    this._id = id;
+  } //-- void setId(java.lang.String)
+
+  /**
+   * Sets the value of field 'userColourScheme'.
+   *
+   * @param userColourScheme the value of field 'userColourScheme'
+   */
+  public void setUserColourScheme(jalview.binding.UserColourScheme
+                                  userColourScheme)
+  {
+    this._userColourScheme = userColourScheme;
+  } //-- void setUserColourScheme(jalview.binding.UserColourScheme)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.
+        UserColours.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index b4237b8..037bd3d 100755
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,570 +7,585 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class VAMSAS.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class VAMSAS implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _alignmentList
-     */
-    private java.util.Vector _alignmentList;
-
-    /**
-     * Field _treeList
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _sequenceSetList
-     */
-    private java.util.Vector _sequenceSetList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSAS() {
-        super();
-        _alignmentList = new Vector();
-        _treeList = new Vector();
-        _sequenceSetList = new Vector();
-    } //-- jalview.binding.VAMSAS()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAlignment
-     * 
-     * 
-     * 
-     * @param vAlignment
-     */
-    public void addAlignment(jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _alignmentList.addElement(vAlignment);
-    } //-- void addAlignment(jalview.binding.Alignment) 
-
-    /**
-     * Method addAlignment
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAlignment
-     */
-    public void addAlignment(int index, jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _alignmentList.insertElementAt(vAlignment, index);
-    } //-- void addAlignment(int, jalview.binding.Alignment) 
-
-    /**
-     * Method addSequenceSet
-     * 
-     * 
-     * 
-     * @param vSequenceSet
-     */
-    public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _sequenceSetList.addElement(vSequenceSet);
-    } //-- void addSequenceSet(jalview.binding.SequenceSet) 
-
-    /**
-     * Method addSequenceSet
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     */
-    public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _sequenceSetList.insertElementAt(vSequenceSet, index);
-    } //-- void addSequenceSet(int, jalview.binding.SequenceSet) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param vTree
-     */
-    public void addTree(java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.addElement(vTree);
-    } //-- void addTree(java.lang.String) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void addTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.insertElementAt(vTree, index);
-    } //-- void addTree(int, java.lang.String) 
-
-    /**
-     * Method enumerateAlignment
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateAlignment()
-    {
-        return _alignmentList.elements();
-    } //-- java.util.Enumeration enumerateAlignment() 
-
-    /**
-     * Method enumerateSequenceSet
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateSequenceSet()
-    {
-        return _sequenceSetList.elements();
-    } //-- java.util.Enumeration enumerateSequenceSet() 
-
-    /**
-     * Method enumerateTree
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateTree()
-    {
-        return _treeList.elements();
-    } //-- java.util.Enumeration enumerateTree() 
-
-    /**
-     * Method getAlignment
-     * 
-     * 
-     * 
-     * @param index
-     * @return Alignment
-     */
-    public jalview.binding.Alignment getAlignment(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _alignmentList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.Alignment) _alignmentList.elementAt(index);
-    } //-- jalview.binding.Alignment getAlignment(int) 
-
-    /**
-     * Method getAlignment
-     * 
-     * 
-     * 
-     * @return Alignment
-     */
-    public jalview.binding.Alignment[] getAlignment()
-    {
-        int size = _alignmentList.size();
-        jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.Alignment[] getAlignment() 
-
-    /**
-     * Method getAlignmentCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getAlignmentCount()
-    {
-        return _alignmentList.size();
-    } //-- int getAlignmentCount() 
-
-    /**
-     * Method getSequenceSet
-     * 
-     * 
-     * 
-     * @param index
-     * @return SequenceSet
-     */
-    public jalview.binding.SequenceSet getSequenceSet(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
-    } //-- jalview.binding.SequenceSet getSequenceSet(int) 
-
-    /**
-     * Method getSequenceSet
-     * 
-     * 
-     * 
-     * @return SequenceSet
-     */
-    public jalview.binding.SequenceSet[] getSequenceSet()
-    {
-        int size = _sequenceSetList.size();
-        jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.SequenceSet[] getSequenceSet() 
-
-    /**
-     * Method getSequenceSetCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getSequenceSetCount()
-    {
-        return _sequenceSetList.size();
-    } //-- int getSequenceSetCount() 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return String
-     */
-    public java.lang.String getTree(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (String)_treeList.elementAt(index);
-    } //-- java.lang.String getTree(int) 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String[] getTree()
-    {
-        int size = _treeList.size();
-        java.lang.String[] mArray = new java.lang.String[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (String)_treeList.elementAt(index);
-        }
-        return mArray;
-    } //-- java.lang.String[] getTree() 
-
-    /**
-     * Method getTreeCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getTreeCount()
-    {
-        return _treeList.size();
-    } //-- int getTreeCount() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAlignment
-     * 
-     * 
-     * 
-     * @param index
-     * @return Alignment
-     */
-    public jalview.binding.Alignment removeAlignment(int index)
-    {
-        java.lang.Object obj = _alignmentList.elementAt(index);
-        _alignmentList.removeElementAt(index);
-        return (jalview.binding.Alignment) obj;
-    } //-- jalview.binding.Alignment removeAlignment(int) 
-
-    /**
-     * Method removeAllAlignment
-     * 
-     */
-    public void removeAllAlignment()
-    {
-        _alignmentList.removeAllElements();
-    } //-- void removeAllAlignment() 
-
-    /**
-     * Method removeAllSequenceSet
-     * 
-     */
-    public void removeAllSequenceSet()
-    {
-        _sequenceSetList.removeAllElements();
-    } //-- void removeAllSequenceSet() 
-
-    /**
-     * Method removeAllTree
-     * 
-     */
-    public void removeAllTree()
-    {
-        _treeList.removeAllElements();
-    } //-- void removeAllTree() 
-
-    /**
-     * Method removeSequenceSet
-     * 
-     * 
-     * 
-     * @param index
-     * @return SequenceSet
-     */
-    public jalview.binding.SequenceSet removeSequenceSet(int index)
-    {
-        java.lang.Object obj = _sequenceSetList.elementAt(index);
-        _sequenceSetList.removeElementAt(index);
-        return (jalview.binding.SequenceSet) obj;
-    } //-- jalview.binding.SequenceSet removeSequenceSet(int) 
-
-    /**
-     * Method removeTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return String
-     */
-    public java.lang.String removeTree(int index)
-    {
-        java.lang.Object obj = _treeList.elementAt(index);
-        _treeList.removeElementAt(index);
-        return (String)obj;
-    } //-- java.lang.String removeTree(int) 
-
-    /**
-     * Method setAlignment
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAlignment
-     */
-    public void setAlignment(int index, jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _alignmentList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _alignmentList.setElementAt(vAlignment, index);
-    } //-- void setAlignment(int, jalview.binding.Alignment) 
-
-    /**
-     * Method setAlignment
-     * 
-     * 
-     * 
-     * @param alignmentArray
-     */
-    public void setAlignment(jalview.binding.Alignment[] alignmentArray)
-    {
-        //-- copy array
-        _alignmentList.removeAllElements();
-        for (int i = 0; i < alignmentArray.length; i++) {
-            _alignmentList.addElement(alignmentArray[i]);
-        }
-    } //-- void setAlignment(jalview.binding.Alignment) 
-
-    /**
-     * Method setSequenceSet
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     */
-    public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _sequenceSetList.setElementAt(vSequenceSet, index);
-    } //-- void setSequenceSet(int, jalview.binding.SequenceSet) 
-
-    /**
-     * Method setSequenceSet
-     * 
-     * 
-     * 
-     * @param sequenceSetArray
-     */
-    public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)
-    {
-        //-- copy array
-        _sequenceSetList.removeAllElements();
-        for (int i = 0; i < sequenceSetArray.length; i++) {
-            _sequenceSetList.addElement(sequenceSetArray[i]);
-        }
-    } //-- void setSequenceSet(jalview.binding.SequenceSet) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void setTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _treeList.setElementAt(vTree, index);
-    } //-- void setTree(int, java.lang.String) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param treeArray
-     */
-    public void setTree(java.lang.String[] treeArray)
-    {
-        //-- copy array
-        _treeList.removeAllElements();
-        for (int i = 0; i < treeArray.length; i++) {
-            _treeList.addElement(treeArray[i]);
-        }
-    } //-- void setTree(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+public class VAMSAS
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _alignmentList
+   */
+  private java.util.Vector _alignmentList;
+
+  /**
+   * Field _treeList
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _sequenceSetList
+   */
+  private java.util.Vector _sequenceSetList;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public VAMSAS()
+  {
+    super();
+    _alignmentList = new Vector();
+    _treeList = new Vector();
+    _sequenceSetList = new Vector();
+  } //-- jalview.binding.VAMSAS()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addAlignment
+   *
+   *
+   *
+   * @param vAlignment
+   */
+  public void addAlignment(jalview.binding.Alignment vAlignment)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _alignmentList.addElement(vAlignment);
+  } //-- void addAlignment(jalview.binding.Alignment)
+
+  /**
+   * Method addAlignment
+   *
+   *
+   *
+   * @param index
+   * @param vAlignment
+   */
+  public void addAlignment(int index, jalview.binding.Alignment vAlignment)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _alignmentList.insertElementAt(vAlignment, index);
+  } //-- void addAlignment(int, jalview.binding.Alignment)
+
+  /**
+   * Method addSequenceSet
+   *
+   *
+   *
+   * @param vSequenceSet
+   */
+  public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _sequenceSetList.addElement(vSequenceSet);
+  } //-- void addSequenceSet(jalview.binding.SequenceSet)
+
+  /**
+   * Method addSequenceSet
+   *
+   *
+   *
+   * @param index
+   * @param vSequenceSet
+   */
+  public void addSequenceSet(int index,
+                             jalview.binding.SequenceSet vSequenceSet)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _sequenceSetList.insertElementAt(vSequenceSet, index);
+  } //-- void addSequenceSet(int, jalview.binding.SequenceSet)
+
+  /**
+   * Method addTree
+   *
+   *
+   *
+   * @param vTree
+   */
+  public void addTree(java.lang.String vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _treeList.addElement(vTree);
+  } //-- void addTree(java.lang.String)
+
+  /**
+   * Method addTree
+   *
+   *
+   *
+   * @param index
+   * @param vTree
+   */
+  public void addTree(int index, java.lang.String vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _treeList.insertElementAt(vTree, index);
+  } //-- void addTree(int, java.lang.String)
+
+  /**
+   * Method enumerateAlignment
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateAlignment()
+  {
+    return _alignmentList.elements();
+  } //-- java.util.Enumeration enumerateAlignment()
+
+  /**
+   * Method enumerateSequenceSet
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateSequenceSet()
+  {
+    return _sequenceSetList.elements();
+  } //-- java.util.Enumeration enumerateSequenceSet()
+
+  /**
+   * Method enumerateTree
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return _treeList.elements();
+  } //-- java.util.Enumeration enumerateTree()
+
+  /**
+   * Method getAlignment
+   *
+   *
+   *
+   * @param index
+   * @return Alignment
+   */
+  public jalview.binding.Alignment getAlignment(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _alignmentList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.Alignment) _alignmentList.elementAt(index);
+  } //-- jalview.binding.Alignment getAlignment(int)
+
+  /**
+   * Method getAlignment
+   *
+   *
+   *
+   * @return Alignment
+   */
+  public jalview.binding.Alignment[] getAlignment()
+  {
+    int size = _alignmentList.size();
+    jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(
+          index);
+    }
+    return mArray;
+  } //-- jalview.binding.Alignment[] getAlignment()
+
+  /**
+   * Method getAlignmentCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getAlignmentCount()
+  {
+    return _alignmentList.size();
+  } //-- int getAlignmentCount()
+
+  /**
+   * Method getSequenceSet
+   *
+   *
+   *
+   * @param index
+   * @return SequenceSet
+   */
+  public jalview.binding.SequenceSet getSequenceSet(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _sequenceSetList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
+  } //-- jalview.binding.SequenceSet getSequenceSet(int)
+
+  /**
+   * Method getSequenceSet
+   *
+   *
+   *
+   * @return SequenceSet
+   */
+  public jalview.binding.SequenceSet[] getSequenceSet()
+  {
+    int size = _sequenceSetList.size();
+    jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(
+          index);
+    }
+    return mArray;
+  } //-- jalview.binding.SequenceSet[] getSequenceSet()
+
+  /**
+   * Method getSequenceSetCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getSequenceSetCount()
+  {
+    return _sequenceSetList.size();
+  } //-- int getSequenceSetCount()
+
+  /**
+   * Method getTree
+   *
+   *
+   *
+   * @param index
+   * @return String
+   */
+  public java.lang.String getTree(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _treeList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (String) _treeList.elementAt(index);
+  } //-- java.lang.String getTree(int)
+
+  /**
+   * Method getTree
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String[] getTree()
+  {
+    int size = _treeList.size();
+    java.lang.String[] mArray = new java.lang.String[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (String) _treeList.elementAt(index);
+    }
+    return mArray;
+  } //-- java.lang.String[] getTree()
+
+  /**
+   * Method getTreeCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getTreeCount()
+  {
+    return _treeList.size();
+  } //-- int getTreeCount()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAlignment
+   *
+   *
+   *
+   * @param index
+   * @return Alignment
+   */
+  public jalview.binding.Alignment removeAlignment(int index)
+  {
+    java.lang.Object obj = _alignmentList.elementAt(index);
+    _alignmentList.removeElementAt(index);
+    return (jalview.binding.Alignment) obj;
+  } //-- jalview.binding.Alignment removeAlignment(int)
+
+  /**
+   * Method removeAllAlignment
+   *
+   */
+  public void removeAllAlignment()
+  {
+    _alignmentList.removeAllElements();
+  } //-- void removeAllAlignment()
+
+  /**
+   * Method removeAllSequenceSet
+   *
+   */
+  public void removeAllSequenceSet()
+  {
+    _sequenceSetList.removeAllElements();
+  } //-- void removeAllSequenceSet()
+
+  /**
+   * Method removeAllTree
+   *
+   */
+  public void removeAllTree()
+  {
+    _treeList.removeAllElements();
+  } //-- void removeAllTree()
+
+  /**
+   * Method removeSequenceSet
+   *
+   *
+   *
+   * @param index
+   * @return SequenceSet
+   */
+  public jalview.binding.SequenceSet removeSequenceSet(int index)
+  {
+    java.lang.Object obj = _sequenceSetList.elementAt(index);
+    _sequenceSetList.removeElementAt(index);
+    return (jalview.binding.SequenceSet) obj;
+  } //-- jalview.binding.SequenceSet removeSequenceSet(int)
+
+  /**
+   * Method removeTree
+   *
+   *
+   *
+   * @param index
+   * @return String
+   */
+  public java.lang.String removeTree(int index)
+  {
+    java.lang.Object obj = _treeList.elementAt(index);
+    _treeList.removeElementAt(index);
+    return (String) obj;
+  } //-- java.lang.String removeTree(int)
+
+  /**
+   * Method setAlignment
+   *
+   *
+   *
+   * @param index
+   * @param vAlignment
+   */
+  public void setAlignment(int index, jalview.binding.Alignment vAlignment)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _alignmentList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _alignmentList.setElementAt(vAlignment, index);
+  } //-- void setAlignment(int, jalview.binding.Alignment)
+
+  /**
+   * Method setAlignment
+   *
+   *
+   *
+   * @param alignmentArray
+   */
+  public void setAlignment(jalview.binding.Alignment[] alignmentArray)
+  {
+    //-- copy array
+    _alignmentList.removeAllElements();
+    for (int i = 0; i < alignmentArray.length; i++)
+    {
+      _alignmentList.addElement(alignmentArray[i]);
+    }
+  } //-- void setAlignment(jalview.binding.Alignment)
+
+  /**
+   * Method setSequenceSet
+   *
+   *
+   *
+   * @param index
+   * @param vSequenceSet
+   */
+  public void setSequenceSet(int index,
+                             jalview.binding.SequenceSet vSequenceSet)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _sequenceSetList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _sequenceSetList.setElementAt(vSequenceSet, index);
+  } //-- void setSequenceSet(int, jalview.binding.SequenceSet)
+
+  /**
+   * Method setSequenceSet
+   *
+   *
+   *
+   * @param sequenceSetArray
+   */
+  public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)
+  {
+    //-- copy array
+    _sequenceSetList.removeAllElements();
+    for (int i = 0; i < sequenceSetArray.length; i++)
+    {
+      _sequenceSetList.addElement(sequenceSetArray[i]);
+    }
+  } //-- void setSequenceSet(jalview.binding.SequenceSet)
+
+  /**
+   * Method setTree
+   *
+   *
+   *
+   * @param index
+   * @param vTree
+   */
+  public void setTree(int index, java.lang.String vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _treeList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _treeList.setElementAt(vTree, index);
+  } //-- void setTree(int, java.lang.String)
+
+  /**
+   * Method setTree
+   *
+   *
+   *
+   * @param treeArray
+   */
+  public void setTree(java.lang.String[] treeArray)
+  {
+    //-- copy array
+    _treeList.removeAllElements();
+    for (int i = 0; i < treeArray.length; i++)
+    {
+      _treeList.addElement(treeArray[i]);
+    }
+  } //-- void setTree(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.
+        VAMSAS.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java
index a4d4362..74aa86e 100755
--- a/src/jalview/binding/VamsasModel.java
+++ b/src/jalview/binding/VamsasModel.java
@@ -1,118 +1,125 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
+
 import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+
+
 /**
  * Class VamsasModel.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class VamsasModel extends VAMSAS 
-implements java.io.Serializable
+public class VamsasModel extends VAMSAS implements java.io.Serializable
 {
-
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public VamsasModel() {
+    //- Constructors -/
+    //----------------/
+    public VamsasModel()
+    {
         super();
-    } //-- jalview.binding.VamsasModel()
+    }
 
-
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.VamsasModel()
     //-----------/
 
     /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
      */
     public boolean isValid()
     {
-        try {
+        try
+        {
             validate();
         }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        catch (org.exolab.castor.xml.ValidationException vex)
+        {
             return false;
         }
+
         return true;
-    } //-- boolean isValid() 
+    }
+
+    //-- boolean isValid() 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+        return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class,
+            reader);
+    }
+
+    //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     * 
+     *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+    public void validate() throws org.exolab.castor.xml.ValidationException
     {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
+    //-- void validate() 
 }
diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java
index 911061b..07622b3 100755
--- a/src/jalview/binding/Viewport.java
+++ b/src/jalview/binding/Viewport.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,1414 +7,1413 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Viewport.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class Viewport implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _conservationSelected
-     */
-    private boolean _conservationSelected;
-
-    /**
-     * keeps track of state for field: _conservationSelected
-     */
-    private boolean _has_conservationSelected;
-
-    /**
-     * Field _pidSelected
-     */
-    private boolean _pidSelected;
-
-    /**
-     * keeps track of state for field: _pidSelected
-     */
-    private boolean _has_pidSelected;
-
-    /**
-     * Field _bgColour
-     */
-    private java.lang.String _bgColour;
-
-    /**
-     * Field _consThreshold
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _title
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _showFullId
-     */
-    private boolean _showFullId;
-
-    /**
-     * keeps track of state for field: _showFullId
-     */
-    private boolean _has_showFullId;
-
-    /**
-     * Field _showText
-     */
-    private boolean _showText;
-
-    /**
-     * keeps track of state for field: _showText
-     */
-    private boolean _has_showText;
-
-    /**
-     * Field _showColourText
-     */
-    private boolean _showColourText;
-
-    /**
-     * keeps track of state for field: _showColourText
-     */
-    private boolean _has_showColourText;
-
-    /**
-     * Field _showBoxes
-     */
-    private boolean _showBoxes;
-
-    /**
-     * keeps track of state for field: _showBoxes
-     */
-    private boolean _has_showBoxes;
-
-    /**
-     * Field _wrapAlignment
-     */
-    private boolean _wrapAlignment;
-
-    /**
-     * keeps track of state for field: _wrapAlignment
-     */
-    private boolean _has_wrapAlignment;
-
-    /**
-     * Field _renderGaps
-     */
-    private boolean _renderGaps;
-
-    /**
-     * keeps track of state for field: _renderGaps
-     */
-    private boolean _has_renderGaps;
-
-    /**
-     * Field _showSequenceFeatures
-     */
-    private boolean _showSequenceFeatures;
-
-    /**
-     * keeps track of state for field: _showSequenceFeatures
-     */
-    private boolean _has_showSequenceFeatures;
-
-    /**
-     * Field _showAnnotation
-     */
-    private boolean _showAnnotation;
-
-    /**
-     * keeps track of state for field: _showAnnotation
-     */
-    private boolean _has_showAnnotation;
-
-    /**
-     * Field _showConservation
-     */
-    private boolean _showConservation;
-
-    /**
-     * keeps track of state for field: _showConservation
-     */
-    private boolean _has_showConservation;
-
-    /**
-     * Field _showQuality
-     */
-    private boolean _showQuality;
-
-    /**
-     * keeps track of state for field: _showQuality
-     */
-    private boolean _has_showQuality;
-
-    /**
-     * Field _showIdentity
-     */
-    private boolean _showIdentity;
-
-    /**
-     * keeps track of state for field: _showIdentity
-     */
-    private boolean _has_showIdentity;
-
-    /**
-     * Field _xpos
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _width
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-    /**
-     * Field _startRes
-     */
-    private int _startRes;
-
-    /**
-     * keeps track of state for field: _startRes
-     */
-    private boolean _has_startRes;
-
-    /**
-     * Field _startSeq
-     */
-    private int _startSeq;
-
-    /**
-     * keeps track of state for field: _startSeq
-     */
-    private boolean _has_startSeq;
-
-    /**
-     * Field _fontName
-     */
-    private java.lang.String _fontName;
-
-    /**
-     * Field _fontSize
-     */
-    private int _fontSize;
-
-    /**
-     * keeps track of state for field: _fontSize
-     */
-    private boolean _has_fontSize;
-
-    /**
-     * Field _fontStyle
-     */
-    private int _fontStyle;
-
-    /**
-     * keeps track of state for field: _fontStyle
-     */
-    private boolean _has_fontStyle;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Viewport() {
-        super();
-    } //-- jalview.binding.Viewport()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteConsThreshold
-     * 
-     */
-    public void deleteConsThreshold()
-    {
-        this._has_consThreshold= false;
-    } //-- void deleteConsThreshold() 
-
-    /**
-     * Method deleteConservationSelected
-     * 
-     */
-    public void deleteConservationSelected()
-    {
-        this._has_conservationSelected= false;
-    } //-- void deleteConservationSelected() 
-
-    /**
-     * Method deleteFontSize
-     * 
-     */
-    public void deleteFontSize()
-    {
-        this._has_fontSize= false;
-    } //-- void deleteFontSize() 
-
-    /**
-     * Method deleteFontStyle
-     * 
-     */
-    public void deleteFontStyle()
-    {
-        this._has_fontStyle= false;
-    } //-- void deleteFontStyle() 
-
-    /**
-     * Method deleteHeight
-     * 
-     */
-    public void deleteHeight()
-    {
-        this._has_height= false;
-    } //-- void deleteHeight() 
-
-    /**
-     * Method deletePidSelected
-     * 
-     */
-    public void deletePidSelected()
-    {
-        this._has_pidSelected= false;
-    } //-- void deletePidSelected() 
-
-    /**
-     * Method deletePidThreshold
-     * 
-     */
-    public void deletePidThreshold()
-    {
-        this._has_pidThreshold= false;
-    } //-- void deletePidThreshold() 
-
-    /**
-     * Method deleteRenderGaps
-     * 
-     */
-    public void deleteRenderGaps()
-    {
-        this._has_renderGaps= false;
-    } //-- void deleteRenderGaps() 
-
-    /**
-     * Method deleteShowAnnotation
-     * 
-     */
-    public void deleteShowAnnotation()
-    {
-        this._has_showAnnotation= false;
-    } //-- void deleteShowAnnotation() 
-
-    /**
-     * Method deleteShowBoxes
-     * 
-     */
-    public void deleteShowBoxes()
-    {
-        this._has_showBoxes= false;
-    } //-- void deleteShowBoxes() 
-
-    /**
-     * Method deleteShowColourText
-     * 
-     */
-    public void deleteShowColourText()
-    {
-        this._has_showColourText= false;
-    } //-- void deleteShowColourText() 
-
-    /**
-     * Method deleteShowConservation
-     * 
-     */
-    public void deleteShowConservation()
-    {
-        this._has_showConservation= false;
-    } //-- void deleteShowConservation() 
-
-    /**
-     * Method deleteShowFullId
-     * 
-     */
-    public void deleteShowFullId()
-    {
-        this._has_showFullId= false;
-    } //-- void deleteShowFullId() 
-
-    /**
-     * Method deleteShowIdentity
-     * 
-     */
-    public void deleteShowIdentity()
-    {
-        this._has_showIdentity= false;
-    } //-- void deleteShowIdentity() 
-
-    /**
-     * Method deleteShowQuality
-     * 
-     */
-    public void deleteShowQuality()
-    {
-        this._has_showQuality= false;
-    } //-- void deleteShowQuality() 
-
-    /**
-     * Method deleteShowSequenceFeatures
-     * 
-     */
-    public void deleteShowSequenceFeatures()
-    {
-        this._has_showSequenceFeatures= false;
-    } //-- void deleteShowSequenceFeatures() 
-
-    /**
-     * Method deleteShowText
-     * 
-     */
-    public void deleteShowText()
-    {
-        this._has_showText= false;
-    } //-- void deleteShowText() 
-
-    /**
-     * Method deleteStartRes
-     * 
-     */
-    public void deleteStartRes()
-    {
-        this._has_startRes= false;
-    } //-- void deleteStartRes() 
-
-    /**
-     * Method deleteStartSeq
-     * 
-     */
-    public void deleteStartSeq()
-    {
-        this._has_startSeq= false;
-    } //-- void deleteStartSeq() 
-
-    /**
-     * Method deleteWidth
-     * 
-     */
-    public void deleteWidth()
-    {
-        this._has_width= false;
-    } //-- void deleteWidth() 
-
-    /**
-     * Method deleteWrapAlignment
-     * 
-     */
-    public void deleteWrapAlignment()
-    {
-        this._has_wrapAlignment= false;
-    } //-- void deleteWrapAlignment() 
-
-    /**
-     * Method deleteXpos
-     * 
-     */
-    public void deleteXpos()
-    {
-        this._has_xpos= false;
-    } //-- void deleteXpos() 
-
-    /**
-     * Method deleteYpos
-     * 
-     */
-    public void deleteYpos()
-    {
-        this._has_ypos= false;
-    } //-- void deleteYpos() 
-
-    /**
-     * Returns the value of field 'bgColour'.
-     * 
-     * @return String
-     * @return the value of field 'bgColour'.
-     */
-    public java.lang.String getBgColour()
-    {
-        return this._bgColour;
-    } //-- java.lang.String getBgColour() 
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'consThreshold'.
-     */
-    public int getConsThreshold()
-    {
-        return this._consThreshold;
-    } //-- int getConsThreshold() 
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return boolean
-     * @return the value of field 'conservationSelected'.
-     */
-    public boolean getConservationSelected()
-    {
-        return this._conservationSelected;
-    } //-- boolean getConservationSelected() 
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return String
-     * @return the value of field 'fontName'.
-     */
-    public java.lang.String getFontName()
-    {
-        return this._fontName;
-    } //-- java.lang.String getFontName() 
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return int
-     * @return the value of field 'fontSize'.
-     */
-    public int getFontSize()
-    {
-        return this._fontSize;
-    } //-- int getFontSize() 
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return int
-     * @return the value of field 'fontStyle'.
-     */
-    public int getFontStyle()
-    {
-        return this._fontStyle;
-    } //-- int getFontStyle() 
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return int
-     * @return the value of field 'height'.
-     */
-    public int getHeight()
-    {
-        return this._height;
-    } //-- int getHeight() 
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return boolean
-     * @return the value of field 'pidSelected'.
-     */
-    public boolean getPidSelected()
-    {
-        return this._pidSelected;
-    } //-- boolean getPidSelected() 
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'pidThreshold'.
-     */
-    public int getPidThreshold()
-    {
-        return this._pidThreshold;
-    } //-- int getPidThreshold() 
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return boolean
-     * @return the value of field 'renderGaps'.
-     */
-    public boolean getRenderGaps()
-    {
-        return this._renderGaps;
-    } //-- boolean getRenderGaps() 
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return boolean
-     * @return the value of field 'showAnnotation'.
-     */
-    public boolean getShowAnnotation()
-    {
-        return this._showAnnotation;
-    } //-- boolean getShowAnnotation() 
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return boolean
-     * @return the value of field 'showBoxes'.
-     */
-    public boolean getShowBoxes()
-    {
-        return this._showBoxes;
-    } //-- boolean getShowBoxes() 
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return boolean
-     * @return the value of field 'showColourText'.
-     */
-    public boolean getShowColourText()
-    {
-        return this._showColourText;
-    } //-- boolean getShowColourText() 
-
-    /**
-     * Returns the value of field 'showConservation'.
-     * 
-     * @return boolean
-     * @return the value of field 'showConservation'.
-     */
-    public boolean getShowConservation()
-    {
-        return this._showConservation;
-    } //-- boolean getShowConservation() 
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return boolean
-     * @return the value of field 'showFullId'.
-     */
-    public boolean getShowFullId()
-    {
-        return this._showFullId;
-    } //-- boolean getShowFullId() 
-
-    /**
-     * Returns the value of field 'showIdentity'.
-     * 
-     * @return boolean
-     * @return the value of field 'showIdentity'.
-     */
-    public boolean getShowIdentity()
-    {
-        return this._showIdentity;
-    } //-- boolean getShowIdentity() 
-
-    /**
-     * Returns the value of field 'showQuality'.
-     * 
-     * @return boolean
-     * @return the value of field 'showQuality'.
-     */
-    public boolean getShowQuality()
-    {
-        return this._showQuality;
-    } //-- boolean getShowQuality() 
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return boolean
-     * @return the value of field 'showSequenceFeatures'.
-     */
-    public boolean getShowSequenceFeatures()
-    {
-        return this._showSequenceFeatures;
-    } //-- boolean getShowSequenceFeatures() 
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return boolean
-     * @return the value of field 'showText'.
-     */
-    public boolean getShowText()
-    {
-        return this._showText;
-    } //-- boolean getShowText() 
-
-    /**
-     * Returns the value of field 'startRes'.
-     * 
-     * @return int
-     * @return the value of field 'startRes'.
-     */
-    public int getStartRes()
-    {
-        return this._startRes;
-    } //-- int getStartRes() 
-
-    /**
-     * Returns the value of field 'startSeq'.
-     * 
-     * @return int
-     * @return the value of field 'startSeq'.
-     */
-    public int getStartSeq()
-    {
-        return this._startSeq;
-    } //-- int getStartSeq() 
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return String
-     * @return the value of field 'title'.
-     */
-    public java.lang.String getTitle()
-    {
-        return this._title;
-    } //-- java.lang.String getTitle() 
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return int
-     * @return the value of field 'width'.
-     */
-    public int getWidth()
-    {
-        return this._width;
-    } //-- int getWidth() 
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return boolean
-     * @return the value of field 'wrapAlignment'.
-     */
-    public boolean getWrapAlignment()
-    {
-        return this._wrapAlignment;
-    } //-- boolean getWrapAlignment() 
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return int
-     * @return the value of field 'xpos'.
-     */
-    public int getXpos()
-    {
-        return this._xpos;
-    } //-- int getXpos() 
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return int
-     * @return the value of field 'ypos'.
-     */
-    public int getYpos()
-    {
-        return this._ypos;
-    } //-- int getYpos() 
-
-    /**
-     * Method hasConsThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasConsThreshold()
-    {
-        return this._has_consThreshold;
-    } //-- boolean hasConsThreshold() 
-
-    /**
-     * Method hasConservationSelected
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasConservationSelected()
-    {
-        return this._has_conservationSelected;
-    } //-- boolean hasConservationSelected() 
-
-    /**
-     * Method hasFontSize
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasFontSize()
-    {
-        return this._has_fontSize;
-    } //-- boolean hasFontSize() 
-
-    /**
-     * Method hasFontStyle
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasFontStyle()
-    {
-        return this._has_fontStyle;
-    } //-- boolean hasFontStyle() 
-
-    /**
-     * Method hasHeight
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasHeight()
-    {
-        return this._has_height;
-    } //-- boolean hasHeight() 
-
-    /**
-     * Method hasPidSelected
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasPidSelected()
-    {
-        return this._has_pidSelected;
-    } //-- boolean hasPidSelected() 
-
-    /**
-     * Method hasPidThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasPidThreshold()
-    {
-        return this._has_pidThreshold;
-    } //-- boolean hasPidThreshold() 
-
-    /**
-     * Method hasRenderGaps
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasRenderGaps()
-    {
-        return this._has_renderGaps;
-    } //-- boolean hasRenderGaps() 
-
-    /**
-     * Method hasShowAnnotation
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowAnnotation()
-    {
-        return this._has_showAnnotation;
-    } //-- boolean hasShowAnnotation() 
-
-    /**
-     * Method hasShowBoxes
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowBoxes()
-    {
-        return this._has_showBoxes;
-    } //-- boolean hasShowBoxes() 
-
-    /**
-     * Method hasShowColourText
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowColourText()
-    {
-        return this._has_showColourText;
-    } //-- boolean hasShowColourText() 
-
-    /**
-     * Method hasShowConservation
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowConservation()
-    {
-        return this._has_showConservation;
-    } //-- boolean hasShowConservation() 
-
-    /**
-     * Method hasShowFullId
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowFullId()
-    {
-        return this._has_showFullId;
-    } //-- boolean hasShowFullId() 
-
-    /**
-     * Method hasShowIdentity
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowIdentity()
-    {
-        return this._has_showIdentity;
-    } //-- boolean hasShowIdentity() 
-
-    /**
-     * Method hasShowQuality
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowQuality()
-    {
-        return this._has_showQuality;
-    } //-- boolean hasShowQuality() 
-
-    /**
-     * Method hasShowSequenceFeatures
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowSequenceFeatures()
-    {
-        return this._has_showSequenceFeatures;
-    } //-- boolean hasShowSequenceFeatures() 
-
-    /**
-     * Method hasShowText
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowText()
-    {
-        return this._has_showText;
-    } //-- boolean hasShowText() 
-
-    /**
-     * Method hasStartRes
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStartRes()
-    {
-        return this._has_startRes;
-    } //-- boolean hasStartRes() 
-
-    /**
-     * Method hasStartSeq
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStartSeq()
-    {
-        return this._has_startSeq;
-    } //-- boolean hasStartSeq() 
-
-    /**
-     * Method hasWidth
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasWidth()
-    {
-        return this._has_width;
-    } //-- boolean hasWidth() 
-
-    /**
-     * Method hasWrapAlignment
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasWrapAlignment()
-    {
-        return this._has_wrapAlignment;
-    } //-- boolean hasWrapAlignment() 
-
-    /**
-     * Method hasXpos
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasXpos()
-    {
-        return this._has_xpos;
-    } //-- boolean hasXpos() 
-
-    /**
-     * Method hasYpos
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasYpos()
-    {
-        return this._has_ypos;
-    } //-- boolean hasYpos() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'bgColour'.
-     * 
-     * @param bgColour the value of field 'bgColour'.
-     */
-    public void setBgColour(java.lang.String bgColour)
-    {
-        this._bgColour = bgColour;
-    } //-- void setBgColour(java.lang.String) 
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(int consThreshold)
-    {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    } //-- void setConsThreshold(int) 
-
-    /**
-     * Sets the value of field 'conservationSelected'.
-     * 
-     * @param conservationSelected the value of field
-     * 'conservationSelected'.
-     */
-    public void setConservationSelected(boolean conservationSelected)
-    {
-        this._conservationSelected = conservationSelected;
-        this._has_conservationSelected = true;
-    } //-- void setConservationSelected(boolean) 
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(java.lang.String fontName)
-    {
-        this._fontName = fontName;
-    } //-- void setFontName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(int fontSize)
-    {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    } //-- void setFontSize(int) 
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(int fontStyle)
-    {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    } //-- void setFontStyle(int) 
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(int height)
-    {
-        this._height = height;
-        this._has_height = true;
-    } //-- void setHeight(int) 
-
-    /**
-     * Sets the value of field 'pidSelected'.
-     * 
-     * @param pidSelected the value of field 'pidSelected'.
-     */
-    public void setPidSelected(boolean pidSelected)
-    {
-        this._pidSelected = pidSelected;
-        this._has_pidSelected = true;
-    } //-- void setPidSelected(boolean) 
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(int pidThreshold)
-    {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    } //-- void setPidThreshold(int) 
-
-    /**
-     * Sets the value of field 'renderGaps'.
-     * 
-     * @param renderGaps the value of field 'renderGaps'.
-     */
-    public void setRenderGaps(boolean renderGaps)
-    {
-        this._renderGaps = renderGaps;
-        this._has_renderGaps = true;
-    } //-- void setRenderGaps(boolean) 
-
-    /**
-     * Sets the value of field 'showAnnotation'.
-     * 
-     * @param showAnnotation the value of field 'showAnnotation'.
-     */
-    public void setShowAnnotation(boolean showAnnotation)
-    {
-        this._showAnnotation = showAnnotation;
-        this._has_showAnnotation = true;
-    } //-- void setShowAnnotation(boolean) 
-
-    /**
-     * Sets the value of field 'showBoxes'.
-     * 
-     * @param showBoxes the value of field 'showBoxes'.
-     */
-    public void setShowBoxes(boolean showBoxes)
-    {
-        this._showBoxes = showBoxes;
-        this._has_showBoxes = true;
-    } //-- void setShowBoxes(boolean) 
-
-    /**
-     * Sets the value of field 'showColourText'.
-     * 
-     * @param showColourText the value of field 'showColourText'.
-     */
-    public void setShowColourText(boolean showColourText)
-    {
-        this._showColourText = showColourText;
-        this._has_showColourText = true;
-    } //-- void setShowColourText(boolean) 
-
-    /**
-     * Sets the value of field 'showConservation'.
-     * 
-     * @param showConservation the value of field 'showConservation'
-     */
-    public void setShowConservation(boolean showConservation)
-    {
-        this._showConservation = showConservation;
-        this._has_showConservation = true;
-    } //-- void setShowConservation(boolean) 
-
-    /**
-     * Sets the value of field 'showFullId'.
-     * 
-     * @param showFullId the value of field 'showFullId'.
-     */
-    public void setShowFullId(boolean showFullId)
-    {
-        this._showFullId = showFullId;
-        this._has_showFullId = true;
-    } //-- void setShowFullId(boolean) 
-
-    /**
-     * Sets the value of field 'showIdentity'.
-     * 
-     * @param showIdentity the value of field 'showIdentity'.
-     */
-    public void setShowIdentity(boolean showIdentity)
-    {
-        this._showIdentity = showIdentity;
-        this._has_showIdentity = true;
-    } //-- void setShowIdentity(boolean) 
-
-    /**
-     * Sets the value of field 'showQuality'.
-     * 
-     * @param showQuality the value of field 'showQuality'.
-     */
-    public void setShowQuality(boolean showQuality)
-    {
-        this._showQuality = showQuality;
-        this._has_showQuality = true;
-    } //-- void setShowQuality(boolean) 
-
-    /**
-     * Sets the value of field 'showSequenceFeatures'.
-     * 
-     * @param showSequenceFeatures the value of field
-     * 'showSequenceFeatures'.
-     */
-    public void setShowSequenceFeatures(boolean showSequenceFeatures)
-    {
-        this._showSequenceFeatures = showSequenceFeatures;
-        this._has_showSequenceFeatures = true;
-    } //-- void setShowSequenceFeatures(boolean) 
-
-    /**
-     * Sets the value of field 'showText'.
-     * 
-     * @param showText the value of field 'showText'.
-     */
-    public void setShowText(boolean showText)
-    {
-        this._showText = showText;
-        this._has_showText = true;
-    } //-- void setShowText(boolean) 
-
-    /**
-     * Sets the value of field 'startRes'.
-     * 
-     * @param startRes the value of field 'startRes'.
-     */
-    public void setStartRes(int startRes)
-    {
-        this._startRes = startRes;
-        this._has_startRes = true;
-    } //-- void setStartRes(int) 
-
-    /**
-     * Sets the value of field 'startSeq'.
-     * 
-     * @param startSeq the value of field 'startSeq'.
-     */
-    public void setStartSeq(int startSeq)
-    {
-        this._startSeq = startSeq;
-        this._has_startSeq = true;
-    } //-- void setStartSeq(int) 
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(java.lang.String title)
-    {
-        this._title = title;
-    } //-- void setTitle(java.lang.String) 
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(int width)
-    {
-        this._width = width;
-        this._has_width = true;
-    } //-- void setWidth(int) 
-
-    /**
-     * Sets the value of field 'wrapAlignment'.
-     * 
-     * @param wrapAlignment the value of field 'wrapAlignment'.
-     */
-    public void setWrapAlignment(boolean wrapAlignment)
-    {
-        this._wrapAlignment = wrapAlignment;
-        this._has_wrapAlignment = true;
-    } //-- void setWrapAlignment(boolean) 
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(int xpos)
-    {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    } //-- void setXpos(int) 
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(int ypos)
-    {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    } //-- void setYpos(int) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+public class Viewport
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _conservationSelected
+   */
+  private boolean _conservationSelected;
+
+  /**
+   * keeps track of state for field: _conservationSelected
+   */
+  private boolean _has_conservationSelected;
+
+  /**
+   * Field _pidSelected
+   */
+  private boolean _pidSelected;
+
+  /**
+   * keeps track of state for field: _pidSelected
+   */
+  private boolean _has_pidSelected;
+
+  /**
+   * Field _bgColour
+   */
+  private java.lang.String _bgColour;
+
+  /**
+   * Field _consThreshold
+   */
+  private int _consThreshold;
+
+  /**
+   * keeps track of state for field: _consThreshold
+   */
+  private boolean _has_consThreshold;
+
+  /**
+   * Field _pidThreshold
+   */
+  private int _pidThreshold;
+
+  /**
+   * keeps track of state for field: _pidThreshold
+   */
+  private boolean _has_pidThreshold;
+
+  /**
+   * Field _title
+   */
+  private java.lang.String _title;
+
+  /**
+   * Field _showFullId
+   */
+  private boolean _showFullId;
+
+  /**
+   * keeps track of state for field: _showFullId
+   */
+  private boolean _has_showFullId;
+
+  /**
+   * Field _showText
+   */
+  private boolean _showText;
+
+  /**
+   * keeps track of state for field: _showText
+   */
+  private boolean _has_showText;
+
+  /**
+   * Field _showColourText
+   */
+  private boolean _showColourText;
+
+  /**
+   * keeps track of state for field: _showColourText
+   */
+  private boolean _has_showColourText;
+
+  /**
+   * Field _showBoxes
+   */
+  private boolean _showBoxes;
+
+  /**
+   * keeps track of state for field: _showBoxes
+   */
+  private boolean _has_showBoxes;
+
+  /**
+   * Field _wrapAlignment
+   */
+  private boolean _wrapAlignment;
+
+  /**
+   * keeps track of state for field: _wrapAlignment
+   */
+  private boolean _has_wrapAlignment;
+
+  /**
+   * Field _renderGaps
+   */
+  private boolean _renderGaps;
+
+  /**
+   * keeps track of state for field: _renderGaps
+   */
+  private boolean _has_renderGaps;
+
+  /**
+   * Field _showSequenceFeatures
+   */
+  private boolean _showSequenceFeatures;
+
+  /**
+   * keeps track of state for field: _showSequenceFeatures
+   */
+  private boolean _has_showSequenceFeatures;
+
+  /**
+   * Field _showAnnotation
+   */
+  private boolean _showAnnotation;
+
+  /**
+   * keeps track of state for field: _showAnnotation
+   */
+  private boolean _has_showAnnotation;
+
+  /**
+   * Field _showConservation
+   */
+  private boolean _showConservation;
+
+  /**
+   * keeps track of state for field: _showConservation
+   */
+  private boolean _has_showConservation;
+
+  /**
+   * Field _showQuality
+   */
+  private boolean _showQuality;
+
+  /**
+   * keeps track of state for field: _showQuality
+   */
+  private boolean _has_showQuality;
+
+  /**
+   * Field _showIdentity
+   */
+  private boolean _showIdentity;
+
+  /**
+   * keeps track of state for field: _showIdentity
+   */
+  private boolean _has_showIdentity;
+
+  /**
+   * Field _xpos
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  /**
+   * Field _width
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  /**
+   * Field _startRes
+   */
+  private int _startRes;
+
+  /**
+   * keeps track of state for field: _startRes
+   */
+  private boolean _has_startRes;
+
+  /**
+   * Field _startSeq
+   */
+  private int _startSeq;
+
+  /**
+   * keeps track of state for field: _startSeq
+   */
+  private boolean _has_startSeq;
+
+  /**
+   * Field _fontName
+   */
+  private java.lang.String _fontName;
+
+  /**
+   * Field _fontSize
+   */
+  private int _fontSize;
+
+  /**
+   * keeps track of state for field: _fontSize
+   */
+  private boolean _has_fontSize;
+
+  /**
+   * Field _fontStyle
+   */
+  private int _fontStyle;
+
+  /**
+   * keeps track of state for field: _fontStyle
+   */
+  private boolean _has_fontStyle;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public Viewport()
+  {
+    super();
+  } //-- jalview.binding.Viewport()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteConsThreshold
+   *
+   */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  } //-- void deleteConsThreshold()
+
+  /**
+   * Method deleteConservationSelected
+   *
+   */
+  public void deleteConservationSelected()
+  {
+    this._has_conservationSelected = false;
+  } //-- void deleteConservationSelected()
+
+  /**
+   * Method deleteFontSize
+   *
+   */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  } //-- void deleteFontSize()
+
+  /**
+   * Method deleteFontStyle
+   *
+   */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  } //-- void deleteFontStyle()
+
+  /**
+   * Method deleteHeight
+   *
+   */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  } //-- void deleteHeight()
+
+  /**
+   * Method deletePidSelected
+   *
+   */
+  public void deletePidSelected()
+  {
+    this._has_pidSelected = false;
+  } //-- void deletePidSelected()
+
+  /**
+   * Method deletePidThreshold
+   *
+   */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  } //-- void deletePidThreshold()
+
+  /**
+   * Method deleteRenderGaps
+   *
+   */
+  public void deleteRenderGaps()
+  {
+    this._has_renderGaps = false;
+  } //-- void deleteRenderGaps()
+
+  /**
+   * Method deleteShowAnnotation
+   *
+   */
+  public void deleteShowAnnotation()
+  {
+    this._has_showAnnotation = false;
+  } //-- void deleteShowAnnotation()
+
+  /**
+   * Method deleteShowBoxes
+   *
+   */
+  public void deleteShowBoxes()
+  {
+    this._has_showBoxes = false;
+  } //-- void deleteShowBoxes()
+
+  /**
+   * Method deleteShowColourText
+   *
+   */
+  public void deleteShowColourText()
+  {
+    this._has_showColourText = false;
+  } //-- void deleteShowColourText()
+
+  /**
+   * Method deleteShowConservation
+   *
+   */
+  public void deleteShowConservation()
+  {
+    this._has_showConservation = false;
+  } //-- void deleteShowConservation()
+
+  /**
+   * Method deleteShowFullId
+   *
+   */
+  public void deleteShowFullId()
+  {
+    this._has_showFullId = false;
+  } //-- void deleteShowFullId()
+
+  /**
+   * Method deleteShowIdentity
+   *
+   */
+  public void deleteShowIdentity()
+  {
+    this._has_showIdentity = false;
+  } //-- void deleteShowIdentity()
+
+  /**
+   * Method deleteShowQuality
+   *
+   */
+  public void deleteShowQuality()
+  {
+    this._has_showQuality = false;
+  } //-- void deleteShowQuality()
+
+  /**
+   * Method deleteShowSequenceFeatures
+   *
+   */
+  public void deleteShowSequenceFeatures()
+  {
+    this._has_showSequenceFeatures = false;
+  } //-- void deleteShowSequenceFeatures()
+
+  /**
+   * Method deleteShowText
+   *
+   */
+  public void deleteShowText()
+  {
+    this._has_showText = false;
+  } //-- void deleteShowText()
+
+  /**
+   * Method deleteStartRes
+   *
+   */
+  public void deleteStartRes()
+  {
+    this._has_startRes = false;
+  } //-- void deleteStartRes()
+
+  /**
+   * Method deleteStartSeq
+   *
+   */
+  public void deleteStartSeq()
+  {
+    this._has_startSeq = false;
+  } //-- void deleteStartSeq()
+
+  /**
+   * Method deleteWidth
+   *
+   */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  } //-- void deleteWidth()
+
+  /**
+   * Method deleteWrapAlignment
+   *
+   */
+  public void deleteWrapAlignment()
+  {
+    this._has_wrapAlignment = false;
+  } //-- void deleteWrapAlignment()
+
+  /**
+   * Method deleteXpos
+   *
+   */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  } //-- void deleteXpos()
+
+  /**
+   * Method deleteYpos
+   *
+   */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  } //-- void deleteYpos()
+
+  /**
+   * Returns the value of field 'bgColour'.
+   *
+   * @return String
+   * @return the value of field 'bgColour'.
+   */
+  public java.lang.String getBgColour()
+  {
+    return this._bgColour;
+  } //-- java.lang.String getBgColour()
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   *
+   * @return int
+   * @return the value of field 'consThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  } //-- int getConsThreshold()
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   *
+   * @return boolean
+   * @return the value of field 'conservationSelected'.
+   */
+  public boolean getConservationSelected()
+  {
+    return this._conservationSelected;
+  } //-- boolean getConservationSelected()
+
+  /**
+   * Returns the value of field 'fontName'.
+   *
+   * @return String
+   * @return the value of field 'fontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  } //-- java.lang.String getFontName()
+
+  /**
+   * Returns the value of field 'fontSize'.
+   *
+   * @return int
+   * @return the value of field 'fontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  } //-- int getFontSize()
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   *
+   * @return int
+   * @return the value of field 'fontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  } //-- int getFontStyle()
+
+  /**
+   * Returns the value of field 'height'.
+   *
+   * @return int
+   * @return the value of field 'height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  } //-- int getHeight()
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   *
+   * @return boolean
+   * @return the value of field 'pidSelected'.
+   */
+  public boolean getPidSelected()
+  {
+    return this._pidSelected;
+  } //-- boolean getPidSelected()
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   *
+   * @return int
+   * @return the value of field 'pidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  } //-- int getPidThreshold()
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   *
+   * @return boolean
+   * @return the value of field 'renderGaps'.
+   */
+  public boolean getRenderGaps()
+  {
+    return this._renderGaps;
+  } //-- boolean getRenderGaps()
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   *
+   * @return boolean
+   * @return the value of field 'showAnnotation'.
+   */
+  public boolean getShowAnnotation()
+  {
+    return this._showAnnotation;
+  } //-- boolean getShowAnnotation()
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   *
+   * @return boolean
+   * @return the value of field 'showBoxes'.
+   */
+  public boolean getShowBoxes()
+  {
+    return this._showBoxes;
+  } //-- boolean getShowBoxes()
+
+  /**
+   * Returns the value of field 'showColourText'.
+   *
+   * @return boolean
+   * @return the value of field 'showColourText'.
+   */
+  public boolean getShowColourText()
+  {
+    return this._showColourText;
+  } //-- boolean getShowColourText()
+
+  /**
+   * Returns the value of field 'showConservation'.
+   *
+   * @return boolean
+   * @return the value of field 'showConservation'.
+   */
+  public boolean getShowConservation()
+  {
+    return this._showConservation;
+  } //-- boolean getShowConservation()
+
+  /**
+   * Returns the value of field 'showFullId'.
+   *
+   * @return boolean
+   * @return the value of field 'showFullId'.
+   */
+  public boolean getShowFullId()
+  {
+    return this._showFullId;
+  } //-- boolean getShowFullId()
+
+  /**
+   * Returns the value of field 'showIdentity'.
+   *
+   * @return boolean
+   * @return the value of field 'showIdentity'.
+   */
+  public boolean getShowIdentity()
+  {
+    return this._showIdentity;
+  } //-- boolean getShowIdentity()
+
+  /**
+   * Returns the value of field 'showQuality'.
+   *
+   * @return boolean
+   * @return the value of field 'showQuality'.
+   */
+  public boolean getShowQuality()
+  {
+    return this._showQuality;
+  } //-- boolean getShowQuality()
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   *
+   * @return boolean
+   * @return the value of field 'showSequenceFeatures'.
+   */
+  public boolean getShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  } //-- boolean getShowSequenceFeatures()
+
+  /**
+   * Returns the value of field 'showText'.
+   *
+   * @return boolean
+   * @return the value of field 'showText'.
+   */
+  public boolean getShowText()
+  {
+    return this._showText;
+  } //-- boolean getShowText()
+
+  /**
+   * Returns the value of field 'startRes'.
+   *
+   * @return int
+   * @return the value of field 'startRes'.
+   */
+  public int getStartRes()
+  {
+    return this._startRes;
+  } //-- int getStartRes()
+
+  /**
+   * Returns the value of field 'startSeq'.
+   *
+   * @return int
+   * @return the value of field 'startSeq'.
+   */
+  public int getStartSeq()
+  {
+    return this._startSeq;
+  } //-- int getStartSeq()
+
+  /**
+   * Returns the value of field 'title'.
+   *
+   * @return String
+   * @return the value of field 'title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  } //-- java.lang.String getTitle()
+
+  /**
+   * Returns the value of field 'width'.
+   *
+   * @return int
+   * @return the value of field 'width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  } //-- int getWidth()
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   *
+   * @return boolean
+   * @return the value of field 'wrapAlignment'.
+   */
+  public boolean getWrapAlignment()
+  {
+    return this._wrapAlignment;
+  } //-- boolean getWrapAlignment()
+
+  /**
+   * Returns the value of field 'xpos'.
+   *
+   * @return int
+   * @return the value of field 'xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  } //-- int getXpos()
+
+  /**
+   * Returns the value of field 'ypos'.
+   *
+   * @return int
+   * @return the value of field 'ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  } //-- int getYpos()
+
+  /**
+   * Method hasConsThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  } //-- boolean hasConsThreshold()
+
+  /**
+   * Method hasConservationSelected
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasConservationSelected()
+  {
+    return this._has_conservationSelected;
+  } //-- boolean hasConservationSelected()
+
+  /**
+   * Method hasFontSize
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  } //-- boolean hasFontSize()
+
+  /**
+   * Method hasFontStyle
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  } //-- boolean hasFontStyle()
+
+  /**
+   * Method hasHeight
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  } //-- boolean hasHeight()
+
+  /**
+   * Method hasPidSelected
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasPidSelected()
+  {
+    return this._has_pidSelected;
+  } //-- boolean hasPidSelected()
+
+  /**
+   * Method hasPidThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  } //-- boolean hasPidThreshold()
+
+  /**
+   * Method hasRenderGaps
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasRenderGaps()
+  {
+    return this._has_renderGaps;
+  } //-- boolean hasRenderGaps()
+
+  /**
+   * Method hasShowAnnotation
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowAnnotation()
+  {
+    return this._has_showAnnotation;
+  } //-- boolean hasShowAnnotation()
+
+  /**
+   * Method hasShowBoxes
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowBoxes()
+  {
+    return this._has_showBoxes;
+  } //-- boolean hasShowBoxes()
+
+  /**
+   * Method hasShowColourText
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowColourText()
+  {
+    return this._has_showColourText;
+  } //-- boolean hasShowColourText()
+
+  /**
+   * Method hasShowConservation
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowConservation()
+  {
+    return this._has_showConservation;
+  } //-- boolean hasShowConservation()
+
+  /**
+   * Method hasShowFullId
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowFullId()
+  {
+    return this._has_showFullId;
+  } //-- boolean hasShowFullId()
+
+  /**
+   * Method hasShowIdentity
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowIdentity()
+  {
+    return this._has_showIdentity;
+  } //-- boolean hasShowIdentity()
+
+  /**
+   * Method hasShowQuality
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowQuality()
+  {
+    return this._has_showQuality;
+  } //-- boolean hasShowQuality()
+
+  /**
+   * Method hasShowSequenceFeatures
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowSequenceFeatures()
+  {
+    return this._has_showSequenceFeatures;
+  } //-- boolean hasShowSequenceFeatures()
+
+  /**
+   * Method hasShowText
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowText()
+  {
+    return this._has_showText;
+  } //-- boolean hasShowText()
+
+  /**
+   * Method hasStartRes
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasStartRes()
+  {
+    return this._has_startRes;
+  } //-- boolean hasStartRes()
+
+  /**
+   * Method hasStartSeq
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasStartSeq()
+  {
+    return this._has_startSeq;
+  } //-- boolean hasStartSeq()
+
+  /**
+   * Method hasWidth
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  } //-- boolean hasWidth()
+
+  /**
+   * Method hasWrapAlignment
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasWrapAlignment()
+  {
+    return this._has_wrapAlignment;
+  } //-- boolean hasWrapAlignment()
+
+  /**
+   * Method hasXpos
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  } //-- boolean hasXpos()
+
+  /**
+   * Method hasYpos
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  } //-- boolean hasYpos()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'bgColour'.
+   *
+   * @param bgColour the value of field 'bgColour'.
+   */
+  public void setBgColour(java.lang.String bgColour)
+  {
+    this._bgColour = bgColour;
+  } //-- void setBgColour(java.lang.String)
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   *
+   * @param consThreshold the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  } //-- void setConsThreshold(int)
+
+  /**
+   * Sets the value of field 'conservationSelected'.
+   *
+   * @param conservationSelected the value of field
+   * 'conservationSelected'.
+   */
+  public void setConservationSelected(boolean conservationSelected)
+  {
+    this._conservationSelected = conservationSelected;
+    this._has_conservationSelected = true;
+  } //-- void setConservationSelected(boolean)
+
+  /**
+   * Sets the value of field 'fontName'.
+   *
+   * @param fontName the value of field 'fontName'.
+   */
+  public void setFontName(java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  } //-- void setFontName(java.lang.String)
+
+  /**
+   * Sets the value of field 'fontSize'.
+   *
+   * @param fontSize the value of field 'fontSize'.
+   */
+  public void setFontSize(int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  } //-- void setFontSize(int)
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   *
+   * @param fontStyle the value of field 'fontStyle'.
+   */
+  public void setFontStyle(int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  } //-- void setFontStyle(int)
+
+  /**
+   * Sets the value of field 'height'.
+   *
+   * @param height the value of field 'height'.
+   */
+  public void setHeight(int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  } //-- void setHeight(int)
+
+  /**
+   * Sets the value of field 'pidSelected'.
+   *
+   * @param pidSelected the value of field 'pidSelected'.
+   */
+  public void setPidSelected(boolean pidSelected)
+  {
+    this._pidSelected = pidSelected;
+    this._has_pidSelected = true;
+  } //-- void setPidSelected(boolean)
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   *
+   * @param pidThreshold the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  } //-- void setPidThreshold(int)
+
+  /**
+   * Sets the value of field 'renderGaps'.
+   *
+   * @param renderGaps the value of field 'renderGaps'.
+   */
+  public void setRenderGaps(boolean renderGaps)
+  {
+    this._renderGaps = renderGaps;
+    this._has_renderGaps = true;
+  } //-- void setRenderGaps(boolean)
+
+  /**
+   * Sets the value of field 'showAnnotation'.
+   *
+   * @param showAnnotation the value of field 'showAnnotation'.
+   */
+  public void setShowAnnotation(boolean showAnnotation)
+  {
+    this._showAnnotation = showAnnotation;
+    this._has_showAnnotation = true;
+  } //-- void setShowAnnotation(boolean)
+
+  /**
+   * Sets the value of field 'showBoxes'.
+   *
+   * @param showBoxes the value of field 'showBoxes'.
+   */
+  public void setShowBoxes(boolean showBoxes)
+  {
+    this._showBoxes = showBoxes;
+    this._has_showBoxes = true;
+  } //-- void setShowBoxes(boolean)
+
+  /**
+   * Sets the value of field 'showColourText'.
+   *
+   * @param showColourText the value of field 'showColourText'.
+   */
+  public void setShowColourText(boolean showColourText)
+  {
+    this._showColourText = showColourText;
+    this._has_showColourText = true;
+  } //-- void setShowColourText(boolean)
+
+  /**
+   * Sets the value of field 'showConservation'.
+   *
+   * @param showConservation the value of field 'showConservation'
+   */
+  public void setShowConservation(boolean showConservation)
+  {
+    this._showConservation = showConservation;
+    this._has_showConservation = true;
+  } //-- void setShowConservation(boolean)
+
+  /**
+   * Sets the value of field 'showFullId'.
+   *
+   * @param showFullId the value of field 'showFullId'.
+   */
+  public void setShowFullId(boolean showFullId)
+  {
+    this._showFullId = showFullId;
+    this._has_showFullId = true;
+  } //-- void setShowFullId(boolean)
+
+  /**
+   * Sets the value of field 'showIdentity'.
+   *
+   * @param showIdentity the value of field 'showIdentity'.
+   */
+  public void setShowIdentity(boolean showIdentity)
+  {
+    this._showIdentity = showIdentity;
+    this._has_showIdentity = true;
+  } //-- void setShowIdentity(boolean)
+
+  /**
+   * Sets the value of field 'showQuality'.
+   *
+   * @param showQuality the value of field 'showQuality'.
+   */
+  public void setShowQuality(boolean showQuality)
+  {
+    this._showQuality = showQuality;
+    this._has_showQuality = true;
+  } //-- void setShowQuality(boolean)
+
+  /**
+   * Sets the value of field 'showSequenceFeatures'.
+   *
+   * @param showSequenceFeatures the value of field
+   * 'showSequenceFeatures'.
+   */
+  public void setShowSequenceFeatures(boolean showSequenceFeatures)
+  {
+    this._showSequenceFeatures = showSequenceFeatures;
+    this._has_showSequenceFeatures = true;
+  } //-- void setShowSequenceFeatures(boolean)
+
+  /**
+   * Sets the value of field 'showText'.
+   *
+   * @param showText the value of field 'showText'.
+   */
+  public void setShowText(boolean showText)
+  {
+    this._showText = showText;
+    this._has_showText = true;
+  } //-- void setShowText(boolean)
+
+  /**
+   * Sets the value of field 'startRes'.
+   *
+   * @param startRes the value of field 'startRes'.
+   */
+  public void setStartRes(int startRes)
+  {
+    this._startRes = startRes;
+    this._has_startRes = true;
+  } //-- void setStartRes(int)
+
+  /**
+   * Sets the value of field 'startSeq'.
+   *
+   * @param startSeq the value of field 'startSeq'.
+   */
+  public void setStartSeq(int startSeq)
+  {
+    this._startSeq = startSeq;
+    this._has_startSeq = true;
+  } //-- void setStartSeq(int)
+
+  /**
+   * Sets the value of field 'title'.
+   *
+   * @param title the value of field 'title'.
+   */
+  public void setTitle(java.lang.String title)
+  {
+    this._title = title;
+  } //-- void setTitle(java.lang.String)
+
+  /**
+   * Sets the value of field 'width'.
+   *
+   * @param width the value of field 'width'.
+   */
+  public void setWidth(int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  } //-- void setWidth(int)
+
+  /**
+   * Sets the value of field 'wrapAlignment'.
+   *
+   * @param wrapAlignment the value of field 'wrapAlignment'.
+   */
+  public void setWrapAlignment(boolean wrapAlignment)
+  {
+    this._wrapAlignment = wrapAlignment;
+    this._has_wrapAlignment = true;
+  } //-- void setWrapAlignment(boolean)
+
+  /**
+   * Sets the value of field 'xpos'.
+   *
+   * @param xpos the value of field 'xpos'.
+   */
+  public void setXpos(int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  } //-- void setXpos(int)
+
+  /**
+   * Sets the value of field 'ypos'.
+   *
+   * @param ypos the value of field 'ypos'.
+   */
+  public void setYpos(int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  } //-- void setYpos(int)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.
+        Viewport.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 817472a..28849b6 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,21 +1,21 @@
 /*
-* 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
-*/
+ * 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.datamodel;
 
 import jalview.analysis.*;
@@ -27,33 +27,56 @@ import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
-public class Alignment implements AlignmentI {
+public class Alignment implements AlignmentI
+{
     protected Vector sequences;
     protected Vector groups = new Vector();
     protected Vector superGroup = new Vector();
     protected char gapCharacter = '-';
+
+    /** DOCUMENT ME!! */
     public AlignmentAnnotation[] annotations;
+
+    /** DOCUMENT ME!! */
     public boolean featuresAdded = false;
 
     /** Make an alignment from an array of Sequences.
-    *
-    * @param sequences
-    */
-    public Alignment(SequenceI[] seqs) {
+     *
+     * @param sequences
+     */
+    public Alignment(SequenceI[] seqs)
+    {
         sequences = new Vector();
 
         for (int i = 0; i < seqs.length; i++)
+        {
             sequences.addElement(seqs[i]);
+        }
 
         getWidth();
     }
 
-    public Vector getSequences() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getSequences()
+    {
         return sequences;
     }
 
-    public SequenceI getSequenceAt(int i) {
-        if (i < sequences.size()) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getSequenceAt(int i)
+    {
+        if (i < sequences.size())
+        {
             return (SequenceI) sequences.elementAt(i);
         }
 
@@ -64,75 +87,73 @@ public class Alignment implements AlignmentI {
      *
      * @param snew
      */
-    public void addSequence(SequenceI snew) {
+    public void addSequence(SequenceI snew)
+    {
         sequences.addElement(snew);
     }
 
-    public void addSequence(SequenceI[] seq) {
-        for (int i = 0; i < seq.length; i++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void addSequence(SequenceI[] seq)
+    {
+        for (int i = 0; i < seq.length; i++)
+        {
             addSequence(seq[i]);
         }
     }
 
     /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-      *
+     *
      * @param snew
      */
-    public void setSequenceAt(int i, SequenceI snew) {
+    public void setSequenceAt(int i, SequenceI snew)
+    {
         SequenceI oldseq = getSequenceAt(i);
         deleteSequence(oldseq);
 
         sequences.setElementAt(snew, i);
     }
 
-    public Vector getGroups() {
-        return groups;
-    }
-
-    /** Sorts the sequences by sequence group size - largest to smallest.
-     * Uses QuickSort.
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
      */
-    public void sortGroups() {
-        float[] arr = new float[groups.size()];
-        Object[] s = new Object[groups.size()];
-
-        for (int i = 0; i < groups.size(); i++) {
-            arr[i] = ((SequenceGroup) groups.elementAt(i)).sequences.size();
-            s[i] = groups.elementAt(i);
-        }
-
-        QuickSort.sort(arr, s);
-
-        Vector newg = new Vector(groups.size());
-
-        for (int i = groups.size() - 1; i >= 0; i--) {
-            newg.addElement(s[i]);
-        }
-
-        groups = newg;
+    public Vector getGroups()
+    {
+        return groups;
     }
 
     /** Takes out columns consisting entirely of gaps (-,.," ")
      */
-    public void removeGaps() {
+    public void removeGaps()
+    {
         SequenceI current;
         int iSize = getWidth();
 
-        for (int i = 0; i < iSize; i++) {
+        for (int i = 0; i < iSize; i++)
+        {
             boolean delete = true;
 
-            for (int j = 0; j < getHeight(); j++) {
+            for (int j = 0; j < getHeight(); j++)
+            {
                 current = getSequenceAt(j);
 
-                if (current.getLength() > i) {
+                if (current.getLength() > i)
+                {
                     /* MC Should move this to a method somewhere */
-                    if (!jalview.util.Comparison.isGap(current.getCharAt(i))) {
+                    if (!jalview.util.Comparison.isGap(current.getCharAt(i)))
+                    {
                         delete = false;
                     }
                 }
             }
 
-            if (delete) {
+            if (delete)
+            {
                 deleteColumns(i, i);
                 iSize--;
                 i--;
@@ -140,59 +161,44 @@ public class Alignment implements AlignmentI {
         }
     }
 
-    /** Returns an array of Sequences containing columns
-     * start to end (inclusive) only.
-     *
-     * @param start start column to fetch
-     * @param end end column to fetch
-     * @return Array of Sequences, ready to put into a new Alignment
-     */
-    public SequenceI[] getColumns(int start, int end) {
-        return getColumns(0, getHeight() - 1, start, end);
-    }
-
     /** Removes a range of columns (start to end inclusive).
      *
      * @param start Start column in the alignment
      * @param end End column in the alignment
      */
-    public void deleteColumns(int start, int end) {
+    public void deleteColumns(int start, int end)
+    {
         deleteColumns(0, getHeight() - 1, start, end);
     }
 
-    public void deleteColumns(int seq1, int seq2, int start, int end) {
-        for (int i = 0; i <= (end - start); i++) {
-            for (int j = seq1; j <= seq2; j++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq1 DOCUMENT ME!
+     * @param seq2 DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public void deleteColumns(int seq1, int seq2, int start, int end)
+    {
+        for (int i = 0; i <= (end - start); i++)
+        {
+            for (int j = seq1; j <= seq2; j++)
+            {
                 getSequenceAt(j).deleteCharAt(start);
             }
         }
     }
 
-    public void insertColumns(SequenceI[] seqs, int pos) {
-        if (seqs.length == getHeight()) {
-            for (int i = 0; i < getHeight(); i++) {
-                String tmp = new String(getSequenceAt(i).getSequence());
-                getSequenceAt(i).setSequence(tmp.substring(0, pos) +
-                    seqs[i].getSequence() + tmp.substring(pos));
-            }
-        }
-    }
-
-    public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {
-        SequenceI[] seqs = new Sequence[(seq2 - seq1) + 1];
-
-        for (int i = seq1; i <= seq2; i++) {
-            seqs[i] = new Sequence(getSequenceAt(i).getName(),
-                    getSequenceAt(i).getSequence().substring(start, end),
-                    getSequenceAt(i).findPosition(start),
-                    getSequenceAt(i).findPosition(end));
-        }
-
-        return seqs;
-    }
-
-    public void trimLeft(int i) {
-        for (int j = 0; j < getHeight(); j++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void trimLeft(int i)
+    {
+        for (int j = 0; j < getHeight(); j++)
+        {
             SequenceI s = getSequenceAt(j);
             int newstart = s.findPosition(i);
 
@@ -201,8 +207,15 @@ public class Alignment implements AlignmentI {
         }
     }
 
-    public void trimRight(int i) {
-        for (int j = 0; j < getHeight(); j++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void trimRight(int i)
+    {
+        for (int j = 0; j < getHeight(); j++)
+        {
             SequenceI s = getSequenceAt(j);
             int newend = s.findPosition(i);
 
@@ -211,36 +224,67 @@ public class Alignment implements AlignmentI {
         }
     }
 
-    public void deleteSequence(SequenceI s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     */
+    public void deleteSequence(SequenceI s)
+    {
         for (int i = 0; i < getHeight(); i++)
-            if (getSequenceAt(i) == s) {
+        {
+            if (getSequenceAt(i) == s)
+            {
                 deleteSequence(i);
             }
+        }
     }
 
-    public void deleteSequence(int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void deleteSequence(int i)
+    {
         sequences.removeElementAt(i);
     }
 
-    public Vector removeRedundancy(float threshold, Vector sel) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param threshold DOCUMENT ME!
+     * @param sel DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector removeRedundancy(float threshold, Vector sel)
+    {
         Vector del = new Vector();
 
-        for (int i = 1; i < sel.size(); i++) {
-            for (int j = 0; j < i; j++) {
+        for (int i = 1; i < sel.size(); i++)
+        {
+            for (int j = 0; j < i; j++)
+            {
                 // Only do the comparison if either have not been deleted
                 if (!del.contains((SequenceI) sel.elementAt(i)) ||
-                        !del.contains((SequenceI) sel.elementAt(j))) {
+                        !del.contains((SequenceI) sel.elementAt(j)))
+                {
                     // use PID instead of Comparison (which is really not pleasant)
                     float pid = Comparison.PID((SequenceI) sel.elementAt(j),
                             (SequenceI) sel.elementAt(i));
 
-                    if (pid >= threshold) {
+                    if (pid >= threshold)
+                    {
                         // Delete the shortest one
                         if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel
                                                                                          .elementAt(
-                                    i)).getSequence().length()) {
+                                    i)).getSequence().length())
+                        {
                             del.addElement(sel.elementAt(i));
-                        } else {
+                        }
+                        else
+                        {
                             del.addElement(sel.elementAt(i));
                         }
                     }
@@ -250,78 +294,28 @@ public class Alignment implements AlignmentI {
 
         // Now delete the sequences
         for (int i = 0; i < del.size(); i++)
+        {
             deleteSequence((SequenceI) del.elementAt(i));
-
-        return del;
-    }
-
-    public void sortByPID(SequenceI s) {
-        float[] scores = new float[getHeight()];
-        SequenceI[] seqs = new SequenceI[getHeight()];
-
-        for (int i = 0; i < getHeight(); i++) {
-            scores[i] = Comparison.compare(getSequenceAt(i), s);
-            seqs[i] = getSequenceAt(i);
         }
 
-        QuickSort.sort(scores, 0, scores.length - 1, seqs);
-
-        int len = 0;
-
-        if ((getHeight() % 2) == 0) {
-            len = getHeight() / 2;
-        } else {
-            len = (getHeight() + 1) / 2;
-        }
-
-        for (int i = 0; i < len; i++) {
-            SequenceI tmp = seqs[i];
-            sequences.setElementAt(seqs[getHeight() - i - 1], i);
-            sequences.setElementAt(tmp, getHeight() - i - 1);
-        }
-    }
-
-    public void sortByID() {
-        String[] ids = new String[getHeight()];
-        SequenceI[] seqs = new SequenceI[getHeight()];
-
-        for (int i = 0; i < getHeight(); i++) {
-            ids[i] = getSequenceAt(i).getName();
-            seqs[i] = getSequenceAt(i);
-        }
-
-        QuickSort.sort(ids, seqs);
-
-        int len = 0;
-
-        if ((getHeight() % 2) == 0) {
-            len = getHeight() / 2;
-        } else {
-            len = (getHeight() + 1) / 2;
-            System.out.println("DEBUG:Sort len is odd = " + len); // log.
-        }
-
-        for (int i = 0; i < len; i++) {
-            System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " +
-                seqs[getHeight() - i - 1].getName()); // log.
-
-            SequenceI tmp = seqs[i];
-            sequences.setElementAt(seqs[getHeight() - i - 1], i);
-            sequences.setElementAt(tmp, getHeight() - i - 1);
-        }
+        return del;
     }
 
     /**    */
-    public SequenceGroup findGroup(int i) {
+    public SequenceGroup findGroup(int i)
+    {
         return findGroup(getSequenceAt(i));
     }
 
     /**    */
-    public SequenceGroup findGroup(SequenceI s) {
-        for (int i = 0; i < this.groups.size(); i++) {
+    public SequenceGroup findGroup(SequenceI s)
+    {
+        for (int i = 0; i < this.groups.size(); i++)
+        {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-            if (sg.sequences.contains(s)) {
+            if (sg.sequences.contains(s))
+            {
                 return sg;
             }
         }
@@ -329,13 +323,23 @@ public class Alignment implements AlignmentI {
         return null;
     }
 
-    public SequenceGroup[] findAllGroups(SequenceI s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceGroup[] findAllGroups(SequenceI s)
+    {
         Vector temp = new Vector();
 
-        for (int i = 0; i < this.groups.size(); i++) {
+        for (int i = 0; i < this.groups.size(); i++)
+        {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-            if (sg.sequences.contains(s)) {
+            if (sg.sequences.contains(s))
+            {
                 temp.addElement(sg);
             }
         }
@@ -343,44 +347,48 @@ public class Alignment implements AlignmentI {
         SequenceGroup[] ret = new SequenceGroup[temp.size()];
 
         for (int i = 0; i < temp.size(); i++)
+        {
             ret[i] = (SequenceGroup) temp.elementAt(i);
-
-        return ret;
-    }
-
-    /**    */
-    public void addToGroup(SequenceGroup g, SequenceI s) {
-        if (!(g.sequences.contains(s))) {
-            g.sequences.addElement(s);
         }
-    }
 
-    /**    */
-    public void removeFromGroup(SequenceGroup g, SequenceI s) {
-        if ((g != null) && (g.sequences != null)) {
-            if (g.sequences.contains(s)) {
-                g.sequences.removeElement(s);
-
-                if (g.sequences.size() == 0) {
-                    groups.removeElement(g);
-                }
-            }
-        }
+        return ret;
     }
 
-    public void addSuperGroup(SuperGroup sg) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void addSuperGroup(SuperGroup sg)
+    {
         superGroup.addElement(sg);
     }
 
-    public void removeSuperGroup(SuperGroup sg) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void removeSuperGroup(SuperGroup sg)
+    {
         superGroup.removeElement(sg);
     }
 
-    public SuperGroup getSuperGroup(SequenceGroup sg) {
-        for (int i = 0; i < this.superGroup.size(); i++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SuperGroup getSuperGroup(SequenceGroup sg)
+    {
+        for (int i = 0; i < this.superGroup.size(); i++)
+        {
             SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
 
-            if (temp.sequenceGroups.contains(sg)) {
+            if (temp.sequenceGroups.contains(sg))
+            {
                 return temp;
             }
         }
@@ -389,19 +397,26 @@ public class Alignment implements AlignmentI {
     }
 
     /**    */
-    public void addGroup(SequenceGroup sg) {
-        if (!groups.contains(sg)) {
+    public void addGroup(SequenceGroup sg)
+    {
+        if (!groups.contains(sg))
+        {
             groups.addElement(sg);
         }
     }
 
-    public void deleteAllGroups() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void deleteAllGroups()
+    {
         groups.removeAllElements();
         superGroup.removeAllElements();
 
         int i = 0;
 
-        while (i < sequences.size()) {
+        while (i < sequences.size())
+        {
             SequenceI s = getSequenceAt(i);
             s.setColor(java.awt.Color.white);
             i++;
@@ -409,20 +424,25 @@ public class Alignment implements AlignmentI {
     }
 
     /**    */
-    public void deleteGroup(SequenceGroup g) {
-        if (groups.contains(g)) {
+    public void deleteGroup(SequenceGroup g)
+    {
+        if (groups.contains(g))
+        {
             groups.removeElement(g);
         }
     }
 
     /**    */
-    public SequenceI findName(String name) {
+    public SequenceI findName(String name)
+    {
         int i = 0;
 
-        while (i < sequences.size()) {
+        while (i < sequences.size())
+        {
             SequenceI s = getSequenceAt(i);
 
-            if (s.getName().equals(name)) {
+            if (s.getName().equals(name))
+            {
                 return s;
             }
 
@@ -433,13 +453,16 @@ public class Alignment implements AlignmentI {
     }
 
     /**    */
-    public SequenceI findbyDisplayId(String name) {
+    public SequenceI findbyDisplayId(String name)
+    {
         int i = 0;
 
-        while (i < sequences.size()) {
+        while (i < sequences.size())
+        {
             SequenceI s = getSequenceAt(i);
 
-            if (s.getDisplayId().equals(name)) {
+            if (s.getDisplayId().equals(name))
+            {
                 return s;
             }
 
@@ -450,11 +473,14 @@ public class Alignment implements AlignmentI {
     }
 
     /**    */
-    public int findIndex(SequenceI s) {
+    public int findIndex(SequenceI s)
+    {
         int i = 0;
 
-        while (i < sequences.size()) {
-            if (s == getSequenceAt(i)) {
+        while (i < sequences.size())
+        {
+            if (s == getSequenceAt(i))
+            {
                 return i;
             }
 
@@ -464,15 +490,29 @@ public class Alignment implements AlignmentI {
         return -1;
     }
 
-    public int getHeight() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getHeight()
+    {
         return sequences.size();
     }
 
-    public int getWidth() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWidth()
+    {
         int maxLength = -1;
 
-        for (int i = 0; i < sequences.size(); i++) {
-            if (getSequenceAt(i).getLength() > maxLength) {
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            if (getSequenceAt(i).getLength() > maxLength)
+            {
                 maxLength = getSequenceAt(i).getLength();
             }
         }
@@ -480,16 +520,24 @@ public class Alignment implements AlignmentI {
         return maxLength;
     }
 
-    public int getMaxIdLength() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMaxIdLength()
+    {
         int max = 0;
         int i = 0;
 
-        while (i < sequences.size()) {
+        while (i < sequences.size())
+        {
             SequenceI seq = getSequenceAt(i);
             String tmp = seq.getName() + "/" + seq.getStart() + "-" +
                 seq.getEnd();
 
-            if (tmp.length() > max) {
+            if (tmp.length() > max)
+            {
                 max = tmp.length();
             }
 
@@ -499,10 +547,17 @@ public class Alignment implements AlignmentI {
         return max;
     }
 
-    public void setGapCharacter(char gc) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gc DOCUMENT ME!
+     */
+    public void setGapCharacter(char gc)
+    {
         gapCharacter = gc;
 
-        for (int i = 0; i < sequences.size(); i++) {
+        for (int i = 0; i < sequences.size(); i++)
+        {
             Sequence seq = (Sequence) sequences.elementAt(i);
             seq.sequence = seq.sequence.replace('.', gc);
             seq.sequence = seq.sequence.replace('-', gc);
@@ -510,29 +565,57 @@ public class Alignment implements AlignmentI {
         }
     }
 
-    public char getGapCharacter() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getGapCharacter()
+    {
         return gapCharacter;
     }
 
-    public Vector getAAFrequency() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getAAFrequency()
+    {
         return AAFrequency.calculate(sequences, 0, getWidth());
     }
 
-    public boolean isAligned() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean isAligned()
+    {
         int width = getWidth();
 
         for (int i = 0; i < sequences.size(); i++)
-            if (getSequenceAt(i).getLength() != width) {
+        {
+            if (getSequenceAt(i).getLength() != width)
+            {
                 return false;
             }
+        }
 
         return true;
     }
 
-    public void deleteAnnotation(AlignmentAnnotation aa) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     */
+    public void deleteAnnotation(AlignmentAnnotation aa)
+    {
         int aSize = 1;
 
-        if (annotations != null) {
+        if (annotations != null)
+        {
             aSize = annotations.length;
         }
 
@@ -540,8 +623,10 @@ public class Alignment implements AlignmentI {
 
         int tIndex = 0;
 
-        for (int i = 0; i < aSize; i++) {
-            if (annotations[i] == aa) {
+        for (int i = 0; i < aSize; i++)
+        {
+            if (annotations[i] == aa)
+            {
                 continue;
             }
 
@@ -552,19 +637,29 @@ public class Alignment implements AlignmentI {
         annotations = temp;
     }
 
-    public void addAnnotation(AlignmentAnnotation aa) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     */
+    public void addAnnotation(AlignmentAnnotation aa)
+    {
         int aSize = 1;
 
-        if (annotations != null) {
+        if (annotations != null)
+        {
             aSize = annotations.length + 1;
         }
 
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
         int i = 0;
 
-        if (aSize > 1) {
+        if (aSize > 1)
+        {
             for (i = 0; i < (aSize - 1); i++)
+            {
                 temp[i] = annotations[i];
+            }
         }
 
         temp[i] = aa;
@@ -572,7 +667,13 @@ public class Alignment implements AlignmentI {
         annotations = temp;
     }
 
-    public AlignmentAnnotation[] getAlignmentAnnotation() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public AlignmentAnnotation[] getAlignmentAnnotation()
+    {
         return annotations;
     }
 }
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 35297b5..9cfdff6 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -18,63 +18,121 @@
 */
 package jalview.datamodel;
 
-public class AlignmentAnnotation {
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentAnnotation
+{
+    /** DOCUMENT ME!! */
     public String label;
+
+    /** DOCUMENT ME!! */
     public String description;
+
+    /** DOCUMENT ME!! */
     public Annotation[] annotations;
+
+    /** DOCUMENT ME!! */
     public boolean isGraph = false;
+
+    /** DOCUMENT ME!! */
     public float graphMin;
+
+    /** DOCUMENT ME!! */
     public float graphMax;
+
+    /** DOCUMENT ME!! */
     public int windowLength;
 
     // Graphical hints and tips
+
+    /** DOCUMENT ME!! */
     public boolean editable = false;
+
+    /** DOCUMENT ME!! */
     public boolean hasIcons; //
+
+    /** DOCUMENT ME!! */
     public boolean hasText;
+
+    /** DOCUMENT ME!! */
     public boolean visible = true;
+
+    /** DOCUMENT ME!! */
     public int height = 0;
 
+    /**
+     * Creates a new AlignmentAnnotation object.
+     *
+     * @param label DOCUMENT ME!
+     * @param description DOCUMENT ME!
+     * @param annotations DOCUMENT ME!
+     */
     public AlignmentAnnotation(String label, String description,
-        Annotation[] annotations) {
+        Annotation[] annotations)
+    {
         // always editable?
         editable = true;
         this.label = label;
         this.description = description;
         this.annotations = annotations;
 
-        for (int i = 0; i < annotations.length; i++) {
+        for (int i = 0; i < annotations.length; i++)
+        {
             if ((annotations[i] != null) &&
                     ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E'))) {
+                    (annotations[i].secondaryStructure == 'E')))
+            {
                 hasIcons = true;
             }
 
             if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0)) {
+                    (annotations[i].displayCharacter.length() > 0))
+            {
                 hasText = true;
             }
         }
     }
 
+    /**
+     * Creates a new AlignmentAnnotation object.
+     *
+     * @param label DOCUMENT ME!
+     * @param description DOCUMENT ME!
+     * @param annotations DOCUMENT ME!
+     * @param min DOCUMENT ME!
+     * @param max DOCUMENT ME!
+     * @param winLength DOCUMENT ME!
+     */
     public AlignmentAnnotation(String label, String description,
-        Annotation[] annotations, float min, float max, int winLength) {
+        Annotation[] annotations, float min, float max, int winLength)
+    {
         // graphs are not editable
         this.label = label;
         this.description = description;
         this.annotations = annotations;
         isGraph = true;
 
-        if (min == max) {
-            for (int i = 0; i < annotations.length; i++) {
-                if (annotations[i] == null) {
+        if (min == max)
+        {
+            for (int i = 0; i < annotations.length; i++)
+            {
+                if (annotations[i] == null)
+                {
                     continue;
                 }
 
-                if (annotations[i].value > max) {
+                if (annotations[i].value > max)
+                {
                     max = annotations[i].value;
                 }
 
-                if (annotations[i].value < min) {
+                if (annotations[i].value < min)
+                {
                     min = annotations[i].value;
                 }
             }
@@ -84,30 +142,46 @@ public class AlignmentAnnotation {
         graphMax = max;
         windowLength = winLength;
 
-        for (int i = 0; i < annotations.length; i++) {
+        for (int i = 0; i < annotations.length; i++)
+        {
             if ((annotations[i] != null) &&
                     ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E'))) {
+                    (annotations[i].secondaryStructure == 'E')))
+            {
                 hasIcons = true;
             }
 
             if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0)) {
+                    (annotations[i].displayCharacter.length() > 0))
+            {
                 hasText = true;
             }
         }
     }
 
-    public String toString() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String toString()
+    {
         StringBuffer buffer = new StringBuffer();
 
-        for (int i = 0; i < annotations.length; i++) {
-            if (annotations[i] != null) {
-                if (isGraph) {
+        for (int i = 0; i < annotations.length; i++)
+        {
+            if (annotations[i] != null)
+            {
+                if (isGraph)
+                {
                     buffer.append(annotations[i].value);
-                } else if (hasIcons) {
+                }
+                else if (hasIcons)
+                {
                     buffer.append(annotations[i].secondaryStructure);
-                } else {
+                }
+                else
+                {
                     buffer.append(annotations[i].displayCharacter);
                 }
             }
@@ -115,11 +189,14 @@ public class AlignmentAnnotation {
             buffer.append(", ");
         }
 
-        if (label.equals("Consensus")) {
+        if (label.equals("Consensus"))
+        {
             buffer.append("\n");
 
-            for (int i = 0; i < annotations.length; i++) {
-                if (annotations[i] != null) {
+            for (int i = 0; i < annotations.length; i++)
+            {
+                if (annotations[i] != null)
+                {
                     buffer.append(annotations[i].description);
                 }
 
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 8a14a08..416be69 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -23,94 +23,270 @@ import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
-public interface AlignmentI {
+public interface AlignmentI
+{
+    /**
+     *  Calculates the number of sequences in an alignment
+     *
+     * @return Number of sequences in alignment
+     */
     public int getHeight();
 
+    /**
+     * Calculates the maximum width of the alignment, including gaps.
+     *
+     * @return Greatest sequence length within alignment.
+     */
     public int getWidth();
 
+    /**
+     * Calculates the longest sequence Id of the alignment
+     *
+     * @return Number of characters in longest sequence Id.
+     */
     public int getMaxIdLength();
 
+    /**
+     * Calculates if this set of sequences is all the same length
+     *
+     * @return true if all sequences in alignment are the same length
+     */
     public boolean isAligned();
 
+    /**
+     * Gets sequences as a Vector
+     *
+     * @return All sequences in alignment.
+     */
     public Vector getSequences();
 
+    /**
+     * Find a specific sequence in this alignment.
+     *
+     * @param i Index of required sequence.
+     *
+     * @return SequenceI at given index.
+     */
     public SequenceI getSequenceAt(int i);
 
+    /**
+     * Add a new sequence to this alignment.
+     *
+     * @param seq New sequence will be added at end of alignment.
+     */
     public void addSequence(SequenceI seq);
 
+    /**
+     * Used to set a particular index of the alignment with the given sequence.
+     *
+     * @param i Index of sequence to be updated.
+     * @param seq New sequence to be inserted.
+     */
     public void setSequenceAt(int i, SequenceI seq);
 
+    /**
+     * Deletes a sequence from the alignment.
+     *
+     * @param s Sequence to be deleted.
+     */
     public void deleteSequence(SequenceI s);
 
+    /**
+     * Deletes a sequence from the alignment.
+     *
+     * @param i Index of sequence to be deleted.
+     */
     public void deleteSequence(int i);
 
-    public SequenceI[] getColumns(int start, int end);
-
-    public SequenceI[] getColumns(int seq1, int seq2, int start, int end);
-
+    /**
+     * Deletes all residues in every sequence of alignment within given columns.
+     *
+     * @param start Start index of columns to delete.
+     * @param end End index to columns to delete.
+     */
     public void deleteColumns(int start, int end);
 
+    /**
+     * Deletes all residues in every sequence of alignment within given columns.
+     *
+     * @param seq1 Index of first sequence to delete columns from.
+     * @param seq2 Index of last sequence to delete columns from.
+     * @param start Start index of columns to delete.
+     * @param end End index of columns to delete.
+     */
     public void deleteColumns(int seq1, int seq2, int start, int end);
 
-    public void insertColumns(SequenceI[] seqs, int pos);
-
+    /**
+     * Finds sequence in alignment using sequence name as query.
+     *
+     * @param name Id of sequence to search for.
+     *
+     * @return Sequence matching query, if found. If not found returns null.
+     */
     public SequenceI findName(String name);
 
+    /**
+     * Finds sequence in alignment using full displayId as query.
+     *
+     * @param name displayId, ie <em>NAME/25-100</em>
+     *
+     * @return Sequence matching query, if found. If not found returns null.
+     */
     public SequenceI findbyDisplayId(String name);
 
+    /**
+     * Finds index of a given sequence in the alignment.
+     *
+     * @param s Sequence to look for.
+     *
+     * @return Index of sequence within the alignment.
+     */
     public int findIndex(SequenceI s);
 
-    // Modifying
+    /**
+    * All sequences will be cut from beginning to given index.
+    *
+    * @param i Remove all residues in sequences up to this column.
+     */
     public void trimLeft(int i);
 
+    /**
+     * All sequences will be cut from given index.
+     *
+     * @param i Remove all residues in sequences beyond this column.
+     */
     public void trimRight(int i);
 
+    /**
+     * Removes all columns containing entirely gap characters.
+     */
     public void removeGaps();
 
+    /**
+     * Removes redundant sequences from alignment.
+     *
+     * @param threshold Remove all sequences above the given threshold.
+     * @param sel Set of sequences which will have redundant sequences removed from.
+     *
+     * @return All sequences below redundancy threshold.
+     */
     public Vector removeRedundancy(float threshold, Vector sel);
 
-    // Grouping methods
+    /**
+     * Finds group that sequence at index i in alignment is part of.
+     *
+     * @param i Index in alignment.
+     *
+     * @return First group found for sequence at position i. WARNING :
+     * Sequences may be members of several groups. This method is incomplete.
+     */
     public SequenceGroup findGroup(int i);
 
+    /**
+     * Finds group that given sequence is part of.
+     *
+     * @param s Sequence in alignment.
+     *
+     * @return First group found for sequence. WARNING :
+     * Sequences may be members of several groups. This method is incomplete.
+     */
     public SequenceGroup findGroup(SequenceI s);
 
+    /**
+     * Finds all groups that a given sequence is part of.
+     *
+     * @param s Sequence in alignment.
+     *
+     * @return All groups containing given sequence.
+     */
     public SequenceGroup[] findAllGroups(SequenceI s);
 
-    public void addToGroup(SequenceGroup g, SequenceI s);
-
-    public void removeFromGroup(SequenceGroup g, SequenceI s);
-
+    /**
+     * Adds a new SequenceGroup to this alignment.
+     *
+     * @param sg New group to be added.
+     */
     public void addGroup(SequenceGroup sg);
 
+    /**
+     * Deletes a specific SequenceGroup
+     *
+     * @param g Group will be deleted from alignment.
+     */
     public void deleteGroup(SequenceGroup g);
 
+    /**
+     * Get all the groups associated with this alignment.
+     *
+     * @return All groups as a Vector.
+     */
     public Vector getGroups();
 
+    /**
+     * Deletes all groups from this alignment.
+     */
     public void deleteAllGroups();
 
+    /**
+     * Adds a super group. A SuperGroup is a group of groups.
+     *
+     * @param sg Adds a new SuperGroup to alignment
+     */
     public void addSuperGroup(SuperGroup sg);
 
+    /**
+     * Removes SuperGroup from alignment.
+     *
+     * @param sg This SuperGroup will be deleted from alignment.
+     */
     public void removeSuperGroup(SuperGroup sg);
 
+    /**
+     * Finds any SuperGroup that a given SequenceGroup may be part of.
+     *
+     * @param sg SequenceGroup to search for.
+     *
+     * @return SuperGroup that contains the given SequenceGroup.
+     */
     public SuperGroup getSuperGroup(SequenceGroup sg);
 
-    // Sorting
-    public void sortGroups();
-
-    public void sortByPID(SequenceI s);
-
-    public void sortByID();
-
-    //Annotations
+    /**
+     * Adds a new AlignmentAnnotation to this alignment
+     */
     public void addAnnotation(AlignmentAnnotation aa);
 
+    /**
+     * Deletes a specific AlignmentAnnotation from the alignment.
+     *
+     * @param aa DOCUMENT ME!
+     */
     public void deleteAnnotation(AlignmentAnnotation aa);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public AlignmentAnnotation[] getAlignmentAnnotation();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gc DOCUMENT ME!
+     */
     public void setGapCharacter(char gc);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public char getGapCharacter();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public Vector getAAFrequency();
 }
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index c0da1fc..1fa3b96 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,125 +1,184 @@
-/*
-* 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
-*/
+/*
+ * 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.datamodel;
 
 import java.util.*;
 
 
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
  */
-public class AlignmentOrder {
+public class AlignmentOrder
+{
     // JBPNote : this method would return a vector containing all sequences in seqset
     // with those also contained in order at the beginning of the vector in the order
     // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method
     // should be here for completeness.
 
-    /*  public Vector getOrder(AlignmentI seqset)
-  {
-    Vector perm = new Vector(seqset.getHeight());
-    for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)
-      perm.setElement(i,...).
-    return Order;
-  }
- */
+    /*  public Vector getOrder(AlignmentI seqset)
+       {
+         Vector perm = new Vector(seqset.getHeight());
+         for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)
+      perm.setElement(i,...).
+         return Order;
+       }
+     */
+
+    /** DOCUMENT ME!! */
     public static final int FILE = 0;
+
+    /** DOCUMENT ME!! */
     public static final int MSA = 1;
+
+    /** DOCUMENT ME!! */
     public static final int USER = 2;
     private int Type = 0;
     private String Name;
     private Vector Order = null;
 
-    public AlignmentOrder() {
+    /**
+     * Creates a new AlignmentOrder object.
+     */
+    public AlignmentOrder()
+    {
     }
 
-    /**
- * AlignmentOrder
- *
- * @param anOrder Vector
- */
-    public AlignmentOrder(Vector anOrder) {
+    /**
+     * AlignmentOrder
+     *
+     * @param anOrder Vector
+     */
+    public AlignmentOrder(Vector anOrder)
+    {
         Order = anOrder;
     }
 
-    /**
- * AlignmentOrder
- *
- * @param orderFrom AlignmentI
- */
-    public AlignmentOrder(AlignmentI orderFrom) {
+    /**
+     * AlignmentOrder
+     *
+     * @param orderFrom AlignmentI
+     */
+    public AlignmentOrder(AlignmentI orderFrom)
+    {
         Order = new Vector();
 
         for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
+        {
             Order.addElement(orderFrom.getSequenceAt(i));
+        }
     }
 
-    public AlignmentOrder(SequenceI[] orderFrom) {
+    /**
+     * Creates a new AlignmentOrder object.
+     *
+     * @param orderFrom DOCUMENT ME!
+     */
+    public AlignmentOrder(SequenceI[] orderFrom)
+    {
         Order = new Vector();
 
         for (int i = 0, ns = orderFrom.length; i < ns; i++)
+        {
             Order.addElement(orderFrom[i]);
+        }
     }
 
-    public void setType(int Type) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Type DOCUMENT ME!
+     */
+    public void setType(int Type)
+    {
         this.Type = Type;
     }
 
-    public int getType() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getType()
+    {
         return Type;
     }
 
-    public void setName(String Name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Name DOCUMENT ME!
+     */
+    public void setName(String Name)
+    {
         this.Name = Name;
     }
 
-    public String getName() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
         return Name;
     }
 
-    public void setOrder(Vector Order) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Order DOCUMENT ME!
+     */
+    public void setOrder(Vector Order)
+    {
         this.Order = Order;
     }
 
-    public Vector getOrder() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getOrder()
+    {
         return Order;
     }
 
-    /**
- * AlignmentOrder
- *
- * @param orderThis AlignmentI
- * @param byThat AlignmentI
- */
+    /**
+     * AlignmentOrder
+     *
+     * @param orderThis AlignmentI
+     * @param byThat AlignmentI
+     */
+
+    /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
+     {
+       // Vector is an ordering of this alignment using the order of sequence objects in byThat,
+       // where ids and unaligned sequences must match
 
-    /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
-{
-  // Vector is an ordering of this alignment using the order of sequence objects in byThat,
-  // where ids and unaligned sequences must match
-
-} */
+     } */
 }
diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 7858e3f..2316d13 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -21,24 +21,59 @@ package jalview.datamodel;
 import java.awt.*;
 
 
-public class Annotation {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Annotation
+{
+    /** DOCUMENT ME!! */
     public String displayCharacter = "";
+
+    /** DOCUMENT ME!! */
     public String description = ""; // currently used as mouse over
+
+    /** DOCUMENT ME!! */
     public char secondaryStructure = ' '; // recognises H and E
+
+    /** DOCUMENT ME!! */
     public float value;
 
     // add visual cues here
+
+    /** DOCUMENT ME!! */
     public Color colour = Color.black;
 
-    public Annotation(String displayChar, String desc, char ss, float val) {
+    /**
+     * Creates a new Annotation object.
+     *
+     * @param displayChar DOCUMENT ME!
+     * @param desc DOCUMENT ME!
+     * @param ss DOCUMENT ME!
+     * @param val DOCUMENT ME!
+     */
+    public Annotation(String displayChar, String desc, char ss, float val)
+    {
         displayCharacter = displayChar;
         description = desc;
         secondaryStructure = ss;
         value = val;
     }
 
+    /**
+     * Creates a new Annotation object.
+     *
+     * @param displayChar DOCUMENT ME!
+     * @param desc DOCUMENT ME!
+     * @param ss DOCUMENT ME!
+     * @param val DOCUMENT ME!
+     * @param colour DOCUMENT ME!
+     */
     public Annotation(String displayChar, String desc, char ss, float val,
-        Color colour) {
+        Color colour)
+    {
         this(displayChar, desc, ss, val);
         this.colour = colour;
     }
diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 850730b..cbec833 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,37 +1,58 @@
-/*
-* 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
-*/
+/*
+ * 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.datamodel;
 
-public class BinaryNode {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BinaryNode
+{
     Object element;
     String name;
     BinaryNode left;
     BinaryNode right;
     BinaryNode parent;
+
+    /** DOCUMENT ME!! */
     public int bootstrap;
 
-    public BinaryNode() {
+    /**
+     * Creates a new BinaryNode object.
+     */
+    public BinaryNode()
+    {
         left = right = parent = null;
         bootstrap = 0;
     }
 
-    public BinaryNode(Object element, BinaryNode parent, String name) {
+    /**
+     * Creates a new BinaryNode object.
+     *
+     * @param element DOCUMENT ME!
+     * @param parent DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     */
+    public BinaryNode(Object element, BinaryNode parent, String name)
+    {
         this.element = element;
         this.parent = parent;
         this.name = name;
@@ -39,72 +60,143 @@ public class BinaryNode {
         left = right = null;
     }
 
-    public Object element() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object element()
+    {
         return element;
     }
 
-    public Object setElement(Object v) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object setElement(Object v)
+    {
         return element = v;
     }
 
-    public BinaryNode left() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode left()
+    {
         return left;
     }
 
-    public BinaryNode setLeft(BinaryNode n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setLeft(BinaryNode n)
+    {
         return left = n;
     }
 
-    public BinaryNode right() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode right()
+    {
         return right;
     }
 
-    public BinaryNode setRight(BinaryNode n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setRight(BinaryNode n)
+    {
         return right = n;
     }
 
-    public BinaryNode parent() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode parent()
+    {
         return parent;
     }
 
-    public BinaryNode setParent(BinaryNode n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setParent(BinaryNode n)
+    {
         return parent = n;
     }
 
-    public boolean isLeaf() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean isLeaf()
+    {
         return (left == null) && (right == null);
     }
 
-    /**
- * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)
- * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to  NULL - you  should use
- * setChild(null), or detach() for this.
- *
- */
-    public void SetChildren(BinaryNode leftchild, BinaryNode rightchild) {
-        if (leftchild != null) {
+    /**
+     * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)
+     * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to  NULL - you  should use
+     * setChild(null), or detach() for this.
+     *
+     */
+    public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+    {
+        if (leftchild != null)
+        {
             this.setLeft(leftchild);
             leftchild.detach();
             leftchild.setParent(this);
         }
 
-        if (rightchild != null) {
+        if (rightchild != null)
+        {
             this.setRight(rightchild);
             rightchild.detach();
             rightchild.setParent(this);
         }
     }
 
-    /**
- * Detaches the node from the binary tree, along with all its child nodes.
- * @return BinaryNode The detached node.
- */
-    public BinaryNode detach() {
-        if (this.parent != null) {
-            if (this.parent.left == this) {
+    /**
+     * Detaches the node from the binary tree, along with all its child nodes.
+     * @return BinaryNode The detached node.
+     */
+    public BinaryNode detach()
+    {
+        if (this.parent != null)
+        {
+            if (this.parent.left == this)
+            {
                 this.parent.left = null;
-            } else {
-                if (this.parent.right == this) {
+            }
+            else
+            {
+                if (this.parent.right == this)
+                {
                     this.parent.right = null;
                 }
             }
@@ -115,48 +207,78 @@ public class BinaryNode {
         return this;
     }
 
-    /**
- * Traverses up through the tree until a node with a free leftchild is discovered.
- * @return BinaryNode
- */
-    public BinaryNode ascendLeft() {
+    /**
+     * Traverses up through the tree until a node with a free leftchild is discovered.
+     * @return BinaryNode
+     */
+    public BinaryNode ascendLeft()
+    {
         BinaryNode c = this;
 
-        do {
+        do
+        {
             c = c.parent();
-        } while ((c != null) && (c.left() != null) && !c.left().isLeaf());
+        }
+        while ((c != null) && (c.left() != null) && !c.left().isLeaf());
 
         return c;
     }
 
-    /**
- * Traverses up through the tree until a node with a free rightchild is discovered.
- * Jalview builds trees by descent on the left, so this may be unused.
- * @return BinaryNode
- */
-    public BinaryNode ascendRight() {
+    /**
+     * Traverses up through the tree until a node with a free rightchild is discovered.
+     * Jalview builds trees by descent on the left, so this may be unused.
+     * @return BinaryNode
+     */
+    public BinaryNode ascendRight()
+    {
         BinaryNode c = this;
 
-        do {
+        do
+        {
             c = c.parent();
-        } while ((c != null) && (c.right() != null) && !c.right().isLeaf());
+        }
+        while ((c != null) && (c.right() != null) && !c.right().isLeaf());
 
         return c;
     }
 
-    public void setName(String name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
         this.name = name;
     }
 
-    public String getName() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
         return this.name;
     }
 
-    public void setBootstrap(int boot) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param boot DOCUMENT ME!
+     */
+    public void setBootstrap(int boot)
+    {
         this.bootstrap = boot;
     }
 
-    public int getBootstrap() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getBootstrap()
+    {
         return bootstrap;
     }
 }
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index a351b04..3cc6910 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -29,40 +29,72 @@ import jalview.schemes.*;
 import java.awt.*;
 
 
-public class BinarySequence extends Sequence {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BinarySequence extends Sequence
+{
     int[] binary;
     double[] dbinary;
 
-    public BinarySequence(SequenceI s) {
+    /**
+     * Creates a new BinarySequence object.
+     *
+     * @param s DOCUMENT ME!
+     */
+    public BinarySequence(SequenceI s)
+    {
         super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());
     }
 
-    public BinarySequence(String name, String sequence, int start, int end) {
+    /**
+     * Creates a new BinarySequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public BinarySequence(String name, String sequence, int start, int end)
+    {
         super(name, sequence, start, end);
     }
 
-    public void encode() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void encode()
+    {
         // Set all matrix to 0
         dbinary = new double[getSequence().length() * 21];
 
         int nores = 21;
 
-        for (int i = 0; i < dbinary.length; i++) {
+        for (int i = 0; i < dbinary.length; i++)
+        {
             dbinary[i] = 0.0;
         }
 
-        for (int i = 0; i < getSequence().length(); i++) {
+        for (int i = 0; i < getSequence().length(); i++)
+        {
             int aanum = 20;
 
-            try {
+            try
+            {
                 aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
                                                                          .substring(i,
                             i + 1))).intValue();
-            } catch (NullPointerException e) {
+            }
+            catch (NullPointerException e)
+            {
                 aanum = 20;
             }
 
-            if (aanum > 20) {
+            if (aanum > 20)
+            {
                 aanum = 20;
             }
 
@@ -70,7 +102,11 @@ public class BinarySequence extends Sequence {
         }
     }
 
-    public void blosumEncode() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void blosumEncode()
+    {
         // Set all matrix to 0
         dbinary = new double[getSequence().length() * 21];
 
@@ -79,35 +115,49 @@ public class BinarySequence extends Sequence {
         //for (int i = 0; i < dbinary.length; i++) {
         //  dbinary[i] = 0.0;
         //}
-        for (int i = 0; i < getSequence().length(); i++) {
+        for (int i = 0; i < getSequence().length(); i++)
+        {
             int aanum = 20;
 
-            try {
+            try
+            {
                 aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
                                                                          .substring(i,
                             i + 1))).intValue();
-            } catch (NullPointerException e) {
+            }
+            catch (NullPointerException e)
+            {
                 aanum = 20;
             }
 
-            if (aanum > 20) {
+            if (aanum > 20)
+            {
                 aanum = 20;
             }
 
             // Do the blosum thing
-            for (int j = 0; j < 20; j++) {
+            for (int j = 0; j < 20; j++)
+            {
                 dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];
             }
         }
     }
 
-    public String toBinaryString() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String toBinaryString()
+    {
         String out = "";
 
-        for (int i = 0; i < binary.length; i++) {
+        for (int i = 0; i < binary.length; i++)
+        {
             out += (new Integer(binary[i])).toString();
 
-            if (i < (binary.length - 1)) {
+            if (i < (binary.length - 1))
+            {
                 out += " ";
             }
         }
@@ -115,11 +165,23 @@ public class BinarySequence extends Sequence {
         return out;
     }
 
-    public double[] getDBinary() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public double[] getDBinary()
+    {
         return dbinary;
     }
 
-    public static void printMemory(Runtime rt) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param rt DOCUMENT ME!
+     */
+    public static void printMemory(Runtime rt)
+    {
         System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.
     }
 }
diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java
index ed119e8..eb4979d 100755
--- a/src/jalview/datamodel/HistoryItem.java
+++ b/src/jalview/datamodel/HistoryItem.java
@@ -21,10 +21,24 @@ package jalview.datamodel;
 import java.util.*;
 
 
-public class HistoryItem {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class HistoryItem
+{
+    /** DOCUMENT ME!! */
     public static final int EDIT = 0;
+
+    /** DOCUMENT ME!! */
     public static final int SORT = 1;
+
+    /** DOCUMENT ME!! */
     public static final int HIDE = 2;
+
+    /** DOCUMENT ME!! */
     public static final int PASTE = 3;
     final int type;
     Vector sequences;
@@ -32,14 +46,23 @@ public class HistoryItem {
     String description;
     Vector hiddenSeqs;
 
-    public HistoryItem(String description, AlignmentI al, int type) {
+    /**
+     * Creates a new HistoryItem object.
+     *
+     * @param description DOCUMENT ME!
+     * @param al DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     */
+    public HistoryItem(String description, AlignmentI al, int type)
+    {
         this.type = type;
         this.description = description;
         sequences = new Vector();
         alignIndex = new Vector();
         hiddenSeqs = new Vector();
 
-        for (int i = 0; i < al.getHeight(); i++) {
+        for (int i = 0; i < al.getHeight(); i++)
+        {
             SequenceI seq = al.getSequenceAt(i);
             sequences.addElement(seq);
             alignIndex.addElement(i + "");
@@ -47,23 +70,55 @@ public class HistoryItem {
         }
     }
 
-    public int getType() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getType()
+    {
         return type;
     }
 
-    public Vector getSequences() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getSequences()
+    {
         return sequences;
     }
 
-    public String getDescription() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDescription()
+    {
         return description;
     }
 
-    public Vector getHidden() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getHidden()
+    {
         return hiddenSeqs;
     }
 
-    public int getAlignIndex(int seq) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getAlignIndex(int seq)
+    {
         return Integer.parseInt(alignIndex.elementAt(seq).toString());
     }
 }
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 3853af9..34c1cd9 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -27,7 +27,14 @@ import java.awt.*;
 import java.util.*;
 
 
-public class Sequence implements SequenceI {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence implements SequenceI
+{
     protected String name;
     protected String sequence;
     protected String description;
@@ -36,9 +43,20 @@ public class Sequence implements SequenceI {
     protected String displayId;
     protected Color color = Color.white;
     String pdbId;
+
+    /** DOCUMENT ME!! */
     public Vector sequenceFeatures = new Vector();
 
-    public Sequence(String name, String sequence, int start, int end) {
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public Sequence(String name, String sequence, int start, int end)
+    {
         this.name = name;
         this.sequence = sequence;
         this.start = start;
@@ -47,137 +65,295 @@ public class Sequence implements SequenceI {
         setDisplayId();
     }
 
-    public Sequence(String name, String sequence) {
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     */
+    public Sequence(String name, String sequence)
+    {
         this(name, sequence, 1, sequence.length());
     }
 
-    public Sequence(SequenceI seq) {
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public Sequence(SequenceI seq)
+    {
         this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
     }
 
-    public void setSequenceFeatures(Vector v) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     */
+    public void setSequenceFeatures(Vector v)
+    {
         sequenceFeatures = v;
     }
 
-    public Vector getSequenceFeatures() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getSequenceFeatures()
+    {
         return sequenceFeatures;
     }
 
-    public void setPDBId(String id) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
+    public void setPDBId(String id)
+    {
         pdbId = id;
     }
 
-    public String getPDBId() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getPDBId()
+    {
         return pdbId;
     }
 
-    public String getDisplayId() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDisplayId()
+    {
         return displayId;
     }
 
-    public void setDisplayId() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void setDisplayId()
+    {
         displayId = name + "/" + start + "-" + end;
     }
 
-    public void setName(String name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
         this.name = name;
         setDisplayId();
     }
 
-    public String getName() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
         return this.name;
     }
 
-    public void setStart(int start) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     */
+    public void setStart(int start)
+    {
         this.start = start;
         setDisplayId();
     }
 
-    public int getStart() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStart()
+    {
         return this.start;
     }
 
-    public void setEnd(int end) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param end DOCUMENT ME!
+     */
+    public void setEnd(int end)
+    {
         this.end = end;
         setDisplayId();
     }
 
-    public int getEnd() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEnd()
+    {
         return this.end;
     }
 
-    public int getLength() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getLength()
+    {
         return this.sequence.length();
     }
 
-    public void setSequence(String seq) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setSequence(String seq)
+    {
         this.sequence = seq;
     }
 
-    public String getSequence() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence()
+    {
         return this.sequence;
     }
 
-    public String getSequence(int start, int end) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence(int start, int end)
+    {
         // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
-        if (start >= sequence.length()) {
+        if (start >= sequence.length())
+        {
             return "";
         }
 
-        if (end >= sequence.length()) {
+        if (end >= sequence.length())
+        {
             end = sequence.length();
         }
 
         return this.sequence.substring(start, end);
     }
 
-    public char getCharAt(int i) {
-        if (i < sequence.length()) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getCharAt(int i)
+    {
+        if (i < sequence.length())
+        {
             return sequence.charAt(i);
-        } else {
+        }
+        else
+        {
             return ' ';
         }
     }
 
-    public void setDescription(String desc) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param desc DOCUMENT ME!
+     */
+    public void setDescription(String desc)
+    {
         this.description = desc;
     }
 
-    public String getDescription() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDescription()
+    {
         return this.description;
     }
 
-    public int findIndex(int pos) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pos DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findIndex(int pos)
+    {
         // returns the alignment position for a residue
         int j = start;
         int i = 0;
 
-        while ((i < sequence.length()) && (j <= end) && (j <= pos)) {
+        while ((i < sequence.length()) && (j <= end) && (j <= pos))
+        {
             char c = sequence.charAt(i);
 
-            if (!jalview.util.Comparison.isGap((c))) {
+            if (!jalview.util.Comparison.isGap((c)))
+            {
                 j++;
             }
 
             i++;
         }
 
-        if ((j == end) && (j < pos)) {
+        if ((j == end) && (j < pos))
+        {
             return end + 1;
-        } else {
+        }
+        else
+        {
             return i;
         }
     }
 
-    public int findPosition(int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findPosition(int i)
+    {
         // Returns the sequence position for an alignment position
         int j = 0;
         int pos = start;
 
-        while ((j < i) && (j < sequence.length())) {
+        while ((j < i) && (j < sequence.length()))
+        {
             char c = sequence.charAt(j);
 
-            if (!jalview.util.Comparison.isGap((c))) {
+            if (!jalview.util.Comparison.isGap((c)))
+            {
                 pos++;
             }
 
@@ -187,15 +363,23 @@ public class Sequence implements SequenceI {
         return pos;
     }
 
-    public int[] gapMap() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] gapMap()
+    {
         // Returns an int array giving the position of each residue in the sequence in the alignment
         String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);
         int[] map = new int[seq.length()];
         int j = 0;
         int p = 0;
 
-        while (j < sequence.length()) {
-            if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {
+        while (j < sequence.length())
+        {
+            if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+            {
                 map[p++] = j;
             }
 
@@ -205,37 +389,73 @@ public class Sequence implements SequenceI {
         return map;
     }
 
-    public void deleteCharAt(int i) {
-        if (i >= sequence.length()) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void deleteCharAt(int i)
+    {
+        if (i >= sequence.length())
+        {
             return;
         }
 
         sequence = sequence.substring(0, i) + sequence.substring(i + 1);
     }
 
-    public void deleteChars(int i, int j) {
-        if (i >= sequence.length()) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void deleteChars(int i, int j)
+    {
+        if (i >= sequence.length())
+        {
             return;
         }
 
-        if (j >= sequence.length()) {
+        if (j >= sequence.length())
+        {
             sequence = sequence.substring(0, i);
-        } else {
+        }
+        else
+        {
             sequence = sequence.substring(0, i) + sequence.substring(j);
         }
     }
 
-    public void insertCharAt(int i, char c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     */
+    public void insertCharAt(int i, char c)
+    {
         insertCharAt(i, c, true);
     }
 
-    public void insertCharAt(int i, char c, boolean chop) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     * @param chop DOCUMENT ME!
+     */
+    public void insertCharAt(int i, char c, boolean chop)
+    {
         String tmp = new String(sequence);
 
-        if (i < sequence.length()) {
+        if (i < sequence.length())
+        {
             sequence = tmp.substring(0, i) + String.valueOf(c) +
                 tmp.substring(i);
-        } else {
+        }
+        else
+        {
             // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
             char[] ch = new char[(1 + i) - sequence.length()];
 
@@ -246,11 +466,23 @@ public class Sequence implements SequenceI {
         }
     }
 
-    public void setColor(Color c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setColor(Color c)
+    {
         this.color = c;
     }
 
-    public Color getColor() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color getColor()
+    {
         return color;
     }
 }
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 702af73..5bf4e88 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,35 +1,56 @@
 /*
-* 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
-*/
+ * 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.datamodel;
 
-public class SequenceFeature {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceFeature
+{
     int begin;
     int end;
     String type;
     String description;
     String status;
 
-    public SequenceFeature() {
+    /**
+     * Creates a new SequenceFeature object.
+     */
+    public SequenceFeature()
+    {
     }
 
+    /**
+     * Creates a new SequenceFeature object.
+     *
+     * @param type DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param description DOCUMENT ME!
+     * @param status DOCUMENT ME!
+     */
     public SequenceFeature(String type, int start, int end, String description,
-        String status) {
+        String status)
+    {
         this.type = type;
         this.begin = start;
         this.end = end;
@@ -37,62 +58,92 @@ public class SequenceFeature {
         this.status = status;
     }
 
-    public int getStart() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStart()
+    {
         return begin;
     }
 
-    public int getEnd() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEnd()
+    {
         return end;
     }
 
-    public String getType() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getType()
+    {
         return type;
     }
 
-    public String getDescription() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDescription()
+    {
         return description;
     }
 
-    public String getStatus() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getStatus()
+    {
         return status;
     }
 
     /*
           <xs:enumeration value="active site" />
-    <xs:enumeration value="binding site" />
-    <xs:enumeration value="calcium-binding region" />
-    <xs:enumeration value="chain" />
-    <xs:enumeration value="cross-link" />
-    <xs:enumeration value="disulfide bond" />
-    <xs:enumeration value="DNA-binding region" />
-    <xs:enumeration value="domain" />
-    <xs:enumeration value="glycosylation site" />
-    <xs:enumeration value="helix" />
-    <xs:enumeration value="initiator methionine" />
-    <xs:enumeration value="lipid moiety-binding region" />
-    <xs:enumeration value="metal ion-binding site" />
-    <xs:enumeration value="modified residue" />
-    <xs:enumeration value="mutagenesis site" />
-    <xs:enumeration value="non-consecutive residues" />
-    <xs:enumeration value="non-terminal residue" />
-    <xs:enumeration value="nucleotide phosphate-binding region" />
-    <xs:enumeration value="peptide" />
-    <xs:enumeration value="propeptide" />
-    <xs:enumeration value="repeat" />
-    <xs:enumeration value="selenocysteine" />
-    <xs:enumeration value="sequence conflict" />
-    <xs:enumeration value="sequence variant" />
-    <xs:enumeration value="signal peptide" />
-    <xs:enumeration value="similar" />
-    <xs:enumeration value="site" />
-    <xs:enumeration value="splice variant" />
-    <xs:enumeration value="strand" />
-    <xs:enumeration value="thioether bond" />
-    <xs:enumeration value="thiolester bond" />
-    <xs:enumeration value="transit peptide" />
-    <xs:enumeration value="transmembrane region" />
-    <xs:enumeration value="turn" />
-    <xs:enumeration value="unsure residue" />
-    <xs:enumeration value="zinc finger region" />
-    */
+         <xs:enumeration value="binding site" />
+         <xs:enumeration value="calcium-binding region" />
+         <xs:enumeration value="chain" />
+         <xs:enumeration value="cross-link" />
+         <xs:enumeration value="disulfide bond" />
+         <xs:enumeration value="DNA-binding region" />
+         <xs:enumeration value="domain" />
+         <xs:enumeration value="glycosylation site" />
+         <xs:enumeration value="helix" />
+         <xs:enumeration value="initiator methionine" />
+         <xs:enumeration value="lipid moiety-binding region" />
+         <xs:enumeration value="metal ion-binding site" />
+         <xs:enumeration value="modified residue" />
+         <xs:enumeration value="mutagenesis site" />
+         <xs:enumeration value="non-consecutive residues" />
+         <xs:enumeration value="non-terminal residue" />
+         <xs:enumeration value="nucleotide phosphate-binding region" />
+         <xs:enumeration value="peptide" />
+         <xs:enumeration value="propeptide" />
+         <xs:enumeration value="repeat" />
+         <xs:enumeration value="selenocysteine" />
+         <xs:enumeration value="sequence conflict" />
+         <xs:enumeration value="sequence variant" />
+         <xs:enumeration value="signal peptide" />
+         <xs:enumeration value="similar" />
+         <xs:enumeration value="site" />
+         <xs:enumeration value="splice variant" />
+         <xs:enumeration value="strand" />
+         <xs:enumeration value="thioether bond" />
+         <xs:enumeration value="thiolester bond" />
+         <xs:enumeration value="transit peptide" />
+         <xs:enumeration value="transmembrane region" />
+         <xs:enumeration value="turn" />
+         <xs:enumeration value="unsure residue" />
+         <xs:enumeration value="zinc finger region" />
+     */
 }
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index a262257..054896b 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -20,311 +20,481 @@ package jalview.datamodel;
 
 import jalview.analysis.*;
 
-import jalview.datamodel.*;
-
 import jalview.schemes.*;
 
 import java.awt.*;
 
-import java.util.Vector;
+import java.util.*;
+
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class SequenceGroup
 {
-  String groupName;
-  Conservation conserve;
-  Vector aaFrequency;
-  boolean displayBoxes;
-  boolean displayText;
-  boolean colourText;
-  public Vector sequences = new Vector();
-  int width = -1;
-  public ColourSchemeI cs;
-  int startRes = 0;
-  int endRes = 0;
-  Color outlineColour = Color.black;
-
-  public SequenceGroup()
-  {
-    groupName = "Group";
-    this.displayBoxes = true;
-    this.displayText = true;
-    this.colourText = false;
-    cs = null;
-  }
-
-  public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme,
-                       boolean displayBoxes, boolean displayText,
-                       boolean colourText,
-                       int start, int end)
-  {
-    this.sequences = sequences;
-    this.groupName = groupName;
-    this.displayBoxes = displayBoxes;
-    this.displayText = displayText;
-    this.colourText = colourText;
-    this.cs = scheme;
-    startRes = start;
-    endRes = end;
-    recalcConservation();
-  }
-
-  public SequenceGroup(String groupName, ColourSchemeI scheme,
-                       boolean displayBoxes, boolean displayText,
-                       boolean colourText,
-                       int start, int end)
-  {
-    this.groupName = groupName;
-    this.displayBoxes = displayBoxes;
-    this.displayText = displayText;
-    this.colourText = colourText;
-    this.cs = scheme;
-    startRes = start;
-    endRes = end;
-  }
-
-  public boolean adjustForRemoveLeft(int col)
-  {
-    // return value is true if the group still exists
-    if (startRes >= col)
+    String groupName;
+    Conservation conserve;
+    Vector aaFrequency;
+    boolean displayBoxes;
+    boolean displayText;
+    boolean colourText;
+
+    /** DOCUMENT ME!! */
+    public Vector sequences = new Vector();
+    int width = -1;
+
+    /** DOCUMENT ME!! */
+    public ColourSchemeI cs;
+    int startRes = 0;
+    int endRes = 0;
+    Color outlineColour = Color.black;
+
+    /**
+     * Creates a new SequenceGroup object.
+     */
+    public SequenceGroup()
     {
-      startRes = startRes - col;
+        groupName = "Group";
+        this.displayBoxes = true;
+        this.displayText = true;
+        this.colourText = false;
+        cs = null;
     }
 
-    if (endRes >= col)
+    /**
+     * Creates a new SequenceGroup object.
+     *
+     * @param sequences DOCUMENT ME!
+     * @param groupName DOCUMENT ME!
+     * @param scheme DOCUMENT ME!
+     * @param displayBoxes DOCUMENT ME!
+     * @param displayText DOCUMENT ME!
+     * @param colourText DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public SequenceGroup(Vector sequences, String groupName,
+        ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
+        boolean colourText, int start, int end)
     {
-      endRes = endRes - col;
+        this.sequences = sequences;
+        this.groupName = groupName;
+        this.displayBoxes = displayBoxes;
+        this.displayText = displayText;
+        this.colourText = colourText;
+        this.cs = scheme;
+        startRes = start;
+        endRes = end;
+        recalcConservation();
+    }
 
-      if (startRes > endRes)
-      {
-        startRes = 0;
-      }
+    /**
+     * Creates a new SequenceGroup object.
+     *
+     * @param groupName DOCUMENT ME!
+     * @param scheme DOCUMENT ME!
+     * @param displayBoxes DOCUMENT ME!
+     * @param displayText DOCUMENT ME!
+     * @param colourText DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public SequenceGroup(String groupName, ColourSchemeI scheme,
+        boolean displayBoxes, boolean displayText, boolean colourText,
+        int start, int end)
+    {
+        this.groupName = groupName;
+        this.displayBoxes = displayBoxes;
+        this.displayText = displayText;
+        this.colourText = colourText;
+        this.cs = scheme;
+        startRes = start;
+        endRes = end;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean adjustForRemoveLeft(int col)
     {
-      // must delete this group!!
-      return false;
+        // return value is true if the group still exists
+        if (startRes >= col)
+        {
+            startRes = startRes - col;
+        }
+
+        if (endRes >= col)
+        {
+            endRes = endRes - col;
+
+            if (startRes > endRes)
+            {
+                startRes = 0;
+            }
+        }
+        else
+        {
+            // must delete this group!!
+            return false;
+        }
+
+        return true;
     }
 
-    return true;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean adjustForRemoveRight(int col)
+    {
+        if (startRes > col)
+        {
+            // delete this group
+            return false;
+        }
+
+        if (endRes >= col)
+        {
+            endRes = col;
+        }
 
-  public boolean adjustForRemoveRight(int col)
-  {
-    if (startRes > col)
+        return true;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
     {
-      // delete this group
-      return false;
+        return groupName;
     }
 
-    if (endRes >= col)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
     {
-      endRes = col;
+        groupName = name;
     }
 
-    return true;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Conservation getConservation()
+    {
+        return conserve;
+    }
 
-  public String getName()
-  {
-    return groupName;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setConservation(Conservation c)
+    {
+        conserve = c;
+    }
 
-  public void setName(String name)
-  {
-    groupName = name;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void addSequence(SequenceI s, boolean recalc)
+    {
+        if (!sequences.contains(s))
+        {
+            sequences.addElement(s);
+        }
 
-  public Conservation getConservation()
-  {
-    return conserve;
-  }
+        if (recalc)
+        {
+            recalcConservation();
+        }
+    }
 
-  public void setConservation(Conservation c)
-  {
-    conserve = c;
-  }
+    /**
+     * DOCUMENT ME!
+     */
+    public void recalcConservation()
+    {
+        if (cs != null)
+        {
+            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+        }
 
-  public void addSequence(SequenceI s, boolean recalc)
-  {
-    if (!sequences.contains(s))
-      sequences.addElement(s);
+        if (cs instanceof ClustalxColourScheme)
+        {
+            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        }
 
-    if(recalc)
-      recalcConservation();
-  }
+        if (cs instanceof ConservationColourScheme)
+        {
+            Conservation c = new Conservation(groupName,
+                    ResidueProperties.propHash, 3, sequences, 0, getWidth());
+            c.calculate();
+            c.verdict(false, 25);
+
+            ConservationColourScheme ccs = (ConservationColourScheme) cs;
+            ccs.conserve = c;
+
+            if (ccs.cs instanceof ClustalxColourScheme)
+            {
+                ((ClustalxColourScheme) ccs.cs).resetClustalX(sequences,
+                    getWidth());
+            }
+        }
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void addOrRemove(SequenceI s, boolean recalc)
+    {
+        if (sequences.contains(s))
+        {
+            deleteSequence(s, recalc);
+        }
+        else
+        {
+            addSequence(s, recalc);
+        }
+    }
 
-  public void recalcConservation()
-  {
-    if (cs != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void deleteSequence(SequenceI s, boolean recalc)
     {
-      cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+        sequences.removeElement(s);
+
+        if (recalc)
+        {
+            recalcConservation();
+        }
     }
 
-    if (cs instanceof ClustalxColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartRes()
     {
-      ( (ClustalxColourScheme) cs).resetClustalX(sequences,getWidth());
+        return startRes;
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndRes()
+    {
+        return endRes;
+    }
 
-    if ( cs  instanceof ConservationColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void setStartRes(int i)
     {
-      Conservation c = new Conservation(groupName,
-                                        ResidueProperties.propHash, 3, sequences,
-                                        0, getWidth());
-      c.calculate();
-      c.verdict(false, 25);
-
-      ConservationColourScheme ccs = (ConservationColourScheme) cs;
-      ccs.conserve = c;
-      if (ccs.cs instanceof ClustalxColourScheme)
-      {
-        ( (ClustalxColourScheme) ccs.cs).resetClustalX(sequences, getWidth());
-      }
+        startRes = i;
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void setEndRes(int i)
+    {
+        endRes = i;
     }
-  }
 
-  public void addOrRemove(SequenceI s, boolean recalc)
-  {
-    if (sequences.contains(s))
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSize()
     {
-      deleteSequence(s, recalc);
+        return sequences.size();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getSequenceAt(int i)
+    {
+        return (SequenceI) sequences.elementAt(i);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setColourText(boolean state)
     {
-      addSequence(s, recalc);
+        colourText = state;
     }
-  }
-
-  public void deleteSequence(SequenceI s, boolean recalc)
-  {
-    sequences.removeElement(s);
-    if(recalc)
-      recalcConservation();
-  }
-
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  public void setStartRes(int i)
-  {
-    startRes = i;
-  }
-
-  public void setEndRes(int i)
-  {
-    endRes = i;
-  }
-
-  public int getSize()
-  {
-    return sequences.size();
-  }
-
-  public SequenceI getSequenceAt(int i)
-  {
-    return (SequenceI) sequences.elementAt(i);
-  }
-
-  public void setColourText(boolean state)
-  {
-    colourText = state;
-  }
-
-  public boolean getColourText()
-  {
-    return colourText;
-  }
-
-  public void setDisplayText(boolean state)
-  {
-    displayText = state;
-  }
-
-  public boolean getDisplayText()
-  {
-    return displayText;
-  }
-
-  public void setDisplayBoxes(boolean state)
-  {
-    displayBoxes = state;
-  }
-
-  public boolean getDisplayBoxes()
-  {
-    return displayBoxes;
-  }
-
-  public int getWidth()
-  {
-    // MC This needs to get reset when characters are inserted and deleted
-    if (sequences.size() > 0)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getColourText()
     {
-      width = ( (SequenceI) sequences.elementAt(0)).getLength();
+        return colourText;
     }
 
-    for (int i = 1; i < sequences.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setDisplayText(boolean state)
     {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
+        displayText = state;
+    }
 
-      if (seq.getLength() > width)
-      {
-        width = seq.getLength();
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getDisplayText()
+    {
+        return displayText;
     }
 
-    return width;
-  }
-
-  public void setOutlineColour(Color c)
-  {
-    outlineColour = c;
-  }
-
-  public Color getOutlineColour()
-  {
-    return outlineColour;
-  }
-
-  /**
-   *
-   * returns the sequences in the group ordered by the ordering given by al
-   *
-   * @param al Alignment
-   * @return SequenceI[]
-   */
-  public SequenceI[] getSequencesInOrder(AlignmentI al)
-  {
-    int sz = sequences.size();
-    java.util.Hashtable orderedSeqs = new java.util.Hashtable();
-    SequenceI[] seqs = new SequenceI[sz];
-
-    for (int i = 0; i < sz; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setDisplayBoxes(boolean state)
     {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
-      int index = al.findIndex(seq);
-      orderedSeqs.put(index + "", seq);
+        displayBoxes = state;
     }
 
-    int index = 0;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getDisplayBoxes()
+    {
+        return displayBoxes;
+    }
 
-    for (int i = 0; i < al.getHeight(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWidth()
     {
-        if (orderedSeqs.containsKey(i + ""))
+        // MC This needs to get reset when characters are inserted and deleted
+        if (sequences.size() > 0)
         {
-          seqs[index++] =  (SequenceI) orderedSeqs.get(i + "");
+            width = ((SequenceI) sequences.elementAt(0)).getLength();
         }
+
+        for (int i = 1; i < sequences.size(); i++)
+        {
+            SequenceI seq = (SequenceI) sequences.elementAt(i);
+
+            if (seq.getLength() > width)
+            {
+                width = seq.getLength();
+            }
+        }
+
+        return width;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setOutlineColour(Color c)
+    {
+        outlineColour = c;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color getOutlineColour()
+    {
+        return outlineColour;
     }
 
-    return seqs;
-  }
+    /**
+     *
+     * returns the sequences in the group ordered by the ordering given by al
+     *
+     * @param al Alignment
+     * @return SequenceI[]
+     */
+    public SequenceI[] getSequencesInOrder(AlignmentI al)
+    {
+        int sz = sequences.size();
+        java.util.Hashtable orderedSeqs = new java.util.Hashtable();
+        SequenceI[] seqs = new SequenceI[sz];
+
+        for (int i = 0; i < sz; i++)
+        {
+            SequenceI seq = (SequenceI) sequences.elementAt(i);
+            int index = al.findIndex(seq);
+            orderedSeqs.put(index + "", seq);
+        }
+
+        int index = 0;
+
+        for (int i = 0; i < al.getHeight(); i++)
+        {
+            if (orderedSeqs.containsKey(i + ""))
+            {
+                seqs[index++] = (SequenceI) orderedSeqs.get(i + "");
+            }
+        }
+
+        return seqs;
+    }
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f16c009..b7c9197 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,82 +1,235 @@
 /*
-* 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
-*/
+ * 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.datamodel;
 
-import jalview.jbgui.*;
-
 import java.awt.*;
 
-import java.util.Vector;
-
-
-public interface SequenceI {
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public interface SequenceI
+{
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
     public void setName(String name);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getName();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     */
     public void setStart(int start);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int getStart();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getDisplayId();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param end DOCUMENT ME!
+     */
     public void setEnd(int end);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int getEnd();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int getLength();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sequence DOCUMENT ME!
+     */
     public void setSequence(String sequence);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getSequence();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getSequence(int start, int end);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public char getCharAt(int i);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param desc DOCUMENT ME!
+     */
     public void setDescription(String desc);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getDescription();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pos DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int findIndex(int pos);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int findPosition(int i);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public int[] gapMap();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
     public void deleteChars(int i, int j);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
     public void deleteCharAt(int i);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     */
     public void insertCharAt(int i, char c);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     * @param chop DOCUMENT ME!
+     */
     public void insertCharAt(int i, char c, boolean chop);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
     public void setColor(Color c);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public Color getColor();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public Vector getSequenceFeatures();
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     */
     public void setSequenceFeatures(Vector v);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
     public void setPDBId(String id);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String getPDBId();
 }
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index f86c63e..ac2e9e2 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,46 +1,88 @@
 /*
-* 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
-*/
+ * 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.datamodel;
 
 import java.awt.*;
 
 
-public class SequenceNode extends BinaryNode {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceNode extends BinaryNode
+{
+    /** DOCUMENT ME!! */
     public float dist;
+
+    /** DOCUMENT ME!! */
     public int count;
+
+    /** DOCUMENT ME!! */
     public float height;
+
+    /** DOCUMENT ME!! */
     public float ycount;
+
+    /** DOCUMENT ME!! */
     public Color color = Color.black;
+
+    /** DOCUMENT ME!! */
     public boolean dummy = false;
     private boolean placeholder = false;
 
-    public SequenceNode() {
+    /**
+     * Creates a new SequenceNode object.
+     */
+    public SequenceNode()
+    {
         super();
     }
 
-    public SequenceNode(Object val, SequenceNode parent, float dist, String name) {
+    /**
+     * Creates a new SequenceNode object.
+     *
+     * @param val DOCUMENT ME!
+     * @param parent DOCUMENT ME!
+     * @param dist DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     */
+    public SequenceNode(Object val, SequenceNode parent, float dist, String name)
+    {
         super(val, parent, name);
         this.dist = dist;
     }
 
+    /**
+     * Creates a new SequenceNode object.
+     *
+     * @param val DOCUMENT ME!
+     * @param parent DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     * @param dist DOCUMENT ME!
+     * @param bootstrap DOCUMENT ME!
+     * @param dummy DOCUMENT ME!
+     */
     public SequenceNode(Object val, SequenceNode parent, String name,
-        float dist, int bootstrap, boolean dummy) {
+        float dist, int bootstrap, boolean dummy)
+    {
         super(val, parent, name);
         this.dist = dist;
         this.bootstrap = bootstrap;
@@ -50,25 +92,41 @@ public class SequenceNode extends BinaryNode {
     /**
      * @param dummy true if node is created for the representation of polytomous trees
      */
-    public boolean isDummy() {
+    public boolean isDummy()
+    {
         return dummy;
     }
 
     /* @param placeholder is true if the sequence refered to in the
      *  element node is not actually present in the associated alignment
      */
-    public boolean isPlaceholder() {
+    public boolean isPlaceholder()
+    {
         return placeholder;
     }
 
-    public boolean setDummy(boolean newstate) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param newstate DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean setDummy(boolean newstate)
+    {
         boolean oldstate = dummy;
         dummy = newstate;
 
         return oldstate;
     }
 
-    public void setPlaceholder(boolean Placeholder) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Placeholder DOCUMENT ME!
+     */
+    public void setPlaceholder(boolean Placeholder)
+    {
         this.placeholder = Placeholder;
     }
 
@@ -76,12 +134,15 @@ public class SequenceNode extends BinaryNode {
      * ascends the tree but doesn't stop until a non-dummy node is discovered.
      * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.
      */
-    public SequenceNode AscendTree() {
+    public SequenceNode AscendTree()
+    {
         SequenceNode c = this;
 
-        do {
+        do
+        {
             c = (SequenceNode) c.parent();
-        } while ((c != null) && c.dummy);
+        }
+        while ((c != null) && c.dummy);
 
         return c;
     }
diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index fa91e59..2c5d2a3 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,35 +1,42 @@
 /*
-* 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
-*/
+ * 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.datamodel;
 
-import java.awt.*;
-
-import java.util.*;
-
-
-public class SequencePoint {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequencePoint
+{
     // SMJS PUBLIC
+
+    /** DOCUMENT ME!! */
     public SequenceI sequence;
+
+    /** DOCUMENT ME!! */
     public float[] coord;
 
     // SMJS ENDPUBLIC
-    public SequencePoint(SequenceI sequence, float[] coord) {
+    public SequencePoint(SequenceI sequence, float[] coord)
+    {
         this.sequence = sequence;
         this.coord = coord;
     }
diff --git a/src/jalview/datamodel/SuperGroup.java b/src/jalview/datamodel/SuperGroup.java
index ad6f703..b2993b5 100755
--- a/src/jalview/datamodel/SuperGroup.java
+++ b/src/jalview/datamodel/SuperGroup.java
@@ -18,8 +18,6 @@
 */
 package jalview.datamodel;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import jalview.schemes.*;
@@ -27,15 +25,28 @@ import jalview.schemes.*;
 import java.util.*;
 
 
-public class SuperGroup {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SuperGroup
+{
     String groupName;
     boolean displayBoxes;
     boolean displayText;
     boolean colourText;
+
+    /** DOCUMENT ME!! */
     public ColourSchemeI cs;
     Vector sequenceGroups = new Vector();
 
-    public SuperGroup() {
+    /**
+     * Creates a new SuperGroup object.
+     */
+    public SuperGroup()
+    {
         groupName = "Super group";
         this.displayBoxes = true;
         this.displayText = true;
@@ -43,8 +54,18 @@ public class SuperGroup {
         cs = null;
     }
 
+    /**
+     * Creates a new SuperGroup object.
+     *
+     * @param groupName DOCUMENT ME!
+     * @param scheme DOCUMENT ME!
+     * @param displayBoxes DOCUMENT ME!
+     * @param displayText DOCUMENT ME!
+     * @param colourText DOCUMENT ME!
+     */
     public SuperGroup(String groupName, ColourSchemeI scheme,
-        boolean displayBoxes, boolean displayText, boolean colourText) {
+        boolean displayBoxes, boolean displayText, boolean colourText)
+    {
         this.groupName = groupName;
         this.displayBoxes = displayBoxes;
         this.displayText = displayText;
@@ -52,39 +73,80 @@ public class SuperGroup {
         this.cs = scheme;
     }
 
-    public String getName() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
         return groupName;
     }
 
-    public void setName(String name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
         groupName = name;
     }
 
-    public void addGroup(SequenceGroup sg) {
-        if (!sequenceGroups.contains(sg)) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void addGroup(SequenceGroup sg)
+    {
+        if (!sequenceGroups.contains(sg))
+        {
             sequenceGroups.addElement(sg);
         }
     }
 
-    public void addOrRemove(SequenceGroup sg) {
-        if (sequenceGroups.contains(sg)) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void addOrRemove(SequenceGroup sg)
+    {
+        if (sequenceGroups.contains(sg))
+        {
             deleteGroup(sg);
-        } else {
+        }
+        else
+        {
             addGroup(sg);
         }
     }
 
-    public void deleteGroup(SequenceGroup sg) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void deleteGroup(SequenceGroup sg)
+    {
         sequenceGroups.removeElement(sg);
     }
 
-    public void setSuperGroupProperties(SequenceGroup sg) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void setSuperGroupProperties(SequenceGroup sg)
+    {
         cs = sg.cs;
         colourText = sg.colourText;
         displayText = sg.displayText;
         displayBoxes = sg.displayBoxes;
 
-        for (int i = 0; i < sequenceGroups.size(); i++) {
+        for (int i = 0; i < sequenceGroups.size(); i++)
+        {
             SequenceGroup temp = (SequenceGroup) sequenceGroups.elementAt(i);
             temp.cs = sg.cs;
             temp.colourText = sg.colourText;
@@ -93,11 +155,25 @@ public class SuperGroup {
         }
     }
 
-    public int getSize() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSize()
+    {
         return sequenceGroups.size();
     }
 
-    public SequenceGroup getGroupeAt(int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceGroup getGroupeAt(int i)
+    {
         return (SequenceGroup) sequenceGroups.elementAt(i);
     }
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7499b4e..d154e2e 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -18,93 +18,185 @@
  */
 package jalview.gui;
 
-import java.beans.*;
-import java.util.*;
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
+import jalview.ws.*;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.event.*;
 import java.awt.print.*;
+
+import java.io.*;
+
+import java.beans.*;
+
+import java.util.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.ws.*;
 
-public class AlignFrame
-    extends GAlignFrame
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame extends GAlignFrame
 {
-  public static final int NEW_WINDOW_WIDTH = 700;
-  public static final int NEW_WINDOW_HEIGHT = 500;
-  final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
-  public String currentFileFormat = "Jalview";
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
-  private int treeCount = 0;
-
-  public AlignFrame(AlignmentI al)
-  {
-    viewport = new AlignViewport(al);
-
-    alignPanel = new AlignmentPanel(this, viewport);
-    alignPanel.annotationPanel.adjustPanelHeight();
-    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
-        annotationPanel.getPreferredSize());
-    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
-        getPreferredSize());
-    alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
-
-    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
-
-    addInternalFrameListener(new InternalFrameAdapter()
-    {
-      public void internalFrameActivated(InternalFrameEvent evt)
-      {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+    /** DOCUMENT ME!! */
+    public static final int NEW_WINDOW_WIDTH = 700;
+
+    /** DOCUMENT ME!! */
+    public static final int NEW_WINDOW_HEIGHT = 500;
+    final AlignmentPanel alignPanel;
+    final AlignViewport viewport;
+
+    /** DOCUMENT ME!! */
+    public String currentFileFormat = null;
+    Stack historyList = new Stack();
+    Stack redoList = new Stack();
+    private int treeCount = 0;
+
+    /**
+     * Creates a new AlignFrame object.
+     *
+     * @param al DOCUMENT ME!
+     */
+    public AlignFrame(AlignmentI al)
+    {
+        viewport = new AlignViewport(al);
+
+        alignPanel = new AlignmentPanel(this, viewport);
+        alignPanel.annotationPanel.adjustPanelHeight();
+        alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+        alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+        alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
+
+        getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+
+        addInternalFrameListener(new InternalFrameAdapter()
+            {
+                public void internalFrameActivated(InternalFrameEvent evt)
+                {
+                    javax.swing.SwingUtilities.invokeLater(new Runnable()
+                        {
+                            public void run()
+                            {
+                                alignPanel.requestFocus();
+                            }
+                        });
+                }
+            });
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void parseGroupsFile(String file)
+    {
+      try{
+        BufferedReader in = new BufferedReader(new FileReader(file));
+        SequenceI seq=null;
+        String line, text, token;
+        UserColourScheme ucs;
+        int index, start, end;
+        StringTokenizer st;
+        SequenceGroup sg;
+        while( (line = in.readLine())!=null)
         {
-          public void run()
+          st = new StringTokenizer(line, "\t");
+          if(st.countTokens()!=6)
           {
-            alignPanel.requestFocus();
+            System.out.println("Groups file "+file+" is invalid. Read help file.");
+            System.exit(1);
           }
-        });
-      }
-    });
-  }
 
-  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"),
-        new String[]
-        {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "jar"
-    },
-        new String[]
+          while(st.hasMoreElements())
+          {
+            text = st.nextToken();
+            token = st.nextToken();
+            if(!token.equals("ID_NOT_SPECIFIED"))
+            {
+              index = viewport.alignment.findIndex(viewport.alignment.findName(
+                  token));
+              st.nextToken();
+            }
+            else
+              index = Integer.parseInt( st.nextToken() );
+
+            start=Integer.parseInt( st.nextToken() );
+            end = Integer.parseInt( st.nextToken() );
+            ucs = new UserColourScheme(st.nextToken());
+
+            seq = viewport.alignment.getSequenceAt(index);
+            start = seq.findIndex(start)-1;
+            end = seq.findIndex(end)-1;
+
+            sg = new SequenceGroup(text,ucs,true,true,false,start,end);
+            sg.addSequence( seq,true);
+
+            viewport.alignment.addGroup(sg);
+          }
+        }
+
+      }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);}
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+    {
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"),
+                new String[]
+                {
+                    "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+                    "jar"
+                },
+                new String[]
+                {
+                    "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+                }, currentFileFormat);
+
+        chooser.setAcceptAllFileFilterUsed(false);
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save Alignment to file");
+        chooser.setToolTipText("Save");
+
+        int value = chooser.showSaveDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
         {
-        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-    }, currentFileFormat);
+            currentFileFormat = chooser.getSelectedFormat();
+            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                currentFileFormat);
 
-    chooser.setAcceptAllFileFilterUsed(false);
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Alignment to file");
-    chooser.setToolTipText("Save");
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
 
-    int value = chooser.showSaveDialog(this);
+            saveAlignment(choice, currentFileFormat);
+        }
+    }
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    public boolean saveAlignment(String file, String format)
     {
-      currentFileFormat = chooser.getSelectedFormat();
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
-                                    currentFileFormat);
-
-      if (currentFileFormat.equals("Jalview"))
+      if (format.equalsIgnoreCase("Jalview"))
       {
         String shortName = title;
 
@@ -114,1536 +206,1931 @@ public class AlignFrame
               java.io.File.separatorChar) + 1);
         }
 
-        String choice = chooser.getSelectedFile().getPath();
-        Jalview2XML.SaveAlignment(this, choice, shortName);
+        Jalview2XML.SaveAlignment(this, file, shortName);
 
         // USE Jalview2XML to save this file
-        return;
-      }
-
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-
-      String output = FormatAdapter.formatSequences(currentFileFormat,
-          viewport.getAlignment().getSequences());
-
-      try
-      {
-        java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
-            FileWriter(
-                choice));
-        out.println(output);
-        out.close();
+        return true;
       }
-      catch (Exception ex)
+      else
       {
+        String output = FormatAdapter.formatSequences(format,
+            viewport.getAlignment().
+            getSequences());
+        if(output==null)
+          return false;
+
+        try
+        {
+          java.io.PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(file));
+          out.println(output);
+          out.close();
+          return true;
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
       }
+      return false;
     }
-  }
-
-  protected void outputText_actionPerformed(ActionEvent e)
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap,
-                             "Alignment output - " + e.getActionCommand(), 600,
-                             500);
-    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().
-                                              getSequences()));
-  }
 
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)
-  {
-    new HTMLOutput(viewport);
-  }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
-  {
-    alignPanel.makePNG();
-  }
-
-  protected void epsFile_actionPerformed(ActionEvent e)
-  {
-    alignPanel.makeEPS();
-  }
-
-  public void printMenuItem_actionPerformed(ActionEvent e)
-  {
-    //Putting in a thread avoids Swing painting problems
-    PrintThread thread = new PrintThread();
-    thread.start();
-  }
-
-  public void closeMenuItem_actionPerformed(ActionEvent e)
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void outputText_actionPerformed(ActionEvent e)
     {
-      this.setClosed(true);
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
+        Desktop.addInternalFrame(cap,
+            "Alignment output - " + e.getActionCommand(), 600, 500);
+        cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+                viewport.getAlignment().getSequences()));
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void htmlMenuItem_actionPerformed(ActionEvent e)
     {
+        new HTMLOutput(viewport);
     }
-  }
 
-  void updateEditMenuBar()
-  {
-    if (historyList.size() > 0)
+    public void createImageMap(File file, String image)
     {
-      undoMenuItem.setEnabled(true);
-
-      HistoryItem hi = (HistoryItem) historyList.peek();
-      undoMenuItem.setText("Undo " + hi.getDescription());
+      alignPanel.makePNGImageMap(file, image);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void createPNG(File f)
     {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setText("Undo");
+        alignPanel.makePNG(f);
     }
 
-    if (redoList.size() > 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void createEPS(File f)
     {
-      redoMenuItem.setEnabled(true);
-
-      HistoryItem hi = (HistoryItem) redoList.peek();
-      redoMenuItem.setText("Redo " + hi.getDescription());
+        alignPanel.makeEPS(f);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void printMenuItem_actionPerformed(ActionEvent e)
     {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setText("Redo");
+        //Putting in a thread avoids Swing painting problems
+        PrintThread thread = new PrintThread();
+        thread.start();
     }
-  }
-
-  public void addHistoryItem(HistoryItem hi)
-  {
-    historyList.push(hi);
-    updateEditMenuBar();
-  }
-
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
-  {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
-                                  HistoryItem.HIDE));
-    restoreHistoryItem(hi);
-  }
-
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
-  {
-    HistoryItem hi = (HistoryItem) redoList.pop();
-    restoreHistoryItem(hi);
-    updateEditMenuBar();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-    alignPanel.repaint();
-  }
 
-  // used by undo and redo
-  void restoreHistoryItem(HistoryItem hi)
-  {
-    if (hi.getType() == HistoryItem.SORT)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void closeMenuItem_actionPerformed(ActionEvent e)
     {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        viewport.alignment.getSequences().setElementAt(hi.getSequences()
-            .elementAt(i),
-            i);
-      }
+        try
+        {
+            this.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
     }
-    else
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
 
-        if (restore.getLength() == 0)
+    /**
+     * DOCUMENT ME!
+     */
+    void updateEditMenuBar()
+    {
+        if (historyList.size() > 0)
         {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-          viewport.alignment.getSequences().insertElementAt(restore,
-              hi.getAlignIndex(i));
+            undoMenuItem.setEnabled(true);
+
+            HistoryItem hi = (HistoryItem) historyList.peek();
+            undoMenuItem.setText("Undo " + hi.getDescription());
         }
         else
         {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
+            undoMenuItem.setEnabled(false);
+            undoMenuItem.setText("Undo");
         }
-      }
 
-      if (hi.getType() == HistoryItem.PASTE)
-      {
-        for (int i = viewport.alignment.getHeight() - 1;
-             i > (hi.getSequences().size() - 1); i--)
+        if (redoList.size() > 0)
         {
-          viewport.alignment.deleteSequence(i);
+            redoMenuItem.setEnabled(true);
+
+            HistoryItem hi = (HistoryItem) redoList.peek();
+            redoMenuItem.setText("Redo " + hi.getDescription());
+        }
+        else
+        {
+            redoMenuItem.setEnabled(false);
+            redoMenuItem.setText("Redo");
         }
-      }
     }
 
-    updateEditMenuBar();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param hi DOCUMENT ME!
+     */
+    public void addHistoryItem(HistoryItem hi)
+    {
+        historyList.push(hi);
+        updateEditMenuBar();
+    }
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void undoMenuItem_actionPerformed(ActionEvent e)
+    {
+        HistoryItem hi = (HistoryItem) historyList.pop();
+        redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
+                HistoryItem.HIDE));
+        restoreHistoryItem(hi);
+    }
 
-  public void moveSelectedSequences(boolean up)
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void redoMenuItem_actionPerformed(ActionEvent e)
+    {
+        HistoryItem hi = (HistoryItem) redoList.pop();
+        restoreHistoryItem(hi);
+        updateEditMenuBar();
+        viewport.updateConsensus();
+        alignPanel.repaint();
+        alignPanel.repaint();
+    }
 
-    if (sg == null)
+    // used by undo and redo
+    void restoreHistoryItem(HistoryItem hi)
     {
-      return;
+        if (hi.getType() == HistoryItem.SORT)
+        {
+            for (int i = 0; i < hi.getSequences().size(); i++)
+            {
+                viewport.alignment.getSequences().setElementAt(hi.getSequences()
+                                                                 .elementAt(i),
+                    i);
+            }
+        }
+        else
+        {
+            for (int i = 0; i < hi.getSequences().size(); i++)
+            {
+                SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
+
+                if (restore.getLength() == 0)
+                {
+                    restore.setSequence(hi.getHidden().elementAt(i).toString());
+                    viewport.alignment.getSequences().insertElementAt(restore,
+                        hi.getAlignIndex(i));
+                }
+                else
+                {
+                    restore.setSequence(hi.getHidden().elementAt(i).toString());
+                }
+            }
+
+            if (hi.getType() == HistoryItem.PASTE)
+            {
+                for (int i = viewport.alignment.getHeight() - 1;
+                        i > (hi.getSequences().size() - 1); i--)
+                {
+                    viewport.alignment.deleteSequence(i);
+                }
+            }
+        }
+
+        updateEditMenuBar();
+
+        viewport.updateConsensus();
+        viewport.updateConservation();
+        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null,
+            viewport.getAlignment().getSequences());
     }
 
-    if (up)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param up DOCUMENT ME!
+     */
+    public void moveSelectedSequences(boolean up)
     {
-      for (int i = 1; i < viewport.alignment.getHeight(); i++)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
+        SequenceGroup sg = viewport.getSelectionGroup();
 
-        if (!sg.sequences.contains(seq))
+        if (sg == null)
         {
-          continue;
+            return;
         }
 
-        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+        if (up)
+        {
+            for (int i = 1; i < viewport.alignment.getHeight(); i++)
+            {
+                SequenceI seq = viewport.alignment.getSequenceAt(i);
+
+                if (!sg.sequences.contains(seq))
+                {
+                    continue;
+                }
+
+                SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
 
-        if (sg.sequences.contains(temp))
+                if (sg.sequences.contains(temp))
+                {
+                    continue;
+                }
+
+                viewport.alignment.getSequences().setElementAt(temp, i);
+                viewport.alignment.getSequences().setElementAt(seq, i - 1);
+            }
+        }
+        else
         {
-          continue;
+            for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+            {
+                SequenceI seq = viewport.alignment.getSequenceAt(i);
+
+                if (!sg.sequences.contains(seq))
+                {
+                    continue;
+                }
+
+                SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+
+                if (sg.sequences.contains(temp))
+                {
+                    continue;
+                }
+
+                viewport.alignment.getSequences().setElementAt(temp, i);
+                viewport.alignment.getSequences().setElementAt(seq, i + 1);
+            }
         }
 
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i - 1);
-      }
+        alignPanel.repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void copy_actionPerformed(ActionEvent e)
     {
-      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
+        if (viewport.getSelectionGroup() == null)
+        {
+            return;
+        }
+
+        SequenceGroup sg = viewport.getSelectionGroup();
 
-        if (!sg.sequences.contains(seq))
+        Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+        StringBuffer buffer = new StringBuffer();
+
+        Hashtable orderedSeqs = new Hashtable();
+
+        for (int i = 0; i < sg.getSize(); i++)
         {
-          continue;
+            SequenceI seq = sg.getSequenceAt(i);
+            int index = viewport.alignment.findIndex(seq);
+            orderedSeqs.put(index + "", seq);
         }
 
-        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+        int index = 0;
 
-        if (sg.sequences.contains(temp))
+        for (int i = 0; i < sg.getSize(); i++)
         {
-          continue;
+            SequenceI seq = null;
+
+            while (seq == null)
+            {
+                if (orderedSeqs.containsKey(index + ""))
+                {
+                    seq = (SequenceI) orderedSeqs.get(index + "");
+                    index++;
+
+                    break;
+                }
+                else
+                {
+                    index++;
+                }
+            }
+
+            buffer.append(seq.getName() + "\t" +
+                seq.findPosition(sg.getStartRes()) + "\t" +
+                seq.findPosition(sg.getEndRes()) + "\t" +
+                sg.getSequenceAt(i).getSequence(sg.getStartRes(),
+                    sg.getEndRes() + 1) + "\n");
         }
 
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i + 1);
-      }
+        c.setContents(new StringSelection(buffer.toString()), null);
     }
 
-    alignPanel.repaint();
-  }
-
-  protected void copy_actionPerformed(ActionEvent e)
-  {
-    if (viewport.getSelectionGroup() == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void pasteNew_actionPerformed(ActionEvent e)
     {
-      return;
+        paste(true);
     }
 
-    SequenceGroup sg = viewport.getSelectionGroup();
-
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    StringBuffer buffer = new StringBuffer();
-
-    Hashtable orderedSeqs = new Hashtable();
-
-    for (int i = 0; i < sg.getSize(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void pasteThis_actionPerformed(ActionEvent e)
     {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.alignment.findIndex(seq);
-      orderedSeqs.put(index + "", seq);
+        addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+                HistoryItem.PASTE));
+        paste(false);
     }
 
-    int index = 0;
-
-    for (int i = 0; i < sg.getSize(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param newAlignment DOCUMENT ME!
+     */
+    void paste(boolean newAlignment)
     {
-      SequenceI seq = null;
-
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
+        try
         {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-
-          break;
+            Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+            Transferable contents = c.getContents(this);
+
+            if (contents == null)
+            {
+                return;
+            }
+
+            String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+            StringTokenizer st = new StringTokenizer(str);
+            ArrayList seqs = new ArrayList();
+
+            while (st.hasMoreElements())
+            {
+                String name = st.nextToken();
+                int start = Integer.parseInt(st.nextToken());
+                int end = Integer.parseInt(st.nextToken());
+                Sequence sequence = new Sequence(name, st.nextToken(), start,
+                        end);
+
+                if (!newAlignment)
+                {
+                    viewport.alignment.addSequence(sequence);
+                }
+                else
+                {
+                    seqs.add(sequence);
+                }
+            }
+
+            if (newAlignment)
+            {
+                SequenceI[] newSeqs = new SequenceI[seqs.size()];
+                seqs.toArray(newSeqs);
+
+                AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+                String newtitle = new String("Copied sequences");
+
+                if (title.startsWith("Copied sequences"))
+                {
+                    newtitle = title;
+                }
+                else
+                {
+                    newtitle = newtitle.concat("- from " + title);
+                }
+
+                Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+                    NEW_WINDOW_HEIGHT);
+            }
+            else
+            {
+                viewport.firePropertyChange("alignment", null,
+                    viewport.getAlignment().getSequences());
+                viewport.setEndSeq(viewport.alignment.getHeight());
+                viewport.alignment.getWidth();
+                viewport.updateConservation();
+                viewport.updateConsensus();
+                alignPanel.repaint();
+            }
         }
-        else
+        catch (Exception ex)
         {
-          index++;
         }
-      }
 
-      buffer.append(seq.getName() + "\t" +
-                    seq.findPosition(sg.getStartRes()) + "\t" +
-                    seq.findPosition(sg.getEndRes()) + "\t" +
-                    sg.getSequenceAt(i).getSequence(sg.getStartRes(),
-          sg.getEndRes() + 1) + "\n");
+        // could be anything being pasted in here
     }
 
-    c.setContents(new StringSelection(buffer.toString()), null);
-  }
-
-  protected void pasteNew_actionPerformed(ActionEvent e)
-  {
-    paste(true);
-  }
-
-  protected void pasteThis_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
-                                   HistoryItem.PASTE));
-    paste(false);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cut_actionPerformed(ActionEvent e)
+    {
+        copy_actionPerformed(null);
+        delete_actionPerformed(null);
+    }
 
-  void paste(boolean newAlignment)
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void delete_actionPerformed(ActionEvent e)
     {
-      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-      Transferable contents = c.getContents(this);
+        boolean seqsdeleted = false;
 
-      if (contents == null)
-      {
-        return;
-      }
+        if (viewport.getSelectionGroup() == null)
+        {
+            return;
+        }
 
-      String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
-      StringTokenizer st = new StringTokenizer(str);
-      ArrayList seqs = new ArrayList();
+        addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                HistoryItem.HIDE));
 
-      while (st.hasMoreElements())
-      {
-        String name = st.nextToken();
-        int start = Integer.parseInt(st.nextToken());
-        int end = Integer.parseInt(st.nextToken());
-        Sequence sequence = new Sequence(name, st.nextToken(), start,
-                                         end);
+        SequenceGroup sg = viewport.getSelectionGroup();
 
-        if (!newAlignment)
+        for (int i = 0; i < sg.sequences.size(); i++)
         {
-          viewport.alignment.addSequence(sequence);
+            SequenceI seq = sg.getSequenceAt(i);
+            int index = viewport.getAlignment().findIndex(seq);
+            seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+
+            if (seq.getSequence().length() < 1)
+            {
+                seqsdeleted = true;
+                viewport.getAlignment().deleteSequence(seq);
+            }
+            else
+            {
+                viewport.getAlignment().getSequences().setElementAt(seq, index);
+            }
         }
-        else
-        {
-          seqs.add(sequence);
-        }
-      }
 
-      if (newAlignment)
-      {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        seqs.toArray(newSeqs);
-
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
-        String newtitle = new String("Copied sequences");
+        viewport.setSelectionGroup(null);
+        viewport.alignment.deleteGroup(sg);
 
-        if (title.startsWith("Copied sequences"))
+        if (seqsdeleted)
         {
-          newtitle = title;
+            viewport.firePropertyChange("alignment", null,
+                viewport.getAlignment().getSequences());
         }
-        else
+
+        viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
+
+        if (viewport.getAlignment().getHeight() < 1)
         {
-          newtitle = newtitle.concat("- from " + title);
+            try
+            {
+                this.setClosed(true);
+            }
+            catch (Exception ex)
+            {
+            }
         }
 
-        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
-                                 NEW_WINDOW_HEIGHT);
-      }
-      else
-      {
-        viewport.firePropertyChange("alignment", null,
-                                    viewport.getAlignment().getSequences());
-        viewport.setEndSeq(viewport.alignment.getHeight());
-        viewport.alignment.getWidth();
         viewport.updateConservation();
         viewport.updateConsensus();
         alignPanel.repaint();
-      }
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void deleteGroups_actionPerformed(ActionEvent e)
     {
+        viewport.alignment.deleteAllGroups();
+        viewport.setSelectionGroup(null);
+        alignPanel.repaint();
     }
 
-    // could be anything being pasted in here
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = new SequenceGroup();
 
-  protected void cut_actionPerformed(ActionEvent e)
-  {
-    copy_actionPerformed(null);
-    delete_actionPerformed(null);
-  }
+        for (int i = 0; i < viewport.getAlignment().getSequences().size();
+                i++)
+        {
+            sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
+        }
 
-  protected void delete_actionPerformed(ActionEvent e)
-  {
-    boolean seqsdeleted = false;
+        sg.setEndRes(viewport.alignment.getWidth());
+        viewport.setSelectionGroup(sg);
+        PaintRefresher.Refresh(null, viewport.alignment);
+    }
 
-    if (viewport.getSelectionGroup() == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
     {
-      return;
+        viewport.setSelectionGroup(null);
+        viewport.getColumnSelection().clear();
+        viewport.setSelectionGroup(null);
+        alignPanel.annotationPanel.activeRes = null;
+        PaintRefresher.Refresh(null, viewport.alignment);
     }
 
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
-
-    SequenceGroup sg = viewport.getSelectionGroup();
-
-    for (int i = 0; i < sg.sequences.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
     {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.getAlignment().findIndex(seq);
-      seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+        SequenceGroup sg = viewport.getSelectionGroup();
 
-      if (seq.getSequence().length() < 1)
-      {
-        seqsdeleted = true;
-        viewport.getAlignment().deleteSequence(seq);
-      }
-      else
-      {
-        viewport.getAlignment().getSequences().setElementAt(seq, index);
-      }
-    }
+        if (sg == null)
+        {
+            selectAllSequenceMenuItem_actionPerformed(null);
 
-    viewport.setSelectionGroup(null);
-    viewport.alignment.deleteGroup(sg);
+            return;
+        }
 
-    if (seqsdeleted)
-    {
-      viewport.firePropertyChange("alignment", null,
-                                  viewport.getAlignment().getSequences());
-    }
+        for (int i = 0; i < viewport.getAlignment().getSequences().size();
+                i++)
+        {
+            sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+        }
 
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
+        PaintRefresher.Refresh(null, viewport.alignment);
+    }
 
-    if (viewport.getAlignment().getHeight() < 1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
     {
-      try
-      {
-        this.setClosed(true);
-      }
-      catch (Exception ex)
-      {
-      }
-    }
+        ColumnSelection colSel = viewport.getColumnSelection();
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-  }
+        if (colSel.size() > 0)
+        {
+            addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
+                    HistoryItem.HIDE));
 
-  protected void deleteGroups_actionPerformed(ActionEvent e)
-  {
-    viewport.alignment.deleteAllGroups();
-    viewport.setSelectionGroup(null);
-    alignPanel.repaint();
-  }
+            int min = colSel.getMin();
+            viewport.getAlignment().trimLeft(min);
+            colSel.compensateForEdit(0, min);
 
-  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = new SequenceGroup();
+            if (viewport.getSelectionGroup() != null)
+            {
+                viewport.getSelectionGroup().adjustForRemoveLeft(min);
+            }
 
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
-    {
-      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
-    }
+            Vector groups = viewport.alignment.getGroups();
 
-    sg.setEndRes(viewport.alignment.getWidth());
-    viewport.setSelectionGroup(sg);
-    PaintRefresher.Refresh(null, viewport.alignment);
-  }
+            for (int i = 0; i < groups.size(); i++)
+            {
+                SequenceGroup sg = (SequenceGroup) groups.get(i);
 
-  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setSelectionGroup(null);
-    viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
-    alignPanel.annotationPanel.activeRes=null;
-    PaintRefresher.Refresh(null, viewport.alignment);
-  }
+                if (!sg.adjustForRemoveLeft(min))
+                {
+                    viewport.alignment.deleteGroup(sg);
+                }
+            }
 
-  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if(sg==null)
-    {
-      selectAllSequenceMenuItem_actionPerformed(null);
-      return;
+            alignPanel.repaint();
+        }
     }
 
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void remove2RightMenuItem_actionPerformed(ActionEvent e)
     {
-      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
-    }
-
-    PaintRefresher.Refresh(null, viewport.alignment);
-  }
+        ColumnSelection colSel = viewport.getColumnSelection();
 
-  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
-  {
-    ColumnSelection colSel = viewport.getColumnSelection();
+        if (colSel.size() > 0)
+        {
+            addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
+                    HistoryItem.HIDE));
 
-    if (colSel.size() > 0)
-    {
-      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
-                                     HistoryItem.HIDE));
+            int max = colSel.getMax();
+            viewport.getAlignment().trimRight(max);
 
-      int min = colSel.getMin();
-      viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0, min);
+            if (viewport.getSelectionGroup() != null)
+            {
+                viewport.getSelectionGroup().adjustForRemoveRight(max);
+            }
 
-      if (viewport.getSelectionGroup() != null)
-      {
-        viewport.getSelectionGroup().adjustForRemoveLeft(min);
-      }
+            Vector groups = viewport.alignment.getGroups();
 
-      Vector groups = viewport.alignment.getGroups();
+            for (int i = 0; i < groups.size(); i++)
+            {
+                SequenceGroup sg = (SequenceGroup) groups.get(i);
 
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
+                if (!sg.adjustForRemoveRight(max))
+                {
+                    viewport.alignment.deleteGroup(sg);
+                }
+            }
 
-        if (!sg.adjustForRemoveLeft(min))
-        {
-          viewport.alignment.deleteGroup(sg);
+            alignPanel.repaint();
         }
-      }
-
-      alignPanel.repaint();
     }
-  }
 
-  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
-  {
-    ColumnSelection colSel = viewport.getColumnSelection();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("Remove Gapped Columns",
+                viewport.alignment, HistoryItem.HIDE));
 
-    if (colSel.size() > 0)
+        viewport.getAlignment().removeGaps();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
     {
-      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
-                                     HistoryItem.HIDE));
+        addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
+                HistoryItem.HIDE));
 
-      int max = colSel.getMax();
-      viewport.getAlignment().trimRight(max);
+        SequenceI current;
+        int jSize;
 
-      if (viewport.getSelectionGroup() != null)
-      {
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
-      }
+        Vector seqs = null;
 
-      Vector groups = viewport.alignment.getGroups();
+        int start = 0;
+        int end = viewport.alignment.getWidth();
 
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if (viewport.getSelectionGroup() != null)
+        {
+            seqs = viewport.getSelectionGroup().sequences;
+            start = viewport.getSelectionGroup().getStartRes();
+            end = viewport.getSelectionGroup().getEndRes();
+        }
+        else
+        {
+            seqs = viewport.alignment.getSequences();
+        }
 
-        if (!sg.adjustForRemoveRight(max))
+        for (int i = 0; i < seqs.size(); i++)
         {
-          viewport.alignment.deleteGroup(sg);
+            current = (SequenceI) seqs.elementAt(i);
+            jSize = current.getLength();
+
+            int j = start;
+
+            do
+            {
+                if (jalview.util.Comparison.isGap(current.getCharAt(j)))
+                {
+                    current.deleteCharAt(j);
+                    j--;
+                    jSize--;
+                }
+
+                j++;
+            }
+            while (j < end);
         }
-      }
 
-      alignPanel.repaint();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
     }
-  }
 
-  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("Remove Gapped Columns",
-                                   viewport.alignment, HistoryItem.HIDE));
-
-    viewport.getAlignment().removeGaps();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void padGapsMenuitem_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
+                HistoryItem.HIDE));
 
-  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
-                                   HistoryItem.HIDE));
+        SequenceI current;
+        int Width = viewport.getAlignment().getWidth();
 
-    SequenceI current;
-    int jSize;
+        for (int i = 0; i < viewport.getAlignment().getSequences().size();
+                i++)
+        {
+            current = viewport.getAlignment().getSequenceAt(i);
 
-    Vector seqs=null;
+            if (current.getLength() < Width)
+            {
+                current.insertCharAt(Width - 1, viewport.getGapCharacter());
+            }
+        }
 
-    int start=0, end = viewport.alignment.getWidth();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
+    }
 
-    if(viewport.getSelectionGroup()!=null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findMenuItem_actionPerformed(ActionEvent e)
     {
-      seqs = viewport.getSelectionGroup().sequences;
-      start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+        JInternalFrame frame = new JInternalFrame();
+        Finder finder = new Finder(viewport, alignPanel, frame);
+        frame.setContentPane(finder);
+        Desktop.addInternalFrame(frame, "Find", 340, 110);
+        frame.setLayer(JLayeredPane.PALETTE_LAYER);
     }
-    else
-      seqs = viewport.alignment.getSequences();
 
-    for (int i = 0; i <seqs.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void font_actionPerformed(ActionEvent e)
     {
-      current = (SequenceI)seqs.elementAt(i);
-      jSize = current.getLength();
-
-      int j = start;
-      do
-      {
-        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
-        {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
-        }
-        j++;
-      }
-      while(j < end);
+        FontChooser fc = new FontChooser(alignPanel);
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-  }
-
-  public void padGapsMenuitem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
-                                   HistoryItem.HIDE));
-
-    SequenceI current;
-    int Width = viewport.getAlignment().getWidth();
-
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void fullSeqId_actionPerformed(ActionEvent e)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
+        viewport.setShowFullId(fullSeqId.isSelected());
 
-      if (current.getLength() < Width)
-      {
-        current.insertCharAt(Width-1, viewport.getGapCharacter());
-      }
+        alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+        alignPanel.repaint();
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-  }
-
-  public void findMenuItem_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    Finder finder = new Finder(viewport, alignPanel, frame);
-    frame.setContentPane(finder);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-  }
-
-  public void font_actionPerformed(ActionEvent e)
-  {
-    FontChooser fc = new FontChooser(alignPanel);
-  }
-
-  protected void fullSeqId_actionPerformed(ActionEvent e)
-  {
-    viewport.setShowFullId(fullSeqId.isSelected());
-
-    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
-    alignPanel.repaint();
-  }
-
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setColourText(colourTextMenuItem.isSelected());
-    alignPanel.repaint();
-  }
-
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setWrapAlignment(wrapMenuItem.isSelected());
-    alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
-    scaleAbove.setVisible(wrapMenuItem.isSelected());
-    scaleLeft.setVisible(wrapMenuItem.isSelected());
-    scaleRight.setVisible(wrapMenuItem.isSelected());
-    alignPanel.repaint();
-  }
-
-  protected void scaleAbove_actionPerformed(ActionEvent e)
-  {
-    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    alignPanel.repaint();
-  }
-
-  protected void scaleLeft_actionPerformed(ActionEvent e)
-  {
-    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
-    alignPanel.repaint();
-  }
-
-  protected void scaleRight_actionPerformed(ActionEvent e)
-  {
-    viewport.setScaleRightWrapped(scaleRight.isSelected());
-    alignPanel.repaint();
-  }
-
-  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
-    alignPanel.repaint();
-  }
-
-  public void viewTextMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setShowText(viewTextMenuItem.isSelected());
-    alignPanel.repaint();
-  }
-
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.repaint();
-  }
-
-  public void sequenceFeatures_actionPerformed(ActionEvent evt)
-  {
-    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-
-    if (viewport.showSequenceFeatures &&
-        ! ( (Alignment) viewport.alignment).featuresAdded)
-    {
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
-          alignment,
-          alignPanel);
-      ( (Alignment) viewport.alignment).featuresAdded = true;
-    }
-
-    alignPanel.repaint();
-  }
-
-  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
-  {
-    if (annotationPanelMenuItem.isSelected() &&
-        viewport.getWrapAlignment())
-    {
-      annotationPanelMenuItem.setSelected(false);
-
-      return;
-    }
-
-    viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
-    alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
-  }
-
-  public void overviewMenuItem_actionPerformed(ActionEvent e)
-  {
-    if (alignPanel.overviewPanel != null)
-    {
-      return;
-    }
-
-    JInternalFrame frame = new JInternalFrame();
-    OverviewPanel overview = new OverviewPanel(alignPanel);
-    frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
-                             frame.getWidth(), frame.getHeight());
-    frame.pack();
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-    {
-      public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
-      {
-        alignPanel.setOverviewPanel(null);
-      }
-      ;
-    });
-
-    alignPanel.setOverviewPanel(overview);
-  }
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    changeColour(null);
-  }
-
-  public void clustalColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new ClustalxColourScheme(
-        viewport.alignment.getSequences(), viewport.alignment.getWidth()));
-  }
-
-  public void zappoColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new ZappoColourScheme());
-  }
-
-  public void taylorColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new TaylorColourScheme());
-  }
-
-  public void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new HydrophobicColourScheme());
-  }
-
-  public void helixColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new HelixColourScheme());
-  }
-
-  public void strandColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new StrandColourScheme());
-  }
-
-  public void turnColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new TurnColourScheme());
-  }
-
-  public void buriedColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new BuriedColourScheme());
-  }
-
-  public void nucleotideColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new NucleotideColourScheme());
-  }
-
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
-  {
-    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
-  }
-
-  void changeColour(ColourSchemeI cs)
-  {
-    int threshold = 0;
-
-    if (viewport.getAbovePIDThreshold())
-    {
-      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                                                 "Background");
-
-      if (cs instanceof ResidueColourScheme)
-      {
-        ( (ResidueColourScheme) cs).setThreshold(threshold);
-      }
-      else if (cs instanceof ScoreColourScheme)
-      {
-        ( (ScoreColourScheme) cs).setThreshold(threshold);
-      }
-
-      viewport.setGlobalColourScheme(cs);
-    }
-    else if (cs instanceof ResidueColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void colourTextMenuItem_actionPerformed(ActionEvent e)
     {
-      ( (ResidueColourScheme) cs).setThreshold(0);
+        viewport.setColourText(colourTextMenuItem.isSelected());
+        alignPanel.repaint();
     }
-    else if (cs instanceof ScoreColourScheme)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void wrapMenuItem_actionPerformed(ActionEvent e)
     {
-      ( (ScoreColourScheme) cs).setThreshold(0);
+        viewport.setWrapAlignment(wrapMenuItem.isSelected());
+        alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+        scaleAbove.setVisible(wrapMenuItem.isSelected());
+        scaleLeft.setVisible(wrapMenuItem.isSelected());
+        scaleRight.setVisible(wrapMenuItem.isSelected());
+        alignPanel.repaint();
     }
 
-    if (viewport.getConservationSelected())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void scaleAbove_actionPerformed(ActionEvent e)
     {
-      ConservationColourScheme ccs = null;
-
-      Alignment al = (Alignment) viewport.alignment;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth() - 1);
-
-      c.calculate();
-      c.verdict(false, viewport.ConsPercGaps);
-
-      ccs = new ConservationColourScheme(c, cs);
+        viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+        alignPanel.repaint();
+    }
 
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus(viewport.vconsensus);
-      viewport.setGlobalColourScheme(ccs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void scaleLeft_actionPerformed(ActionEvent e)
+    {
+        viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+        alignPanel.repaint();
+    }
 
-      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
-                                                  "Background");
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void scaleRight_actionPerformed(ActionEvent e)
+    {
+        viewport.setScaleRightWrapped(scaleRight.isSelected());
+        alignPanel.repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
     {
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      if (cs != null)
-      {
-        cs.setConsensus(viewport.vconsensus);
-      }
+        viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+        alignPanel.repaint();
+    }
 
-      viewport.setGlobalColourScheme(cs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void viewTextMenuItem_actionPerformed(ActionEvent e)
+    {
+        viewport.setShowText(viewTextMenuItem.isSelected());
+        alignPanel.repaint();
     }
 
-    if (viewport.getColourAppliesToAllGroups())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
     {
-      Vector groups = viewport.alignment.getGroups();
+        viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+        alignPanel.repaint();
+    }
 
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void sequenceFeatures_actionPerformed(ActionEvent evt)
+    {
+        viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 
-        if (cs == null)
-        {
-          sg.cs = null;
-        }
-        else if (cs instanceof ClustalxColourScheme)
-        {
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
-        }
-        else if (cs instanceof UserColourScheme)
+        if (viewport.showSequenceFeatures &&
+                !((Alignment) viewport.alignment).featuresAdded)
         {
-          sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
-        }
-        else
-        {
-          try
-          {
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
-          }
-          catch (Exception ex)
-          {
-          }
+            SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,
+                    alignPanel);
+            ((Alignment) viewport.alignment).featuresAdded = true;
         }
 
-        if (viewport.getAbovePIDThreshold())
+        alignPanel.repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+    {
+        if (annotationPanelMenuItem.isSelected() &&
+                viewport.getWrapAlignment())
         {
-          if (sg.cs instanceof ResidueColourScheme)
-          {
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-          }
-          else if (sg.cs instanceof ScoreColourScheme)
-          {
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-          }
+            annotationPanelMenuItem.setSelected(false);
 
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-              sg.getWidth()));
+            return;
         }
 
-        if (viewport.getConservationSelected())
-        {
-          Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.sequences, 0,
-                                            viewport.alignment.getWidth() - 1);
-          c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
-
-          ConservationColourScheme ccs = new ConservationColourScheme(c,
-              sg.cs);
+        viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
+        alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+    }
 
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                                 sg.getWidth()));
-          sg.cs = ccs;
-        }
-        else if (cs != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void overviewMenuItem_actionPerformed(ActionEvent e)
+    {
+        if (alignPanel.overviewPanel != null)
         {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-              sg.getWidth()));
+            return;
         }
-      }
+
+        JInternalFrame frame = new JInternalFrame();
+        OverviewPanel overview = new OverviewPanel(alignPanel);
+        frame.setContentPane(overview);
+        Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+            frame.getWidth(), frame.getHeight());
+        frame.pack();
+        frame.setLayer(JLayeredPane.PALETTE_LAYER);
+        frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+                public void internalFrameClosed(
+                    javax.swing.event.InternalFrameEvent evt)
+                {
+                    alignPanel.setOverviewPanel(null);
+                }
+                ;
+            });
+
+        alignPanel.setOverviewPanel(overview);
     }
 
-    if (alignPanel.getOverviewPanel() != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void noColourmenuItem_actionPerformed(ActionEvent e)
     {
-      alignPanel.getOverviewPanel().updateOverviewImage();
+        changeColour(null);
     }
 
-    alignPanel.repaint();
-  }
-
-  protected void modifyPID_actionPerformed(ActionEvent e)
-  {
-    if (viewport.getAbovePIDThreshold())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void clustalColour_actionPerformed(ActionEvent e)
     {
-      SliderPanel.setPIDSliderSource(alignPanel,
-                                     viewport.getGlobalColourScheme(),
-                                     "Background");
-      SliderPanel.showPIDSlider();
+        changeColour(new ClustalxColourScheme(
+                viewport.alignment.getSequences(), viewport.alignment.getWidth()));
     }
-  }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
-  {
-    if (viewport.getConservationSelected())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void zappoColour_actionPerformed(ActionEvent e)
     {
-      SliderPanel.setConservationSlider(alignPanel,
-                                        viewport.globalColourScheme,
-                                        "Background");
-      SliderPanel.showConservationSlider();
+        changeColour(new ZappoColourScheme());
     }
-  }
-
-  protected void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if (cs instanceof ConservationColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void taylorColour_actionPerformed(ActionEvent e)
     {
-      changeColour( ( (ConservationColourScheme) cs).cs);
+        changeColour(new TaylorColourScheme());
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void hydrophobicityColour_actionPerformed(ActionEvent e)
     {
-      changeColour(cs);
+        changeColour(new HydrophobicColourScheme());
     }
 
-    modifyConservation_actionPerformed(null);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void helixColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new HelixColourScheme());
+    }
 
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
-  {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void strandColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new StrandColourScheme());
+    }
 
-    conservationMenuItem.setSelected(false);
-    viewport.setConservationSelected(false);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void turnColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new TurnColourScheme());
+    }
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void buriedColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new BuriedColourScheme());
+    }
 
-    if (cs instanceof ConservationColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void nucleotideColour_actionPerformed(ActionEvent e)
     {
-      changeColour( ( (ConservationColourScheme) cs).cs);
+        changeColour(new NucleotideColourScheme());
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void applyToAllGroups_actionPerformed(ActionEvent e)
     {
-      changeColour(cs);
+        viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
     }
 
-    modifyPID_actionPerformed(null);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     */
+    void changeColour(ColourSchemeI cs)
+    {
+        int threshold = 0;
 
-  public void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    new UserDefinedColours(alignPanel, null);
-  }
+        if (viewport.getAbovePIDThreshold())
+        {
+            threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                    "Background");
+
+            if (cs instanceof ResidueColourScheme)
+            {
+                ((ResidueColourScheme) cs).setThreshold(threshold);
+            }
+            else if (cs instanceof ScoreColourScheme)
+            {
+                ((ScoreColourScheme) cs).setThreshold(threshold);
+            }
+
+            viewport.setGlobalColourScheme(cs);
+        }
+        else if (cs instanceof ResidueColourScheme)
+        {
+            ((ResidueColourScheme) cs).setThreshold(0);
+        }
+        else if (cs instanceof ScoreColourScheme)
+        {
+            ((ScoreColourScheme) cs).setThreshold(0);
+        }
 
-  public void PIDColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new PIDColourScheme());
-  }
+        if (viewport.getConservationSelected())
+        {
+            ConservationColourScheme ccs = null;
 
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new Blosum62ColourScheme());
-  }
+            Alignment al = (Alignment) viewport.alignment;
+            Conservation c = new Conservation("All",
+                    ResidueProperties.propHash, 3, al.getSequences(), 0,
+                    al.getWidth() - 1);
 
-  public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
-                                   HistoryItem.SORT));
-    AlignmentSorter.sortByPID(viewport.getAlignment(),
-                              viewport.getAlignment().getSequenceAt(0));
-    alignPanel.repaint();
-  }
+            c.calculate();
+            c.verdict(false, viewport.ConsPercGaps);
 
-  public void sortIDMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
-                                   HistoryItem.SORT));
-    AlignmentSorter.sortByID(viewport.getAlignment());
-    alignPanel.repaint();
-  }
+            ccs = new ConservationColourScheme(c, cs);
 
-  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+            // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+            ccs.setConsensus(viewport.vconsensus);
+            viewport.setGlobalColourScheme(ccs);
 
-    AlignmentSorter.sortByGroup(viewport.getAlignment());
-    alignPanel.repaint();
-  }
+            ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
+                    "Background");
+        }
+        else
+        {
+            // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+            if (cs != null)
+            {
+                cs.setConsensus(viewport.vconsensus);
+            }
 
-  public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
-  {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
-                             100, false);
-  }
+            viewport.setGlobalColourScheme(cs);
+        }
 
-  public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
-  {
-    if ( (viewport.getSelectionGroup() == null) ||
-        (viewport.getSelectionGroup().getSize() < 2))
-    {
-      JOptionPane.showInternalMessageDialog(this,
-                                            "You must select at least 2 sequences.",
-                                            "Invalid Selection",
-                                            JOptionPane.WARNING_MESSAGE);
+        if (viewport.getColourAppliesToAllGroups())
+        {
+            Vector groups = viewport.alignment.getGroups();
+
+            for (int i = 0; i < groups.size(); i++)
+            {
+                SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+                if (cs == null)
+                {
+                    sg.cs = null;
+                }
+                else if (cs instanceof ClustalxColourScheme)
+                {
+                    sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+                }
+                else if (cs instanceof UserColourScheme)
+                {
+                    sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
+                }
+                else
+                {
+                    try
+                    {
+                        sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+                    }
+                    catch (Exception ex)
+                    {
+                    }
+                }
+
+                if (viewport.getAbovePIDThreshold())
+                {
+                    if (sg.cs instanceof ResidueColourScheme)
+                    {
+                        ((ResidueColourScheme) sg.cs).setThreshold(threshold);
+                    }
+                    else if (sg.cs instanceof ScoreColourScheme)
+                    {
+                        ((ScoreColourScheme) sg.cs).setThreshold(threshold);
+                    }
+
+                    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                            sg.getWidth()));
+                }
+
+                if (viewport.getConservationSelected())
+                {
+                    Conservation c = new Conservation("Group",
+                            ResidueProperties.propHash, 3, sg.sequences, 0,
+                            viewport.alignment.getWidth() - 1);
+                    c.calculate();
+                    c.verdict(false, viewport.ConsPercGaps);
+
+                    ConservationColourScheme ccs = new ConservationColourScheme(c,
+                            sg.cs);
+
+                    // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+                    ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                            sg.getWidth()));
+                    sg.cs = ccs;
+                }
+                else if (cs != null)
+                {
+                    // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+                    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                            sg.getWidth()));
+                }
+            }
+        }
+
+        if (alignPanel.getOverviewPanel() != null)
+        {
+            alignPanel.getOverviewPanel().updateOverviewImage();
+        }
+
+        alignPanel.repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void modifyPID_actionPerformed(ActionEvent e)
     {
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(new PairwiseAlignPanel(viewport));
-      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+        if (viewport.getAbovePIDThreshold())
+        {
+            SliderPanel.setPIDSliderSource(alignPanel,
+                viewport.getGlobalColourScheme(), "Background");
+            SliderPanel.showPIDSlider();
+        }
     }
-  }
 
-  public void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-    if ( ( (viewport.getSelectionGroup() != null) &&
-          (viewport.getSelectionGroup().getSize() < 4) &&
-          (viewport.getSelectionGroup().getSize() > 0)) ||
-        (viewport.getAlignment().getHeight() < 4))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void modifyConservation_actionPerformed(ActionEvent e)
     {
-      JOptionPane.showInternalMessageDialog(this,
-                                            "Principal component analysis must take\n" +
-                                            "at least 4 input sequences.",
-                                            "Sequence selection insufficient",
-                                            JOptionPane.WARNING_MESSAGE);
-
-      return;
+        if (viewport.getConservationSelected())
+        {
+            SliderPanel.setConservationSlider(alignPanel,
+                viewport.globalColourScheme, "Background");
+            SliderPanel.showConservationSlider();
+        }
     }
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void conservationMenuItem_actionPerformed(ActionEvent e)
     {
-      PCAPanel pcaPanel = new PCAPanel(viewport, null);
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(pcaPanel);
-      Desktop.addInternalFrame(frame, "Principal component analysis",
-                               400, 400);
-    }
-    catch (java.lang.OutOfMemoryError ex)
-    {
-      JOptionPane.showInternalMessageDialog(this,
-                                            "Too many sequences selected\nfor Principal Component Analysis!!",
-                                            "Out of memory",
-                                            JOptionPane.WARNING_MESSAGE);
-    }
-  }
-
-  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
-  }
-
-  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
-  }
-
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
-  }
-
-  void NewTreePanel(String type, String pwType, String title)
-  {
-    final TreePanel tp;
-
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 3))
-    {
-      int s = 0;
-      SequenceGroup sg = viewport.getSelectionGroup();
+        viewport.setConservationSelected(conservationMenuItem.isSelected());
 
-      /* Decide if the selection is a column region */
-      while (s < sg.sequences.size())
-      {
-        if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
-            sg.getEndRes())
-        {
-          JOptionPane.showMessageDialog(Desktop.desktop,
-                                        "The selected region to create a tree may\nonly contain residues or gaps.\n" +
-                                        "Try using the Pad function in the edit menu,\n" +
-                                        "or one of the multiple sequence alignment web services.",
-                                        "Sequences in selection are not aligned",
-                                        JOptionPane.WARNING_MESSAGE);
+        viewport.setAbovePIDThreshold(false);
+        abovePIDThreshold.setSelected(false);
+
+        ColourSchemeI cs = viewport.getGlobalColourScheme();
 
-          return;
+        if (cs instanceof ConservationColourScheme)
+        {
+            changeColour(((ConservationColourScheme) cs).cs);
+        }
+        else
+        {
+            changeColour(cs);
         }
-      }
 
-      title = title + " on region";
-      tp = new TreePanel(viewport,
-                         viewport.getSelectionGroup().sequences, type, pwType,
-                         sg.getStartRes(), sg.getEndRes());
+        modifyConservation_actionPerformed(null);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void abovePIDThreshold_actionPerformed(ActionEvent e)
     {
-      //are the sequences aligned?
-      if (!viewport.alignment.isAligned())
-      {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "The sequences must be aligned before creating a tree.\n" +
-                                      "Try using the Pad function in the edit menu,\n" +
-                                      "or one of the multiple sequence alignment web services.",
-                                      "Sequences not aligned",
-                                      JOptionPane.WARNING_MESSAGE);
-
-        return;
-      }
+        viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
-      tp = new TreePanel(viewport,
-                         viewport.getAlignment().getSequences(), type, pwType,
-                         0,
-                         viewport.alignment.getWidth());
-    }
+        conservationMenuItem.setSelected(false);
+        viewport.setConservationSelected(false);
 
-    addTreeMenuItem(tp, title);
-    viewport.setCurrentTree(tp.getTree());
+        ColourSchemeI cs = viewport.getGlobalColourScheme();
 
-    Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
-  }
+        if (cs instanceof ConservationColourScheme)
+        {
+            changeColour(((ConservationColourScheme) cs).cs);
+        }
+        else
+        {
+            changeColour(cs);
+        }
 
-  public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
-  {
-    final JMenuItem item = new JMenuItem("by " + title);
-    sort.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
+        modifyPID_actionPerformed(null);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void userDefinedColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-                                       HistoryItem.SORT));
+        new UserDefinedColours(alignPanel, null);
+    }
 
-        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
-        AlignmentSorter.sortBy(viewport.getAlignment(), order);
-        alignPanel.repaint();
-      }
-    });
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void PIDColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new PIDColourScheme());
+    }
 
-  void addTreeMenuItem(final TreePanel treePanel, String title)
-  {
-    final JMenuItem item = new JMenuItem(title);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new Blosum62ColourScheme());
+    }
 
-    treeCount++;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+                HistoryItem.SORT));
+        AlignmentSorter.sortByPID(viewport.getAlignment(),
+            viewport.getAlignment().getSequenceAt(0));
+        alignPanel.repaint();
+    }
 
-    if (treeCount == 1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void sortIDMenuItem_actionPerformed(ActionEvent e)
     {
-      sort.add(sortByTreeMenu);
+        addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+                HistoryItem.SORT));
+        AlignmentSorter.sortByID(viewport.getAlignment());
+        alignPanel.repaint();
     }
 
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void sortGroupMenuItem_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        addHistoryItem(new HistoryItem("Tree Sort",
-                                       viewport.alignment, HistoryItem.SORT));
-        AlignmentSorter.sortByTree(viewport.getAlignment(),
-                                   treePanel.getTree());
+        addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+                HistoryItem.SORT));
+
+        AlignmentSorter.sortByGroup(viewport.getAlignment());
         alignPanel.repaint();
-      }
-    });
+    }
 
-    treePanel.addInternalFrameListener(new javax.swing.event.
-                                       InternalFrameAdapter()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
     {
-      public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
-      {
-        treeCount--;
-        sortByTreeMenu.remove(item);
+        RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
+        JInternalFrame frame = new JInternalFrame();
+        frame.setContentPane(sp);
+        Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
+            100, false);
+    }
 
-        if (treeCount == 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+    {
+        if ((viewport.getSelectionGroup() == null) ||
+                (viewport.getSelectionGroup().getSize() < 2))
         {
-          sort.remove(sortByTreeMenu);
+            JOptionPane.showInternalMessageDialog(this,
+                "You must select at least 2 sequences.", "Invalid Selection",
+                JOptionPane.WARNING_MESSAGE);
         }
-      }
-      ;
-    });
-    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
-    {
-      public void propertyChange(PropertyChangeEvent evt)
-      {
-        if (evt.getPropertyName().equals("alignment"))
+        else
         {
-          treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
-          treePanel.repaint();
+            JInternalFrame frame = new JInternalFrame();
+            frame.setContentPane(new PairwiseAlignPanel(viewport));
+            Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
         }
-      }
-    });
-  }
-
-  public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-    // TODO:resolve which menu item was actually selected
-    // Now, check we have enough sequences
-    SequenceI[] msa = null;
-
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 1))
-    {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
-      int sz;
-      msa = new SequenceI[sz = seqs.getSize()];
-
-      for (int i = 0; i < sz; i++)
-      {
-        msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void PCAMenuItem_actionPerformed(ActionEvent e)
     {
-      Vector seqs = viewport.getAlignment().getSequences();
+        if (((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() < 4) &&
+                (viewport.getSelectionGroup().getSize() > 0)) ||
+                (viewport.getAlignment().getHeight() < 4))
+        {
+            JOptionPane.showInternalMessageDialog(this,
+                "Principal component analysis must take\n" +
+                "at least 4 input sequences.",
+                "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);
 
-      if (seqs.size() > 1)
-      {
-        msa = new SequenceI[seqs.size()];
+            return;
+        }
 
-        for (int i = 0; i < seqs.size(); i++)
+        try
         {
-          msa[i] = (SequenceI) seqs.elementAt(i);
+            PCAPanel pcaPanel = new PCAPanel(viewport, null);
+            JInternalFrame frame = new JInternalFrame();
+            frame.setContentPane(pcaPanel);
+            Desktop.addInternalFrame(frame, "Principal component analysis",
+                400, 400);
+        }
+        catch (java.lang.OutOfMemoryError ex)
+        {
+            JOptionPane.showInternalMessageDialog(this,
+                "Too many sequences selected\nfor Principal Component Analysis!!",
+                "Out of memory", JOptionPane.WARNING_MESSAGE);
         }
-      }
     }
 
-    if (msa != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
     {
-      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
-          title, msa, false, true);
+        NewTreePanel("AV", "PID", "Average distance tree using PID");
     }
-  }
 
-  public void ClustalRealign_actionPerformed(ActionEvent e)
-  {
-    // TODO:resolve which menu item was actually selected
-    // Now, check we have enough sequences
-    SequenceI[] msa = null;
-
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 1))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
     {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
-      int sz;
-      msa = new SequenceI[sz = seqs.getSize()];
+        NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+    }
 
-      for (int i = 0; i < sz; i++)
-      {
-        msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+    {
+        NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
     {
-      Vector seqs = viewport.getAlignment().getSequences();
+        NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+    }
 
-      if (seqs.size() > 1)
-      {
-        msa = new SequenceI[seqs.size()];
+    /**
+     * DOCUMENT ME!
+     *
+     * @param type DOCUMENT ME!
+     * @param pwType DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     */
+    void NewTreePanel(String type, String pwType, String title)
+    {
+        final TreePanel tp;
 
-        for (int i = 0; i < seqs.size(); i++)
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 3))
         {
-          msa[i] = (SequenceI) seqs.elementAt(i);
+            int s = 0;
+            SequenceGroup sg = viewport.getSelectionGroup();
+
+            /* Decide if the selection is a column region */
+            while (s < sg.sequences.size())
+            {
+                if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())
+                {
+                    JOptionPane.showMessageDialog(Desktop.desktop,
+                        "The selected region to create a tree may\nonly contain residues or gaps.\n" +
+                        "Try using the Pad function in the edit menu,\n" +
+                        "or one of the multiple sequence alignment web services.",
+                        "Sequences in selection are not aligned",
+                        JOptionPane.WARNING_MESSAGE);
+
+                    return;
+                }
+            }
+
+            title = title + " on region";
+            tp = new TreePanel(viewport,
+                    viewport.getSelectionGroup().sequences, type, pwType,
+                    sg.getStartRes(), sg.getEndRes());
         }
-      }
+        else
+        {
+            //are the sequences aligned?
+            if (!viewport.alignment.isAligned())
+            {
+                JOptionPane.showMessageDialog(Desktop.desktop,
+                    "The sequences must be aligned before creating a tree.\n" +
+                    "Try using the Pad function in the edit menu,\n" +
+                    "or one of the multiple sequence alignment web services.",
+                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+
+                return;
+            }
+
+            tp = new TreePanel(viewport,
+                    viewport.getAlignment().getSequences(), type, pwType, 0,
+                    viewport.alignment.getWidth());
+        }
+
+        addTreeMenuItem(tp, title);
+        viewport.setCurrentTree(tp.getTree());
+
+        Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
     }
 
-    if (msa != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param title DOCUMENT ME!
+     * @param order DOCUMENT ME!
+     */
+    public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
     {
-      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
-          title, msa, true, true);
-    }
-  }
+        final JMenuItem item = new JMenuItem("by " + title);
+        sort.add(item);
+        item.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+                            HistoryItem.SORT));
 
-  protected void jpred_actionPerformed(ActionEvent e)
-  {
-    SequenceI seq = null;
-    SequenceI[] msa = null;
+                    // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+                    AlignmentSorter.sortBy(viewport.getAlignment(), order);
+                    alignPanel.repaint();
+                }
+            });
+    }
 
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 0))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param treePanel DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     */
+    void addTreeMenuItem(final TreePanel treePanel, String title)
     {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
+        final JMenuItem item = new JMenuItem(title);
 
-      if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
-      {
-        seq = (SequenceI) seqs.getSequenceAt(0);
-      }
-      else
-      {
-        int sz;
-        msa = new SequenceI[sz = seqs.getSize()];
+        treeCount++;
 
-        for (int i = 0; i < sz; i++)
+        if (treeCount == 1)
         {
-          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+            sort.add(sortByTreeMenu);
         }
-      }
-    }
-    else
-    {
-      Vector seqs = viewport.getAlignment().getSequences();
 
-      if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
-      {
-        seq = (SequenceI) seqs.elementAt(0);
-      }
-      else
-      {
-        msa = new SequenceI[seqs.size()];
+        sortByTreeMenu.add(item);
+        item.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    addHistoryItem(new HistoryItem("Tree Sort",
+                            viewport.alignment, HistoryItem.SORT));
+                    AlignmentSorter.sortByTree(viewport.getAlignment(),
+                        treePanel.getTree());
+                    alignPanel.repaint();
+                }
+            });
+
+        treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+                public void internalFrameClosed(
+                    javax.swing.event.InternalFrameEvent evt)
+                {
+                    treeCount--;
+                    sortByTreeMenu.remove(item);
+
+                    if (treeCount == 0)
+                    {
+                        sort.remove(sortByTreeMenu);
+                    }
+                }
+                ;
+            });
+        viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+            {
+                public void propertyChange(PropertyChangeEvent evt)
+                {
+                    if (evt.getPropertyName().equals("alignment"))
+                    {
+                        treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());
+                        treePanel.repaint();
+                    }
+                }
+            });
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+    {
+        // TODO:resolve which menu item was actually selected
+        // Now, check we have enough sequences
+        SequenceI[] msa = null;
+
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 1))
+        {
+            // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+            SequenceGroup seqs = viewport.getSelectionGroup();
+            int sz;
+            msa = new SequenceI[sz = seqs.getSize()];
+
+            for (int i = 0; i < sz; i++)
+            {
+                msa[i] = (SequenceI) seqs.getSequenceAt(i);
+            }
+        }
+        else
+        {
+            Vector seqs = viewport.getAlignment().getSequences();
 
-        for (int i = 0; i < seqs.size(); i++)
+            if (seqs.size() > 1)
+            {
+                msa = new SequenceI[seqs.size()];
+
+                for (int i = 0; i < seqs.size(); i++)
+                {
+                    msa[i] = (SequenceI) seqs.elementAt(i);
+                }
+            }
+        }
+
+        if (msa != null)
         {
-          msa[i] = (SequenceI) seqs.elementAt(i);
+            jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
+                    title, msa, false, true);
         }
-      }
     }
 
-    if (msa != null)
-    {
-      JPredClient ct = new JPredClient(title, msa);
-    }
-    else if (seq != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ClustalRealign_actionPerformed(ActionEvent e)
     {
-      JPredClient ct = new JPredClient(title, seq);
-    }
-    else
-    {
-      System.err.print(
-          "JALVIEW ERROR! - Unexpected JPred selection state!\n");
-    }
-  }
+        // TODO:resolve which menu item was actually selected
+        // Now, check we have enough sequences
+        SequenceI[] msa = null;
+
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 1))
+        {
+            // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+            SequenceGroup seqs = viewport.getSelectionGroup();
+            int sz;
+            msa = new SequenceI[sz = seqs.getSize()];
+
+            for (int i = 0; i < sz; i++)
+            {
+                msa[i] = (SequenceI) seqs.getSequenceAt(i);
+            }
+        }
+        else
+        {
+            Vector seqs = viewport.getAlignment().getSequences();
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-    // TODO:resolve which menu item was actually selected
-    // Now, check we have enough sequences
-    SequenceI[] msa = null;
+            if (seqs.size() > 1)
+            {
+                msa = new SequenceI[seqs.size()];
 
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 1))
-    {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
-      int sz;
-      msa = new SequenceI[sz = seqs.getSize()];
+                for (int i = 0; i < seqs.size(); i++)
+                {
+                    msa[i] = (SequenceI) seqs.elementAt(i);
+                }
+            }
+        }
 
-      for (int i = 0; i < sz; i++)
-      {
-        msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      }
+        if (msa != null)
+        {
+            jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
+                    title, msa, true, true);
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void jpred_actionPerformed(ActionEvent e)
     {
-      Vector seqs = viewport.getAlignment().getSequences();
+        SequenceI seq = null;
+        SequenceI[] msa = null;
 
-      if (seqs.size() > 1)
-      {
-        msa = new SequenceI[seqs.size()];
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 0))
+        {
+            // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+            SequenceGroup seqs = viewport.getSelectionGroup();
+
+            if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())
+            {
+                seq = (SequenceI) seqs.getSequenceAt(0);
+            }
+            else
+            {
+                int sz;
+                msa = new SequenceI[sz = seqs.getSize()];
+
+                for (int i = 0; i < sz; i++)
+                {
+                    msa[i] = (SequenceI) seqs.getSequenceAt(i);
+                }
+            }
+        }
+        else
+        {
+            Vector seqs = viewport.getAlignment().getSequences();
+
+            if ((seqs.size() == 1) || !viewport.alignment.isAligned())
+            {
+                seq = (SequenceI) seqs.elementAt(0);
+            }
+            else
+            {
+                msa = new SequenceI[seqs.size()];
+
+                for (int i = 0; i < seqs.size(); i++)
+                {
+                    msa[i] = (SequenceI) seqs.elementAt(i);
+                }
+            }
+        }
 
-        for (int i = 0; i < seqs.size(); i++)
+        if (msa != null)
         {
-          msa[i] = (SequenceI) seqs.elementAt(i);
+            JPredClient ct = new JPredClient(title, msa);
+        }
+        else if (seq != null)
+        {
+            JPredClient ct = new JPredClient(title, seq);
+        }
+        else
+        {
+            System.err.print(
+                "JALVIEW ERROR! - Unexpected JPred selection state!\n");
         }
-      }
     }
 
-    if (msa != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
     {
-      MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
-                                                  false, true);
-    }
-  }
+        // TODO:resolve which menu item was actually selected
+        // Now, check we have enough sequences
+        SequenceI[] msa = null;
 
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    // Pick the tree file
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"));
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Select a newick-like tree file");
-    chooser.setToolTipText("Load a tree file");
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 1))
+        {
+            // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+            SequenceGroup seqs = viewport.getSelectionGroup();
+            int sz;
+            msa = new SequenceI[sz = seqs.getSize()];
+
+            for (int i = 0; i < sz; i++)
+            {
+                msa[i] = (SequenceI) seqs.getSequenceAt(i);
+            }
+        }
+        else
+        {
+            Vector seqs = viewport.getAlignment().getSequences();
 
-    int value = chooser.showOpenDialog(null);
+            if (seqs.size() > 1)
+            {
+                msa = new SequenceI[seqs.size()];
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+                for (int i = 0; i < seqs.size(); i++)
+                {
+                    msa[i] = (SequenceI) seqs.elementAt(i);
+                }
+            }
+        }
 
-      try
-      {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
-            "File");
-        viewport.setCurrentTree( ShowNewickTree(fin, choice).getTree() );
-      }
-      catch (Exception ex)
-      {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "Problem reading tree file",
-                                      ex.getMessage(),
-                                      JOptionPane.WARNING_MESSAGE);
-        ex.printStackTrace();
-      }
+        if (msa != null)
+        {
+            MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
+                    false, true);
+        }
     }
-  }
 
-  public TreePanel ShowNewickTree(NewickFile nf, String title)
-  {
-    TreePanel tp = null;
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
     {
-      nf.parse();
-      if (nf.getTree() != null)
-      {
-        tp = new TreePanel(viewport,
-                                     viewport.getAlignment().getSequences(), nf,
-                                     "FromFile",
-                                     title);
-        Desktop.addInternalFrame(tp, title, 600, 500);
-        addTreeMenuItem(tp, title);
-      }
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
+        // Pick the tree file
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Select a newick-like tree file");
+        chooser.setToolTipText("Load a tree file");
+
+        int value = chooser.showOpenDialog(null);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+
+            try
+            {
+                jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
+                        "File");
+                viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+            }
+            catch (Exception ex)
+            {
+                JOptionPane.showMessageDialog(Desktop.desktop,
+                    "Problem reading tree file", ex.getMessage(),
+                    JOptionPane.WARNING_MESSAGE);
+                ex.printStackTrace();
+            }
+        }
     }
-    return tp;
-  }
 
-  class PrintThread
-      extends Thread
-  {
-    public void run()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param nf DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public TreePanel ShowNewickTree(NewickFile nf, String title)
     {
-      PrinterJob printJob = PrinterJob.getPrinterJob();
-      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-      printJob.setPrintable(alignPanel, pf);
+        TreePanel tp = null;
 
-      if (printJob.printDialog())
-      {
         try
         {
-          printJob.print();
+            nf.parse();
+
+            if (nf.getTree() != null)
+            {
+                tp = new TreePanel(viewport,
+                        viewport.getAlignment().getSequences(), nf, "FromFile",
+                        title);
+                Desktop.addInternalFrame(tp, title, 600, 500);
+                addTreeMenuItem(tp, title);
+            }
         }
-        catch (Exception PrintException)
+        catch (Exception ex)
         {
-          PrintException.printStackTrace();
+            ex.printStackTrace();
+        }
+
+        return tp;
+    }
+
+    class PrintThread extends Thread
+    {
+        public void run()
+        {
+            PrinterJob printJob = PrinterJob.getPrinterJob();
+            PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+            printJob.setPrintable(alignPanel, pf);
+
+            if (printJob.printDialog())
+            {
+                try
+                {
+                    printJob.print();
+                }
+                catch (Exception PrintException)
+                {
+                    PrintException.printStackTrace();
+                }
+            }
         }
-      }
     }
-  }
 }
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 44b7432..e8f34d8 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -18,670 +18,1017 @@
  */
 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)));
-    }
-    else
-    {
-      setFont(font);
-    }
-
-    alignment.setGapCharacter(Preferences.gapSymbol);
-
-    // We must set conservation and consensus before setting colour,
-    // as Blosum and Clustal require this to be done
-    updateConservation();
-    updateConsensus();
-
-    if (Preferences.defaultColour != null)
-    {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-          Preferences.defaultColour);
-
-      if (globalColourScheme instanceof UserColourScheme)
-      {
-        globalColourScheme = UserDefinedColours.loadDefaultColours();
-      }
-
-      if (globalColourScheme != null)
-      {
-        globalColourScheme.setConsensus(vconsensus);
-      }
-    }
-  }
-
-  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
-      {
-        value = Integer.parseInt(sequence.charAt(i) + "");
-      }
-      catch (Exception ex)
-      {
-        if (sequence.charAt(i) == '*')
+    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;
+
+    /** 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);
+
+    /**
+     * 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 = 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))
         {
-          value = 11;
+            int style = 0;
+
+            if (fontStyle.equals("bold"))
+            {
+                style = 1;
+            }
+            else if (fontStyle.equals("italic"))
+            {
+                style = 2;
+            }
+
+            setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
         }
+        else
+        {
+            setFont(font);
+        }
+
+        alignment.setGapCharacter(Preferences.gapSymbol);
 
-        if (sequence.charAt(i) == '+')
+        // We must set conservation and consensus before setting colour,
+        // as Blosum and Clustal require this to be done
+        updateConservation();
+        updateConsensus();
+
+        if (Preferences.defaultColour != null)
         {
-          value = 10;
+            globalColourScheme = ColourSchemeProperty.getColour(alignment,
+                    Preferences.defaultColour);
+
+            if (globalColourScheme instanceof UserColourScheme)
+            {
+                globalColourScheme = UserDefinedColours.loadDefaultColours();
+            }
+
+            if (globalColourScheme != null)
+            {
+                globalColourScheme.setConsensus(vconsensus);
+            }
         }
-      }
+    }
 
-      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)));
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void showSequenceFeatures(boolean b)
+    {
+        showSequenceFeatures = b;
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    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
+            {
+                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)));
+        }
 
-      // 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();
+        }
     }
 
-    if (conservation == null)
+    /**
+     * DOCUMENT ME!
+     */
+    public void updateConsensus()
     {
-      conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than " +
-                                             ConsPercGaps + "% gaps",
-                                             annotations, 0f, // cons.qualityRange[0].floatValue(),
-                                             11f, // cons.qualityRange[1].floatValue()
-                                             1);
+        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 = Float.parseFloat(hash.get("maxCount").toString());
+            value /= Float.parseFloat(hash.get("size").toString());
+
+            value *= 100;
+
+            String maxRes = hash.get("maxResidue") + " ";
+            String mouseOver = hash.get("maxResidue") + " ";
+
+            if (maxRes.length() > 2)
+            {
+                mouseOver = "[" + maxRes + "] ";
+                maxRes = "+ ";
+            }
+
+            mouseOver += ((int) value + "%");
+            annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+        }
 
-      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 (showQuality)
-      {
-        alignment.addAnnotation(quality);
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceGroup getSelectionGroup()
+    {
+        return selectionGroup;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void setSelectionGroup(SequenceGroup sg)
     {
-      conservation.annotations = annotations;
-      quality.annotations = qannotations;
-      quality.graphMax = cons.qualityRange[1].floatValue();
+        selectionGroup = sg;
     }
-  }
 
-  public void updateConsensus()
-  {
-    Annotation[] annotations = new Annotation[alignment.getWidth()];
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getConservationSelected()
+    {
+        return conservationColourSelected;
+    }
 
-    // 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!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setConservationSelected(boolean b)
     {
-      vconsensus = alignment.getAAFrequency();
+        conservationColourSelected = b;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getAbovePIDThreshold()
     {
-      Vector temp = alignment.getAAFrequency();
-      vconsensus.clear();
+        return abovePIDThreshold;
+    }
 
-      Enumeration e = temp.elements();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAbovePIDThreshold(boolean b)
+    {
+        abovePIDThreshold = b;
+    }
 
-      while (e.hasMoreElements())
-      {
-        vconsensus.add(e.nextElement());
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartRes()
+    {
+        return startRes;
     }
 
-    Hashtable hash = null;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndRes()
+    {
+        return endRes;
+    }
 
-    for (int i = 0; i < alignment.getWidth(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartSeq()
     {
-      hash = (Hashtable) vconsensus.elementAt(i);
+        return startSeq;
+    }
 
-      float value = Float.parseFloat(hash.get("maxCount").toString());
-      value /= Float.parseFloat(hash.get("size").toString());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     */
+    public void setGlobalColourScheme(ColourSchemeI cs)
+    {
+        globalColourScheme = cs;
+    }
 
-      value *= 100;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public ColourSchemeI getGlobalColourScheme()
+    {
+        return globalColourScheme;
+    }
 
-      String maxRes = hash.get("maxResidue") + " ";
-      String mouseOver = hash.get("maxResidue") + " ";
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     */
+    public void setStartRes(int res)
+    {
+        this.startRes = res;
+    }
 
-      if (maxRes.length() > 2)
-      {
-        mouseOver = "[" + maxRes + "] ";
-        maxRes = "+ ";
-      }
+    /**
+     * 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;
+        }
 
-      mouseOver += ( (int) value + "%");
-      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+        this.endRes = res;
     }
 
-    if (consensus == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setEndSeq(int seq)
     {
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-                                          annotations, 0f, 100f, 1);
+        if (seq > alignment.getHeight())
+        {
+            seq = alignment.getHeight();
+        }
+
+        if (seq < 0)
+        {
+            seq = 0;
+        }
 
-      if (showIdentity)
-      {
-        alignment.addAnnotation(consensus);
-      }
+        this.endSeq = seq;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndSeq()
     {
-      consensus.annotations = annotations;
+        return endSeq;
     }
-  }
 
-  public SequenceGroup getSelectionGroup()
-  {
-    return selectionGroup;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param f DOCUMENT ME!
+     */
+    public void setFont(Font f)
+    {
+        font = f;
+
+        javax.swing.JFrame temp = new javax.swing.JFrame();
+        temp.addNotify();
 
-  public void setSelectionGroup(SequenceGroup sg)
-  {
-    selectionGroup = sg;
-  }
+        java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);
+        setCharHeight(fm.getHeight());
+        setCharWidth(fm.charWidth('M'));
+    }
 
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Font getFont()
+    {
+        return font;
+    }
 
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param w DOCUMENT ME!
+     */
+    public void setCharWidth(int w)
+    {
+        this.charWidth = w;
+    }
 
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getCharWidth()
+    {
+        return charWidth;
+    }
 
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param h DOCUMENT ME!
+     */
+    public void setCharHeight(int h)
+    {
+        this.charHeight = h;
+    }
 
-  public int getStartRes()
-  {
-    return startRes;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getCharHeight()
+    {
+        return charHeight;
+    }
 
-  public int getEndRes()
-  {
-    return endRes;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param w DOCUMENT ME!
+     */
+    public void setChunkWidth(int w)
+    {
+        this.chunkWidth = w;
+    }
 
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getChunkWidth()
+    {
+        return chunkWidth;
+    }
 
-  public void setGlobalColourScheme(ColourSchemeI cs)
-  {
-    globalColourScheme = cs;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param h DOCUMENT ME!
+     */
+    public void setChunkHeight(int h)
+    {
+        this.chunkHeight = h;
+    }
 
-  public ColourSchemeI getGlobalColourScheme()
-  {
-    return globalColourScheme;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getChunkHeight()
+    {
+        return chunkHeight;
+    }
 
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public AlignmentI getAlignment()
+    {
+        return alignment;
+    }
 
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param align DOCUMENT ME!
+     */
+    public void setAlignment(AlignmentI align)
+    {
+        this.alignment = align;
+    }
 
-  public void setEndRes(int res)
-  {
-    if (res > (alignment.getWidth() - 1))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setWrapAlignment(boolean state)
     {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-      res = alignment.getWidth() - 1;
+        wrapAlignment = state;
     }
 
-    if (res < 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowText(boolean state)
     {
-      res = 0;
+        showText = state;
     }
 
-    this.endRes = res;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setRenderGaps(boolean state)
+    {
+        renderGaps = state;
+    }
 
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getColourText()
     {
-      seq = alignment.getHeight();
+        return showColourText;
     }
 
-    if (seq < 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setColourText(boolean state)
     {
-      seq = 0;
+        showColourText = state;
     }
 
-    this.endSeq = seq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowBoxes(boolean state)
+    {
+        showBoxes = 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!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getWrapAlignment()
+    {
+        return wrapAlignment;
+    }
 
-  public void setCharHeight(int h)
-  {
-    this.charHeight = h;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowText()
+    {
+        return showText;
+    }
 
-  public int getCharHeight()
-  {
-    return charHeight;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowBoxes()
+    {
+        return showBoxes;
+    }
 
-  public void setChunkWidth(int w)
-  {
-    this.chunkWidth = w;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getGapCharacter()
+    {
+        return getAlignment().getGapCharacter();
+    }
 
-  public int getChunkWidth()
-  {
-    return chunkWidth;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gap DOCUMENT ME!
+     */
+    public void setGapCharacter(char gap)
+    {
+        if (getAlignment() != null)
+        {
+            getAlignment().setGapCharacter(gap);
+        }
+    }
 
-  public void setChunkHeight(int h)
-  {
-    this.chunkHeight = h;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param thresh DOCUMENT ME!
+     */
+    public void setThreshold(int thresh)
+    {
+        threshold = thresh;
+    }
 
-  public int getChunkHeight()
-  {
-    return chunkHeight;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getThreshold()
+    {
+        return threshold;
+    }
 
-  public AlignmentI getAlignment()
-  {
-    return alignment;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param inc DOCUMENT ME!
+     */
+    public void setIncrement(int inc)
+    {
+        increment = inc;
+    }
 
-  public void setAlignment(AlignmentI align)
-  {
-    this.alignment = align;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getIncrement()
+    {
+        return increment;
+    }
 
-  public void setWrapAlignment(boolean state)
-  {
-    wrapAlignment = state;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param y DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getIndex(int y)
+    {
+        int y1 = 0;
+        int starty = getStartSeq();
+        int endy = getEndSeq();
 
-  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();
-
-        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;
-      }
-    }
-
-    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);
-  }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public ColumnSelection getColumnSelection()
+    {
+        return colSel;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param height DOCUMENT ME!
+     */
+    public void resetSeqLimits(int height)
+    {
+        setEndSeq(height / getCharHeight());
+    }
+
+    /**
+     * 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;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @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);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @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);
+    }
 }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 1a48af6..e312510 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -18,804 +18,1040 @@
  */
 package jalview.gui;
 
-import java.io.*;
-import javax.imageio.*;
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
+import org.jibble.epsgraphics.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
 import java.awt.print.*;
+
+import java.io.*;
+
+import javax.imageio.*;
+
 import javax.swing.*;
 
-import org.jibble.epsgraphics.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
 
-public class AlignmentPanel
-    extends GAlignmentPanel implements AdjustmentListener, Printable
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentPanel extends GAlignmentPanel
+    implements AdjustmentListener, Printable
 {
-  AlignViewport av;
-  OverviewPanel overviewPanel;
-  SeqPanel seqPanel;
-  IdPanel idPanel;
-  IdwidthAdjuster idwidthAdjuster;
-  public AlignFrame alignFrame;
-  ScalePanel scalePanel;
-  AnnotationPanel annotationPanel;
-  AnnotationLabels alabels;
-
-  // this value is set false when selection area being dragged
-  boolean fastPaint = true;
-  int hextent = 0;
-  int vextent = 0;
-
-  public AlignmentPanel(AlignFrame af, final AlignViewport av)
-  {
-    alignFrame = af;
-    this.av = av;
-    seqPanel = new SeqPanel(av, this);
-    idPanel = new IdPanel(av, this);
-
-    scalePanel = new ScalePanel(av, this);
-
-    idPanelHolder.add(idPanel, BorderLayout.CENTER);
-    idwidthAdjuster = new IdwidthAdjuster(this);
-    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
-
-    annotationPanel = new AnnotationPanel(this);
-    alabels = new AnnotationLabels(this);
-
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
-    annotationScroller.setViewportView(annotationPanel);
-    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
-
-    fontChanged();
-
-    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-
-    setScrollValues(0, 0);
-
-    hscroll.addAdjustmentListener(this);
-    vscroll.addAdjustmentListener(this);
-
-    setFocusable(true);
-    addKeyListener(new KeyAdapter()
+    AlignViewport av;
+    OverviewPanel overviewPanel;
+    SeqPanel seqPanel;
+    IdPanel idPanel;
+    IdwidthAdjuster idwidthAdjuster;
+
+    /** DOCUMENT ME!! */
+    public AlignFrame alignFrame;
+    ScalePanel scalePanel;
+    AnnotationPanel annotationPanel;
+    AnnotationLabels alabels;
+
+    // this value is set false when selection area being dragged
+    boolean fastPaint = true;
+    int hextent = 0;
+    int vextent = 0;
+
+    /**
+     * Creates a new AlignmentPanel object.
+     *
+     * @param af DOCUMENT ME!
+     * @param av DOCUMENT ME!
+     */
+    public AlignmentPanel(AlignFrame af, final AlignViewport av)
     {
-      public void keyPressed(KeyEvent evt)
-      {
-        switch (evt.getKeyCode())
-        {
-          case 27: // escape key
-            av.setSelectionGroup(null);
-            repaint();
+        alignFrame = af;
+        this.av = av;
+        seqPanel = new SeqPanel(av, this);
+        idPanel = new IdPanel(av, this);
 
-            break;
+        scalePanel = new ScalePanel(av, this);
 
-          case KeyEvent.VK_DOWN:
-            alignFrame.moveSelectedSequences(false);
+        idPanelHolder.add(idPanel, BorderLayout.CENTER);
+        idwidthAdjuster = new IdwidthAdjuster(this);
+        idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
 
-            break;
+        annotationPanel = new AnnotationPanel(this);
+        alabels = new AnnotationLabels(this);
 
-          case KeyEvent.VK_UP:
-            alignFrame.moveSelectedSequences(true);
+        annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+        annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+        annotationScroller.setViewportView(annotationPanel);
+        annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
-            break;
-        }
-      }
-    });
-  }
-
-  public void fontChanged()
-  {
-    // set idCanvas bufferedImage to null
-    // to prevent drawing old image
-    FontMetrics fm = getFontMetrics(av.getFont());
-
-    scalePanelHolder.setPreferredSize(new Dimension(10,
-        av.charHeight + fm.getDescent()));
-    idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
-        av.charHeight + fm.getDescent()));
-
-    idPanel.idCanvas.gg = null;
-    annotationPanel.adjustPanelHeight();
-
-    Dimension d = calculateIdWidth();
-    d.setSize(d.width + 4, d.height);
-    idPanel.idCanvas.setPreferredSize(d);
-    hscrollFillerPanel.setPreferredSize(d);
-    repaint();
-  }
-
-  Dimension calculateIdWidth()
-  {
-    Graphics g = this.getGraphics();
-
-    if (g == null)
-    {
-      javax.swing.JFrame f = new javax.swing.JFrame();
-      f.addNotify();
-      g = f.getGraphics();
-    }
+        fontChanged();
 
-    FontMetrics fm = g.getFontMetrics(av.font);
-    AlignmentI al = av.getAlignment();
+        scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+        seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
-    int i = 0;
-    int idWidth = 0;
-    String id;
+        setScrollValues(0, 0);
 
-    while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
-    {
-      SequenceI s = al.getSequenceAt(i);
+        hscroll.addAdjustmentListener(this);
+        vscroll.addAdjustmentListener(this);
 
-      if (av.getShowFullId())
-      {
-        id = s.getDisplayId();
-      }
-      else
-      {
-        id = s.getName();
-      }
+        setFocusable(true);
+        addKeyListener(new KeyAdapter()
+            {
+                public void keyPressed(KeyEvent evt)
+                {
+                    switch (evt.getKeyCode())
+                    {
+                    case 27: // escape key
+                        av.setSelectionGroup(null);
+                        repaint();
 
-      if (fm.stringWidth(id) > idWidth)
-      {
-        idWidth = fm.stringWidth(id);
-      }
+                        break;
+
+                    case KeyEvent.VK_DOWN:
+                        alignFrame.moveSelectedSequences(false);
 
-      i++;
+                        break;
+
+                    case KeyEvent.VK_UP:
+                        alignFrame.moveSelectedSequences(true);
+
+                        break;
+                    }
+                }
+            });
     }
 
-    // Also check annotation label widths
-    i = 0;
+    /**
+     * DOCUMENT ME!
+     */
+    public void fontChanged()
+    {
+        // set idCanvas bufferedImage to null
+        // to prevent drawing old image
+        FontMetrics fm = getFontMetrics(av.getFont());
+
+        scalePanelHolder.setPreferredSize(new Dimension(10,
+                av.charHeight + fm.getDescent()));
+        idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
+                av.charHeight + fm.getDescent()));
+
+        idPanel.idCanvas.gg = null;
+        annotationPanel.adjustPanelHeight();
+
+        Dimension d = calculateIdWidth();
+        d.setSize(d.width + 4, d.height);
+        idPanel.idCanvas.setPreferredSize(d);
+        hscrollFillerPanel.setPreferredSize(d);
+        repaint();
+    }
 
-    if (al.getAlignmentAnnotation() != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension calculateIdWidth()
     {
-      fm = g.getFontMetrics(alabels.getFont());
+        Graphics g = this.getGraphics();
 
-      while (i < al.getAlignmentAnnotation().length)
-      {
-        String label = al.getAlignmentAnnotation()[i].label;
+        if (g == null)
+        {
+            javax.swing.JFrame f = new javax.swing.JFrame();
+            f.addNotify();
+            g = f.getGraphics();
+        }
+
+        FontMetrics fm = g.getFontMetrics(av.font);
+        AlignmentI al = av.getAlignment();
 
-        if (fm.stringWidth(label) > idWidth)
+        int i = 0;
+        int idWidth = 0;
+        String id;
+
+        while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
         {
-          idWidth = fm.stringWidth(label);
+            SequenceI s = al.getSequenceAt(i);
+
+            if (av.getShowFullId())
+            {
+                id = s.getDisplayId();
+            }
+            else
+            {
+                id = s.getName();
+            }
+
+            if (fm.stringWidth(id) > idWidth)
+            {
+                idWidth = fm.stringWidth(id);
+            }
+
+            i++;
         }
 
-        i++;
-      }
-    }
+        // Also check annotation label widths
+        i = 0;
 
-    return new Dimension(idWidth, 12);
-  }
+        if (al.getAlignmentAnnotation() != null)
+        {
+            fm = g.getFontMetrics(alabels.getFont());
 
-  public void highlightSearchResults(int[] results)
-  {
-    seqPanel.seqCanvas.highlightSearchResults(results);
+            while (i < al.getAlignmentAnnotation().length)
+            {
+                String label = al.getAlignmentAnnotation()[i].label;
 
-    // do we need to scroll the panel?
-    if (results != null)
-    {
-      SequenceI seq = av.alignment.getSequenceAt(results[0]);
-      int start = seq.findIndex(results[1]) - 1;
-      int end = seq.findIndex(results[2]) - 1;
+                if (fm.stringWidth(label) > idWidth)
+                {
+                    idWidth = fm.stringWidth(label);
+                }
 
-      if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
-          ( (av.getStartSeq() > results[0]) ||
-           (av.getEndSeq() < results[0])))
-      {
-        setScrollValues(start, results[0]);
-      }
+                i++;
+            }
+        }
+
+        return new Dimension(idWidth, 12);
     }
-  }
-
-  public OverviewPanel getOverviewPanel()
-  {
-    return overviewPanel;
-  }
-
-  public void setOverviewPanel(OverviewPanel op)
-  {
-    overviewPanel = op;
-  }
-
-  public void setAnnotationVisible(boolean b)
-  {
-    annotationSpaceFillerHolder.setVisible(b);
-    annotationScroller.setVisible(b);
-  }
-
-  public void setWrapAlignment(boolean wrap)
-  {
-    scalePanelHolder.setVisible(!wrap);
-    hscroll.setVisible(!wrap);
-    idwidthAdjuster.setVisible(!wrap);
-
-    av.setShowAnnotation(!wrap);
-    annotationScroller.setVisible(!wrap);
-    annotationSpaceFillerHolder.setVisible(!wrap);
-    idSpaceFillerPanel1.setVisible(!wrap);
-
-    repaint();
-  }
-
-  public void setColourScheme()
-  {
-    ColourSchemeI cs = av.getGlobalColourScheme();
-
-    if (av.getConservationSelected())
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param results DOCUMENT ME!
+     */
+    public void highlightSearchResults(int[] results)
     {
-      Alignment al = (Alignment) av.getAlignment();
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth());
+        seqPanel.seqCanvas.highlightSearchResults(results);
 
-      c.calculate();
-      c.verdict(false, av.ConsPercGaps);
+        // do we need to scroll the panel?
+        if (results != null)
+        {
+            SequenceI seq = av.alignment.getSequenceAt(results[0]);
+            int start = seq.findIndex(results[1]) - 1;
+            int end = seq.findIndex(results[2]) - 1;
+
+            if ((av.getStartRes() > start) || (av.getEndRes() < end) ||
+                    ((av.getStartSeq() > results[0]) ||
+                    (av.getEndSeq() < results[0])))
+            {
+                setScrollValues(start, results[0]);
+            }
+        }
+    }
 
-      ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public OverviewPanel getOverviewPanel()
+    {
+        return overviewPanel;
+    }
 
-      av.setGlobalColourScheme(ccs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param op DOCUMENT ME!
+     */
+    public void setOverviewPanel(OverviewPanel op)
+    {
+        overviewPanel = op;
     }
 
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAnnotationVisible(boolean b)
+    {
+        annotationSpaceFillerHolder.setVisible(b);
+        annotationScroller.setVisible(b);
+    }
 
-  // return value is true if the scroll is valid
-  public boolean scrollUp(boolean up)
-  {
-    if (up)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param wrap DOCUMENT ME!
+     */
+    public void setWrapAlignment(boolean wrap)
     {
-      if (vscroll.getValue() < 1)
-      {
-        return false;
-      }
+        scalePanelHolder.setVisible(!wrap);
+        hscroll.setVisible(!wrap);
+        idwidthAdjuster.setVisible(!wrap);
 
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() - 1);
+        av.setShowAnnotation(!wrap);
+        annotationScroller.setVisible(!wrap);
+        annotationSpaceFillerHolder.setVisible(!wrap);
+        idSpaceFillerPanel1.setVisible(!wrap);
+
+        repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void setColourScheme()
     {
-      if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
-      {
-        return false;
-      }
+        ColourSchemeI cs = av.getGlobalColourScheme();
 
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() + 1);
-    }
+        if (av.getConservationSelected())
+        {
+            Alignment al = (Alignment) av.getAlignment();
+            Conservation c = new Conservation("All",
+                    ResidueProperties.propHash, 3, al.getSequences(), 0,
+                    al.getWidth());
 
-    fastPaint = true;
+            c.calculate();
+            c.verdict(false, av.ConsPercGaps);
 
-    return true;
-  }
+            ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
-  public boolean scrollRight(boolean right)
-  {
-    if (right)
-    {
-      if (hscroll.getValue() < 1)
-      {
-        return false;
-      }
+            av.setGlobalColourScheme(ccs);
+        }
 
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() - 1);
+        repaint();
     }
-    else
+
+    // return value is true if the scroll is valid
+    public boolean scrollUp(boolean up)
     {
-      if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
-      {
-        return false;
-      }
+        if (up)
+        {
+            if (vscroll.getValue() < 1)
+            {
+                return false;
+            }
+
+            fastPaint = false;
+            vscroll.setValue(vscroll.getValue() - 1);
+        }
+        else
+        {
+            if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+            {
+                return false;
+            }
 
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() + 1);
+            fastPaint = false;
+            vscroll.setValue(vscroll.getValue() + 1);
+        }
+
+        fastPaint = true;
+
+        return true;
     }
 
-    fastPaint = true;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param right DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean scrollRight(boolean right)
+    {
+        if (right)
+        {
+            if (hscroll.getValue() < 1)
+            {
+                return false;
+            }
 
-    return true;
-  }
+            fastPaint = false;
+            hscroll.setValue(hscroll.getValue() - 1);
+        }
+        else
+        {
+            if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+            {
+                return false;
+            }
 
-  public void setScrollValues(int x, int y)
-  {
-    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
-                 1);
+            fastPaint = false;
+            hscroll.setValue(hscroll.getValue() + 1);
+        }
 
-    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
-    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+        fastPaint = true;
 
-    if (hextent > av.alignment.getWidth())
-    {
-      hextent = av.alignment.getWidth();
+        return true;
     }
 
-    if (vextent > av.alignment.getHeight())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param x DOCUMENT ME!
+     * @param y DOCUMENT ME!
+     */
+    public void setScrollValues(int x, int y)
     {
-      vextent = av.alignment.getHeight();
-    }
+        av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
+            1);
 
-    if ( (hextent + x) > av.getAlignment().getWidth())
-    {
-      x = av.getAlignment().getWidth() - hextent;
-    }
+        hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+        vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if ( (vextent + y) > av.getAlignment().getHeight())
-    {
-      y = av.getAlignment().getHeight() - vextent;
-    }
+        if (hextent > av.alignment.getWidth())
+        {
+            hextent = av.alignment.getWidth();
+        }
 
-    if (y < 0)
-    {
-      y = 0;
-    }
+        if (vextent > av.alignment.getHeight())
+        {
+            vextent = av.alignment.getHeight();
+        }
 
-    if (x < 0)
-    {
-      x = 0;
-    }
+        if ((hextent + x) > av.getAlignment().getWidth())
+        {
+            x = av.getAlignment().getWidth() - hextent;
+        }
 
-    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
-    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
-  }
+        if ((vextent + y) > av.getAlignment().getHeight())
+        {
+            y = av.getAlignment().getHeight() - vextent;
+        }
 
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
+        if (y < 0)
+        {
+            y = 0;
+        }
 
-    if (evt.getSource() == hscroll)
-    {
-      int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes( (x +
-                     (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+        if (x < 0)
+        {
+            x = 0;
+        }
+
+        hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
+        vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
     }
 
-    if (evt.getSource() == vscroll)
+    public void this_mouseWheelMoved(MouseWheelEvent e)
     {
-      int offy = vscroll.getValue();
-
-      if (av.getWrapAlignment())
-      {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-            seqCanvas.getWidth());
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes( (vscroll.getValue() + 1) * rowSize);
-      }
+      if(e.getWheelRotation()>0)
+        scrollUp(false);
       else
-      {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy +
-                     (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
-      }
+        scrollUp(true);
     }
 
-    if (overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
-    }
 
-    if (av.getWrapAlignment() || !fastPaint)
-    {
-      repaint();
-    }
-    else
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void adjustmentValueChanged(AdjustmentEvent evt)
     {
-      idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
-      seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
-                                   av.getStartSeq() - oldY);
+        int oldX = av.getStartRes();
+        int oldY = av.getStartSeq();
 
-      scalePanel.repaint();
+        if (evt.getSource() == hscroll)
+        {
+            int x = hscroll.getValue();
+            av.setStartRes(x);
+            av.setEndRes((x +
+                (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+        }
 
-      if (av.getShowAnnotation())
-      {
-        annotationPanel.fastPaint(av.getStartRes() - oldX);
-      }
-    }
-  }
+        if (evt.getSource() == vscroll)
+        {
+            int offy = vscroll.getValue();
+
+            if (av.getWrapAlignment())
+            {
+                int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+                av.setStartRes(vscroll.getValue() * rowSize);
+                av.setEndRes((vscroll.getValue() + 1) * rowSize);
+            }
+            else
+            {
+                av.setStartSeq(offy);
+                av.setEndSeq(offy +
+                    (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+            }
+        }
 
-  public void paintComponent(Graphics g)
-  {
-    invalidate();
+        if (overviewPanel != null)
+        {
+            overviewPanel.setBoxPosition();
+        }
 
-    Dimension d = idPanel.idCanvas.getPreferredSize();
-    idPanelHolder.setPreferredSize(d);
-    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
-    validate();
+        if (av.getWrapAlignment() || !fastPaint)
+        {
+            repaint();
+        }
+        else
+        {
+            idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
+            seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
+                av.getStartSeq() - oldY);
 
-    if (av.getWrapAlignment())
-    {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-      vscroll.setMaximum(max);
-      vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
-    }
-    else
-    {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+            scalePanel.repaint();
+
+            if (av.getShowAnnotation())
+            {
+                annotationPanel.fastPaint(av.getStartRes() - oldX);
+            }
+        }
     }
-  }
 
-  public int print(Graphics pg, PageFormat pf, int pi)
-      throws PrinterException
-  {
-    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
+    {
+        invalidate();
 
-    int pwidth = (int) pf.getImageableWidth();
-    int pheight = (int) pf.getImageableHeight();
+        Dimension d = idPanel.idCanvas.getPreferredSize();
+        idPanelHolder.setPreferredSize(d);
+        hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+        validate();
 
-    if (av.getWrapAlignment())
-    {
-      return printWrappedAlignment(pg, pwidth, pheight, pi);
+        if (av.getWrapAlignment())
+        {
+            int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+            vscroll.setMaximum(max);
+            vscroll.setUnitIncrement(1);
+            vscroll.setVisibleAmount(1);
+        }
+        else
+        {
+            setScrollValues(av.getStartRes(), av.getStartSeq());
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pg DOCUMENT ME!
+     * @param pf DOCUMENT ME!
+     * @param pi DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     *
+     * @throws PrinterException DOCUMENT ME!
+     */
+    public int print(Graphics pg, PageFormat pf, int pi)
+        throws PrinterException
     {
-      return printUnwrapped(pg, pwidth, pheight, pi);
-    }
-  }
+        pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
 
-  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
-      throws PrinterException
-  {
-    int idWidth = calculateIdWidth().width + 4;
-    FontMetrics fm = getFontMetrics(av.getFont());
-    int scaleHeight = av.charHeight + fm.getDescent();
+        int pwidth = (int) pf.getImageableWidth();
+        int pheight = (int) pf.getImageableHeight();
 
-    pg.setColor(Color.white);
-    pg.fillRect(0, 0, pwidth, pheight);
-    pg.setFont(av.getFont());
+        if (av.getWrapAlignment())
+        {
+            return printWrappedAlignment(pg, pwidth, pheight, pi);
+        }
+        else
+        {
+            return printUnwrapped(pg, pwidth, pheight, pi);
+        }
+    }
 
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
-    int totalRes = (pwidth - idWidth) / av.getCharWidth();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pg DOCUMENT ME!
+     * @param pwidth DOCUMENT ME!
+     * @param pheight DOCUMENT ME!
+     * @param pi DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     *
+     * @throws PrinterException DOCUMENT ME!
+     */
+    public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+        throws PrinterException
+    {
+        int idWidth = calculateIdWidth().width + 4;
+        FontMetrics fm = getFontMetrics(av.getFont());
+        int scaleHeight = av.charHeight + fm.getDescent();
 
-    int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
-        1;
+        pg.setColor(Color.white);
+        pg.fillRect(0, 0, pwidth, pheight);
+        pg.setFont(av.getFont());
 
-    int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+        ////////////////////////////////////
+        /// How many sequences and residues can we fit on a printable page?
+        int totalRes = (pwidth - idWidth) / av.getCharWidth();
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
-    int startRes;
+        int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -
+            1;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
-    int endRes;
+        int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
-    int startSeq;
+        /////////////////////////////
+        /// Only print these sequences and residues on this page
+        int startRes;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
-    int endSeq;
-    startRes = (pi % pagesWide) * totalRes;
-    endRes = (startRes + totalRes) - 1;
+        /////////////////////////////
+        /// Only print these sequences and residues on this page
+        int endRes;
 
-    if (endRes > (av.getAlignment().getWidth() - 1))
-    {
-      endRes = av.getAlignment().getWidth() - 1;
-    }
+        /////////////////////////////
+        /// Only print these sequences and residues on this page
+        int startSeq;
 
-    startSeq = (pi / pagesWide) * totalSeq;
-    endSeq = startSeq + totalSeq;
+        /////////////////////////////
+        /// Only print these sequences and residues on this page
+        int endSeq;
+        startRes = (pi % pagesWide) * totalRes;
+        endRes = (startRes + totalRes) - 1;
 
-    if (endSeq > av.getAlignment().getHeight())
-    {
-      endSeq = av.getAlignment().getHeight();
-    }
+        if (endRes > (av.getAlignment().getWidth() - 1))
+        {
+            endRes = av.getAlignment().getWidth() - 1;
+        }
 
-    int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
+        startSeq = (pi / pagesWide) * totalSeq;
+        endSeq = startSeq + totalSeq;
 
-    if (av.showAnnotation)
-    {
-      pagesHigh += annotationPanel.getHeight();
-    }
+        if (endSeq > av.getAlignment().getHeight())
+        {
+            endSeq = av.getAlignment().getHeight();
+        }
 
-    pagesHigh /= pheight;
+        int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
 
-    if (pi >= (pagesWide * pagesHigh))
-    {
-      return Printable.NO_SUCH_PAGE;
-    }
+        if (av.showAnnotation)
+        {
+            pagesHigh += annotationPanel.getHeight();
+        }
 
-    //draw Scale
-    pg.translate(idWidth, 0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
-    pg.translate( -idWidth, scaleHeight);
+        pagesHigh /= pheight;
 
-    ////////////////
-    // Draw the ids
-    Color currentColor = null;
-    Color currentTextColor = null;
+        if (pi >= (pagesWide * pagesHigh))
+        {
+            return Printable.NO_SUCH_PAGE;
+        }
 
-    for (int i = startSeq; i < endSeq; i++)
-    {
-      if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().sequences.contains(
-              av.getAlignment().getSequenceAt(i)))
-      {
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
-      {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
-        currentTextColor = Color.black;
-      }
+        //draw Scale
+        pg.translate(idWidth, 0);
+        scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+        pg.translate(-idWidth, scaleHeight);
 
-      pg.setColor(currentColor);
-      pg.fillRect(0,
-                  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
-          av.getCharHeight()), idWidth, av.getCharHeight());
+        ////////////////
+        // Draw the ids
+        Color currentColor = null;
+        Color currentTextColor = null;
 
-      pg.setColor(currentTextColor);
+        for (int i = startSeq; i < endSeq; i++)
+        {
+            if ((av.getSelectionGroup() != null) &&
+                    av.getSelectionGroup().sequences.contains(
+                        av.getAlignment().getSequenceAt(i)))
+            {
+                currentColor = Color.gray;
+                currentTextColor = Color.black;
+            }
+            else
+            {
+                currentColor = av.getAlignment().getSequenceAt(i).getColor();
+                currentTextColor = Color.black;
+            }
+
+            pg.setColor(currentColor);
+            pg.fillRect(0, (i-startSeq) * av.charHeight, idWidth,
+                av.getCharHeight());
+
+            pg.setColor(currentTextColor);
+
+            String string = av.getAlignment().getSequenceAt(i).getName();
+
+            if (av.getShowFullId())
+            {
+                string = av.getAlignment().getSequenceAt(i).getDisplayId();
+            }
+
+            pg.drawString(string, 0,
+                (((i-startSeq) * av.charHeight) + av.getCharHeight()) -
+                (av.getCharHeight() / 5));
+        }
 
-      String string = av.getAlignment().getSequenceAt(i).getName();
+        // draw main sequence panel
+        pg.translate(idWidth, 0);
+        seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
+            startRes, startSeq, 0);
 
-      if (av.getShowFullId())
-      {
-        string = av.getAlignment().getSequenceAt(i).getDisplayId();
-      }
+        if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+        {
+            pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight);
+            alabels.drawComponent((Graphics2D) pg);
+            pg.translate(idWidth, 0);
+            annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +
+                1);
+        }
 
-      pg.drawString(string, 0,
-                    (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
-          av.getCharHeight()) + av.getCharHeight()) -
-                    (av.getCharHeight() / 5));
+        return Printable.PAGE_EXISTS;
     }
 
-    // draw main sequence panel
-    pg.translate(idWidth, 0);
-    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
-                                 startRes, startSeq, 0);
-
-    if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pg DOCUMENT ME!
+     * @param pwidth DOCUMENT ME!
+     * @param pheight DOCUMENT ME!
+     * @param pi DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     *
+     * @throws PrinterException DOCUMENT ME!
+     */
+    public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+        int pi) throws PrinterException
     {
-      pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
-      alabels.drawComponent( (Graphics2D) pg);
-      pg.translate(idWidth, 0);
-      annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
-                                    1);
-    }
+        int idWidth = calculateIdWidth().width + 4;
 
-    return Printable.PAGE_EXISTS;
-  }
+        int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+                idWidth);
+        int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +
+                1) * av.charHeight;
 
-  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
-                                   int pi)
-      throws PrinterException
-  {
-    int idWidth = calculateIdWidth().width + 4;
+        pg.setColor(Color.white);
+        pg.fillRect(0, 0, pwidth, pheight);
+        pg.setFont(av.getFont());
 
-    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
-        idWidth);
-    int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
-        ( (av.alignment.getWidth() / resWidth) +
-         1) * av.charHeight;
+        ////////////////
+        // Draw the ids
+        pg.setColor(Color.black);
 
-    pg.setColor(Color.white);
-    pg.fillRect(0, 0, pwidth, pheight);
-    pg.setFont(av.getFont());
+        pg.translate(0, -pi * pheight);
 
-    ////////////////
-    // Draw the ids
-    pg.setColor(Color.black);
+        pg.setClip(0, pi * pheight, pwidth, pheight);
 
-    pg.translate(0, -pi * pheight);
+        int ypos = 2 * av.charHeight;
 
-    pg.setClip(0, pi * pheight, pwidth, pheight);
+        do
+        {
+            for (int i = 0; i < av.alignment.getHeight(); i++)
+            {
+                SequenceI s = av.alignment.getSequenceAt(i);
+                String string = s.getName();
+
+                if (av.getShowFullId())
+                {
+                    string = s.getDisplayId();
+                }
+
+                pg.drawString(string, 0,
+                    ((i * av.charHeight) + ypos + av.charHeight) -
+                    (av.charHeight / 5));
+            }
+
+            ypos += ((av.alignment.getHeight() + 2) * av.charHeight);
+        }
+        while (ypos < totalHeight);
 
-    int ypos = 2 * av.charHeight;
+        pg.translate(idWidth, 0);
 
-    do
-    {
-      for (int i = 0; i < av.alignment.getHeight(); i++)
-      {
-        SequenceI s = av.alignment.getSequenceAt(i);
-        String string = s.getName();
+        seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
 
-        if (av.getShowFullId())
+        if ((pi * pheight) < totalHeight)
+        {
+            return Printable.PAGE_EXISTS;
+        }
+        else
         {
-          string = s.getDisplayId();
+            return Printable.NO_SUCH_PAGE;
         }
+    }
 
-        pg.drawString(string, 0,
-                      (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
-                       av.charHeight) - (av.charHeight / 5));
-      }
+    /**
+     * DOCUMENT ME!
+     */
+    public void makeEPS(File epsFile)
+    {
+        if(epsFile == null)
+        {
+          jalview.io.JalviewFileChooser chooser = new jalview.io.
+              JalviewFileChooser(jalview.bin.Cache.getProperty(
+                  "LAST_DIRECTORY"), new String[]
+                                 {"eps"},
+                                 new String[]
+                                 {"Encapsulated Postscript"},
+                                 "Encapsulated Postscript");
+          chooser.setFileView(new jalview.io.JalviewFileView());
+          chooser.setDialogTitle("Create EPS file from alignment");
+          chooser.setToolTipText("Save");
+
+          int value = chooser.showSaveDialog(this);
+
+          if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+          {
+            return;
+          }
+
+          epsFile = chooser.getSelectedFile();
+
+          jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                        chooser.getSelectedFile().getParent());
+        }
 
-      ypos += ( (av.alignment.getHeight() + 2) * av.charHeight);
-    }
-    while (ypos < totalHeight);
+        int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+        int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
 
-    pg.translate(idWidth, 0);
+        if (av.getWrapAlignment())
+        {
+          height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
+              av.chunkHeight;
+          width = seqPanel.getWidth() + idPanel.getWidth();
 
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+        }
 
-    if ( (pi * pheight) < totalHeight)
-    {
-      return Printable.PAGE_EXISTS;
-    }
-    else
-    {
-      return Printable.NO_SUCH_PAGE;
-    }
-  }
 
-  public void makeEPS()
-  {
-    int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
-        av.chunkHeight;
-    int width = seqPanel.getWidth() + idPanel.getWidth();
+        if (av.getShowAnnotation())
+        {
+            height += annotationPanel.getPreferredSize().height;
+        }
 
-    if (!av.getWrapAlignment())
-    {
-      height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
-      width = idPanel.getWidth() +
-          (av.alignment.getWidth() * av.charWidth);
+        try
+         {
+            FileOutputStream out = new FileOutputStream(epsFile);
+            EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
+                    height);
+
+            if (av.getWrapAlignment())
+            {
+                printWrappedAlignment(pg, width, height, 0);
+            }
+            else
+            {
+                printUnwrapped(pg, width, height, 0);
+            }
+
+            pg.flush();
+            pg.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
     }
 
-    if (av.getShowAnnotation())
+
+    public void makePNGImageMap(File imgMapFile, String imageName)
     {
-      height += annotationPanel.getPreferredSize().height;
+      ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+      //////////////////////////////////////////////
+      int idWidth = calculateIdWidth().width + 4;
+      FontMetrics fm = getFontMetrics(av.getFont());
+      int scaleHeight = av.charHeight + fm.getDescent();
+
+        // Gen image map
+         //////////////////////////////////
+         if(imgMapFile!=null)
+         {
+           try
+           {
+             PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+             out.println(jalview.io.HTMLOutput.getImageMapHTML());
+             out.println("<img src=\"" + imageName +
+                       "\" border=\"0\" usemap=\"#Map\" >"
+                       +"<map name=\"Map\">");
+
+             for (int s = 0; s < av.alignment.getHeight(); s++)
+             {
+               SequenceI seq = av.alignment.getSequenceAt(s);
+               SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+               for (int i = 0; i < groups.length; i++)
+               {
+                 int sy = s * av.charHeight + scaleHeight;
+                 for (int res = groups[i].getStartRes();
+                      res < groups[i].getEndRes() + 1; res++)
+                 {
+                   int alIndex = seq.findPosition(res);
+                   Object obj = ResidueProperties.aa2Triplet.get(
+                       seq.getCharAt(res) + "");
+                   if (obj == null)
+                     continue;
+
+                   String triplet = obj.toString();
+
+                   out.println(
+                       "<area shape=\"rect\" coords=\""
+                       + (idWidth + res * av.charWidth) + ","
+                       + sy + ","
+                       + (idWidth + (res + 1) * av.charWidth) + ","
+                       + (av.charHeight + sy) + "\""
+                       + " onMouseOver=\"toolTip('"
+                       + alIndex + " " + triplet +
+                       "<br><em>" + groups[i].getName() +
+                       "</em>')\"; onMouseOut=\"toolTip()\"; "
+                       + " href=\"#\">");
+                 }
+               }
+             }
+
+             out.println("</map></body></html>");
+             out.close();
+
+           }
+           catch (Exception ex)
+           {
+             ex.printStackTrace();
+           }
+         }///////////END OF IMAGE MAP
+
     }
 
-    try
+    /**
+     * DOCUMENT ME!
+     */
+    public void makePNG(File pngFile)
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-          jalview.bin.Cache.getProperty(
-              "LAST_DIRECTORY"), new String[]
-          {"eps"},
-          new String[]
-          {"Encapsulated Postscript"},
-          "Encapsulated Postscript");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from alignment");
-      chooser.setToolTipText("Save");
-
-      int value = chooser.showSaveDialog(this);
-
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      if(pngFile==null)
       {
-        return;
+        jalview.io.JalviewFileChooser chooser = new jalview.io.
+            JalviewFileChooser(jalview.bin.Cache.getProperty(
+                "LAST_DIRECTORY"), new String[]
+                               {"png"},
+                               new String[]
+                               {"Portable network graphics"},
+                               "Portable network graphics");
+        chooser.setFileView(new jalview.io.JalviewFileView());
+        chooser.setDialogTitle("Create EPS file from alignment");
+        chooser.setToolTipText("Save");
+
+        int value = chooser.showSaveDialog(this);
+
+        if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        {
+          return;
+        }
+
+        pngFile = chooser.getSelectedFile();
+
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                      chooser.getSelectedFile().getParent());
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
 
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-      EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
-                                           height);
+
+      int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+      int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
 
       if (av.getWrapAlignment())
       {
-        printWrappedAlignment(pg, width, height, 0);
-      }
-      else
-      {
-        printUnwrapped(pg, width, height, 0);
-      }
+        height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
+            av.chunkHeight;
+        width = seqPanel.getWidth() + idPanel.getWidth();
 
-      pg.flush();
-      pg.close();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
+      }
 
-  public void makePNG()
-  {
-    int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
-        av.chunkHeight;
-    int width = seqPanel.getWidth() + idPanel.getWidth();
 
-    if (!av.getWrapAlignment())
-    {
-      height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
-      width = idPanel.getWidth() +
-          (av.alignment.getWidth() * av.charWidth);
-    }
+        if (av.getShowAnnotation())
+        {
+            height += annotationPanel.getPreferredSize().height;
+        }
 
-    if (av.getShowAnnotation())
-    {
-      height += annotationPanel.getPreferredSize().height;
-    }
+        try
+        {
 
-    try
-    {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-          jalview.bin.Cache.getProperty(
-              "LAST_DIRECTORY"), new String[]
-          {"png"},
-          new String[]
-          {"Portable network graphics"},
-          "Portable network graphics");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from alignment");
-      chooser.setToolTipText("Save");
-
-      int value = chooser.showSaveDialog(this);
-
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-      {
-        return;
-      }
+            FileOutputStream out = new FileOutputStream(pngFile);
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+            BufferedImage bi = new BufferedImage(width, height,
+                    BufferedImage.TYPE_INT_RGB);
+            Graphics2D png = (Graphics2D) bi.getGraphics();
 
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                RenderingHints.VALUE_ANTIALIAS_ON);
 
-      BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
-      Graphics2D png = (Graphics2D) bi.getGraphics();
+            if (av.getWrapAlignment())
+            {
+                printWrappedAlignment(png, width, height, 0);
+            }
+            else
+            {
+                printUnwrapped(png, width, height, 0);
+            }
 
-      png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                           RenderingHints.VALUE_ANTIALIAS_ON);
+            ImageIO.write(bi, "png", out);
+            out.close();
+        }
+        catch(OutOfMemoryError err)
+        {
+          System.out.println("########################\n"
+                             +"OUT OF MEMORY "+pngFile+"\n"
+                             +"########################");
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
+}
 
-      if (av.getWrapAlignment())
-      {
-        printWrappedAlignment(png, width, height, 0);
-      }
-      else
-      {
-        printUnwrapped(png, width, height, 0);
-      }
 
-      ImageIO.write(bi, "png", out);
-      out.close();
-    }
-    catch (Exception ex)
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+class Preview extends JFrame
+{
+    /**
+     * Creates a new Preview object.
+     *
+     * @param image DOCUMENT ME!
+     */
+    public Preview(Image image)
     {
-      ex.printStackTrace();
+        setResizable(true);
+        setSize(image.getWidth(this), image.getHeight(this));
+        setVisible(true);
+        getContentPane().setLayout(new BorderLayout());
+        getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
+        validate();
+        repaint();
     }
-  }
 }
 
-class Preview
-    extends JFrame
-{
-  public Preview(Image image)
-  {
-    setResizable(true);
-    setSize(image.getWidth(this), image.getHeight(this));
-    setVisible(true);
-    getContentPane().setLayout(new BorderLayout());
-    getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
-    validate();
-    repaint();
-  }
-}
 
-class PreviewPanel
-    extends JPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+class PreviewPanel extends JPanel
 {
-  Image image;
-
-  public PreviewPanel(Image image)
-  {
-    this.image = image;
-  }
-
-  public void paintComponent(Graphics g)
-  {
-    if (image != null)
+    Image image;
+
+    /**
+     * Creates a new PreviewPanel object.
+     *
+     * @param image DOCUMENT ME!
+     */
+    public PreviewPanel(Image image)
     {
-      g.drawImage(image, 0, 0, this);
+        this.image = image;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      System.out.println("DEBUG:image is null");
+        if (image != null)
+        {
+            g.drawImage(image, 0, 0, this);
+        }
+        else
+        {
+            System.out.println("DEBUG:image is null");
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 9b9e2db..2a972ea 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -18,316 +18,386 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.*;
+
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
+
 import javax.swing.*;
 
-import jalview.datamodel.*;
 
-public class AnnotationLabels
-    extends JPanel implements MouseListener,
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationLabels extends JPanel implements MouseListener,
     MouseMotionListener, ActionListener
 {
-  static String ADDNEW = "Add New Row";
-  static String HIDE = "Hide This Row";
-  static String DELETE = "Delete This Row";
-  static String SHOWALL = "Show All Hidden Rows";
-  static String OUTPUT_TEXT = "Show Values In Textbox";
-  boolean active = false;
-  Image image;
-  AlignmentPanel ap;
-  boolean resizing = false;
-  int oldY;
-  int mouseX;
-  int selectedRow = 0;
-  int scrollOffset = 0;
-
-  public AnnotationLabels(AlignmentPanel ap)
-  {
-    this.ap = ap;
-
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-    Image temp = null;
-
-    if (url != null)
+    static String ADDNEW = "Add New Row";
+    static String HIDE = "Hide This Row";
+    static String DELETE = "Delete This Row";
+    static String SHOWALL = "Show All Hidden Rows";
+    static String OUTPUT_TEXT = "Show Values In Textbox";
+    boolean active = false;
+    Image image;
+    AlignmentPanel ap;
+    boolean resizing = false;
+    int oldY;
+    int mouseX;
+    int selectedRow = 0;
+    int scrollOffset = 0;
+
+    /**
+     * Creates a new AnnotationLabels object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public AnnotationLabels(AlignmentPanel ap)
     {
-      temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-    }
+        this.ap = ap;
 
-    try
-    {
-      MediaTracker mt = new MediaTracker(this);
-      mt.addImage(temp, 0);
-      mt.waitForID(0);
+        java.net.URL url = getClass().getResource("/images/idwidth.gif");
+        Image temp = null;
+
+        if (url != null)
+        {
+            temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+        }
+
+        try
+        {
+            MediaTracker mt = new MediaTracker(this);
+            mt.addImage(temp, 0);
+            mt.waitForID(0);
+        }
+        catch (Exception ex)
+        {
+        }
+
+        BufferedImage bi = new BufferedImage(temp.getHeight(this),
+                temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
+        Graphics2D g = (Graphics2D) bi.getGraphics();
+        g.rotate(Math.toRadians(90));
+        g.drawImage(temp, 0, -bi.getWidth(this), this);
+        image = (Image) bi;
+
+        addMouseListener(this);
+        addMouseMotionListener(this);
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param y DOCUMENT ME!
+     */
+    public void setScrollOffset(int y)
     {
+        scrollOffset = y;
+        repaint();
     }
 
-    BufferedImage bi = new BufferedImage(temp.getHeight(this),
-                                         temp.getWidth(this),
-                                         BufferedImage.TYPE_INT_RGB);
-    Graphics2D g = (Graphics2D) bi.getGraphics();
-    g.rotate(Math.toRadians(90));
-    g.drawImage(temp, 0, -bi.getWidth(this), this);
-    image = (Image) bi;
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public void setScrollOffset(int y)
-  {
-    scrollOffset = y;
-    repaint();
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    int dif = 0;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-    if (evt.getActionCommand().equals(ADDNEW))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void actionPerformed(ActionEvent evt)
     {
-      String label = JOptionPane.showInputDialog(this,
-                                                 "Label for annotation");
-      if (label == null)
-        label = "";
+        int dif = 0;
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-      ap.av.alignment.addAnnotation(new AlignmentAnnotation(label,
-          "New description",
-          new Annotation[ap.av.alignment.getWidth()]));
+        if (evt.getActionCommand().equals(ADDNEW))
+        {
+            String label = JOptionPane.showInputDialog(this,
+                    "Label for annotation");
 
-      dif = aa[aa.length-1].height;
-    }
-    else if (evt.getActionCommand().equals(HIDE))
-    {
-      aa[selectedRow].visible = false;
+            if (label == null)
+            {
+                label = "";
+            }
+
+            ap.av.alignment.addAnnotation(new AlignmentAnnotation(label,
+                    "New description",
+                    new Annotation[ap.av.alignment.getWidth()]));
+
+            dif = aa[aa.length - 1].height;
+        }
+        else if (evt.getActionCommand().equals(HIDE))
+        {
+            aa[selectedRow].visible = false;
+
+            if (aa[selectedRow].label.equals("Conservation"))
+            {
+                ap.av.showConservation = false;
+            }
 
-      if (aa[selectedRow].label.equals("Conservation"))
-      {
-        ap.av.showConservation = false;
-      }
+            if (aa[selectedRow].label.equals("Quality"))
+            {
+                ap.av.showQuality = false;
+            }
 
-      if (aa[selectedRow].label.equals("Quality"))
-      {
-        ap.av.showQuality = false;
-      }
+            if (aa[selectedRow].label.equals("Consensus"))
+            {
+                ap.av.showIdentity = false;
+            }
+
+            dif = aa[selectedRow].height * -1;
+        }
+        else if (evt.getActionCommand().equals(DELETE))
+        {
+            ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+            dif = aa[selectedRow].height * -1;
+        }
+        else if (evt.getActionCommand().equals(SHOWALL))
+        {
+            for (int i = 0; i < aa.length; i++)
+            {
+                if (!aa[i].visible)
+                {
+                    dif += aa[i].height;
+                    aa[i].visible = true;
+                }
+            }
+        }
+        else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+        {
+            CutAndPasteTransfer cap = new CutAndPasteTransfer();
+            Desktop.addInternalFrame(cap,
+                ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
+                100);
+            cap.setText(aa[selectedRow].toString());
+        }
 
-      if (aa[selectedRow].label.equals("Consensus"))
-      {
-        ap.av.showIdentity = false;
-      }
+        ap.annotationPanel.adjustPanelHeight();
 
-      dif = aa[selectedRow].height*-1;
+        Dimension d = ap.annotationScroller.getPreferredSize();
+        ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+                d.height + dif));
+        d = ap.annotationSpaceFillerHolder.getPreferredSize();
+        ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,
+                d.height + dif));
+
+        ap.addNotify();
     }
-    else if (evt.getActionCommand().equals(DELETE))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
     {
-      ap.av.alignment.deleteAnnotation(aa[selectedRow]);
-      dif = aa[selectedRow].height*-1;
+        oldY = evt.getY();
     }
-    else if (evt.getActionCommand().equals(SHOWALL))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
     {
-      for (int i = 0; i < aa.length; i++)
-      {
-        if(!aa[i].visible)
-         {
-           dif+=aa[i].height;
-           aa[i].visible = true;
-         }
-      }
+        active = false;
+        repaint();
     }
-    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();
-      Desktop.addInternalFrame(cap,
-                               ap.alignFrame.getTitle() + " - " +
-                               aa[selectedRow].label, 500,
-                               100);
-      cap.setText(aa[selectedRow].toString());
+        active = true;
+        repaint();
     }
 
-    ap.annotationPanel.adjustPanelHeight();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
+    {
+        active = false;
+        repaint();
+    }
 
-    Dimension d = ap.annotationScroller.getPreferredSize();
-    ap.annotationScroller.setPreferredSize(new Dimension(d.width, d.height+dif));
-    d = ap.annotationSpaceFillerHolder.getPreferredSize();
-    ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-        d.width, d.height+dif));
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
+    {
+        active = true;
 
-      ap.addNotify();
+        Dimension d = ap.annotationScroller.getPreferredSize();
+        int dif = evt.getY() - oldY;
 
+        dif /= ap.av.charHeight;
+        dif *= ap.av.charHeight;
 
-  }
+        if ((d.height - dif) > 20)
+        {
+            ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+                    d.height - dif));
+            d = ap.annotationSpaceFillerHolder.getPreferredSize();
+            ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+                    d.width, d.height - dif));
+            ap.repaint();
+        }
 
-  public void mousePressed(MouseEvent evt)
-  {
-    oldY = evt.getY();
-  }
+        ap.addNotify();
+    }
 
-  public void mouseReleased(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
+    {
+    }
 
-  public void mouseEntered(MouseEvent evt)
-  {
-    active = true;
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
+    {
+        int y = evt.getY() - scrollOffset;
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-  public void mouseExited(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
+        if ((aa == null) || (aa.length == 0))
+        {
+            JPopupMenu pop = new JPopupMenu("Annotations");
+            JMenuItem item = new JMenuItem(ADDNEW);
+            item.addActionListener(this);
+            pop.add(item);
+            pop.show(this, evt.getX(), evt.getY());
 
-  public void mouseDragged(MouseEvent evt)
-  {
-    active = true;
+            return;
+        }
 
-    Dimension d = ap.annotationScroller.getPreferredSize();
-    int dif = evt.getY() - oldY;
+        int height = 0;
 
-    dif /= ap.av.charHeight;
-    dif *= ap.av.charHeight;
+        for (int i = 0; i < aa.length; i++)
+        {
+            if (!aa[i].visible)
+            {
+                continue;
+            }
 
-    if ( (d.height - dif) > 20)
-    {
-      ap.annotationScroller.setPreferredSize(new Dimension(d.width,
-          d.height - dif));
-      d = ap.annotationSpaceFillerHolder.getPreferredSize();
-      ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-          d.width, d.height - dif));
-      ap.repaint();
-    }
+            height += aa[i].height;
 
-    ap.addNotify();
-  }
+            if (y < height)
+            {
+                selectedRow = i;
 
-  public void mouseMoved(MouseEvent evt)
-  {
-  }
+                break;
+            }
+        }
 
-  public void mouseClicked(MouseEvent evt)
-  {
-    int y = evt.getY() - scrollOffset;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+        JPopupMenu pop = new JPopupMenu("Annotations");
+        JMenuItem item = new JMenuItem(ADDNEW);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(HIDE);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(DELETE);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(SHOWALL);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(OUTPUT_TEXT);
+        item.addActionListener(this);
+        pop.add(item);
+        pop.show(this, evt.getX(), evt.getY());
+    }
 
-    if ( (aa == null) || (aa.length == 0))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g1 DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g1)
     {
-      JPopupMenu pop = new JPopupMenu("Annotations");
-      JMenuItem item = new JMenuItem(ADDNEW);
-      item.addActionListener(this);
-      pop.add(item);
-      pop.show(this, evt.getX(), evt.getY());
+        Graphics2D g = (Graphics2D) g1;
+        g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
 
-      return;
+        drawComponent(g);
     }
 
-    int height = 0;
-
-    for (int i = 0; i < aa.length; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void drawComponent(Graphics2D g)
     {
-      if (!aa[i].visible)
-      {
-        continue;
-      }
+        FontMetrics fm = g.getFontMetrics(g.getFont());
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
 
-      height += aa[i].height;
+        g.translate(0, scrollOffset);
+        g.setColor(Color.black);
 
-      if (y < height)
-      {
-        selectedRow = i;
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+        int y = g.getFont().getSize();
+        int x = 0;
+        int width = getWidth();
+        if(width==0)
+         width = ap.calculateIdWidth().width + 4;
 
-        break;
-      }
-    }
-
-    JPopupMenu pop = new JPopupMenu("Annotations");
-    JMenuItem item = new JMenuItem(ADDNEW);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new JMenuItem(HIDE);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new JMenuItem(DELETE);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new JMenuItem(SHOWALL);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new JMenuItem(OUTPUT_TEXT);
-    item.addActionListener(this);
-    pop.add(item);
-    pop.show(this, evt.getX(), evt.getY());
-  }
-
-  public void paintComponent(Graphics g1)
-  {
-    Graphics2D g = (Graphics2D) g1;
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                       RenderingHints.VALUE_ANTIALIAS_ON);
-
-    drawComponent(g);
-  }
-
-  public void drawComponent(Graphics2D g)
-  {
-    FontMetrics fm = g.getFontMetrics(g.getFont());
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    g.translate(0, scrollOffset);
-    g.setColor(Color.black);
-
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-    int y = g.getFont().getSize();
-    int x = 0;
-
-    if (aa != null)
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (!aa[i].visible)
+        if (aa != null)
         {
-          continue;
+            for (int i = 0; i < aa.length; i++)
+            {
+                if (!aa[i].visible)
+                {
+                    continue;
+                }
+
+                x = width - fm.stringWidth(aa[i].label) - 3;
+
+                if (aa[i].isGraph)
+                {
+                    y += (aa[i].height / 3);
+                }
+
+                g.drawString(aa[i].label, x, y);
+
+                if (aa[i].isGraph)
+                {
+                    y += ((2 * aa[i].height) / 3);
+                }
+                else
+                {
+                    y += aa[i].height;
+                }
+            }
         }
 
-        x = getWidth() - fm.stringWidth(aa[i].label) - 3;
-
-        if (aa[i].isGraph)
+        if (active)
         {
-          y += (aa[i].height / 3);
+            if (image != null)
+            {
+                g.drawImage(image, 2, 0, this);
+            }
         }
 
-        g.drawString(aa[i].label, x, y);
-
-        if (aa[i].isGraph)
+        if ((aa == null) || (aa.length < 1))
         {
-          y += ( (2 * aa[i].height) / 3);
+            g.drawString("Right click", 2, 8);
+            g.drawString("to add annotation", 2, 18);
         }
-        else
-        {
-          y += aa[i].height;
-        }
-      }
-    }
-
-    if (active)
-    {
-      if (image != null)
-      {
-        g.drawImage(image, 2, 0, this);
-      }
-    }
-
-    if ( (aa == null) || (aa.length < 1))
-    {
-      g.drawString("Right click", 2, 8);
-      g.drawString("to add annotation", 2, 18);
     }
-  }
 }
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index a6c2055..9ae103e 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -18,751 +18,841 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
+
+import java.util.*;
+
 import javax.swing.*;
 
-import jalview.datamodel.*;
 
-public class AnnotationPanel
-    extends JPanel implements MouseListener,
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationPanel extends JPanel implements MouseListener,
     MouseMotionListener, ActionListener, AdjustmentListener
 {
-  static String HELIX = "Helix";
-  static String SHEET = "Sheet";
-  static String LABEL = "Label";
-  static String REMOVE = "Remove Annotation";
-  static String COLOUR = "Colour";
-  static Color HELIX_COLOUR = Color.red.darker();
-  static Color SHEET_COLOUR = Color.green.darker().darker();
-
-  public static int GRAPH_HEIGHT = 40;
-  AlignViewport av;
-  AlignmentPanel ap;
-  int activeRow = -1;
-  Vector activeRes;
-  BufferedImage image;
-  Graphics2D gg;
-  FontMetrics fm;
-  int imgWidth = 0;
-  boolean fastPaint = false;
-
-  public AnnotationPanel(AlignmentPanel ap)
-  {
-    ToolTipManager.sharedInstance().registerComponent(this);
-    ToolTipManager.sharedInstance().setInitialDelay(0);
-    ToolTipManager.sharedInstance().setDismissDelay(10000);
-    this.ap = ap;
-    av = ap.av;
-    this.setLayout(null);
-    addMouseListener(this);
-    addMouseMotionListener(this);
-    ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
-  }
-
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    ap.alabels.setScrollOffset( -evt.getValue());
-  }
-
-  public void adjustPanelHeight()
-  {
-    // setHeight of panels
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    int height = 0;
-
-    if (aa != null)
+    static String HELIX = "Helix";
+    static String SHEET = "Sheet";
+    static String LABEL = "Label";
+    static String REMOVE = "Remove Annotation";
+    static String COLOUR = "Colour";
+    static Color HELIX_COLOUR = Color.red.darker();
+    static Color SHEET_COLOUR = Color.green.darker().darker();
+
+    /** DOCUMENT ME!! */
+    public static int GRAPH_HEIGHT = 40;
+    AlignViewport av;
+    AlignmentPanel ap;
+    int activeRow = -1;
+    Vector activeRes;
+    BufferedImage image;
+    Graphics2D gg;
+    FontMetrics fm;
+    int imgWidth = 0;
+    boolean fastPaint = false;
+
+    /**
+     * Creates a new AnnotationPanel object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public AnnotationPanel(AlignmentPanel ap)
     {
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (!aa[i].visible)
-        {
-          continue;
-        }
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
+        this.ap = ap;
+        av = ap.av;
+        this.setLayout(null);
+        addMouseListener(this);
+        addMouseMotionListener(this);
+        ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
+    }
 
-        aa[i].height = 0;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void adjustmentValueChanged(AdjustmentEvent evt)
+    {
+        ap.alabels.setScrollOffset(-evt.getValue());
+    }
 
-        if (aa[i].hasText)
+    /**
+     * DOCUMENT ME!
+     */
+    public void adjustPanelHeight()
+    {
+        // setHeight of panels
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        int height = 0;
+
+        if (aa != null)
         {
-          aa[i].height += av.charHeight;
+            for (int i = 0; i < aa.length; i++)
+            {
+                if (!aa[i].visible)
+                {
+                    continue;
+                }
+
+                aa[i].height = 0;
+
+                if (aa[i].hasText)
+                {
+                    aa[i].height += av.charHeight;
+                }
+
+                if (aa[i].hasIcons)
+                {
+                    aa[i].height += 16;
+                }
+
+                if (aa[i].isGraph)
+                {
+                    aa[i].height += GRAPH_HEIGHT;
+                }
+
+                if (aa[i].height == 0)
+                {
+                    aa[i].height = 20;
+                }
+
+                height += aa[i].height;
+            }
         }
-
-        if (aa[i].hasIcons)
+        else
         {
-          aa[i].height += 16;
+            height = 20;
         }
 
-        if (aa[i].isGraph)
+        this.setPreferredSize(new Dimension(1, height));
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     */
+    public void removeEditableColumn(int col)
+    {
+        if (activeRow == -1)
         {
-          aa[i].height += GRAPH_HEIGHT;
+            AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+            for (int j = 0; j < aa.length; j++)
+            {
+                if (aa[j].editable)
+                {
+                    activeRow = j;
+
+                    break;
+                }
+            }
         }
 
-        if (aa[i].height == 0)
+        if ((activeRes != null) && activeRes.contains(String.valueOf(col)))
         {
-          aa[i].height = 20;
+            activeRes.removeElement(String.valueOf(col));
         }
 
-        height += aa[i].height;
-      }
+        repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     */
+    public void addEditableColumn(int col)
     {
-      height = 20;
-    }
+        if (activeRow == -1)
+        {
+            AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    this.setPreferredSize(new Dimension(1, height));
-  }
+            for (int j = 0; j < aa.length; j++)
+            {
+                if (aa[j].editable)
+                {
+                    activeRow = j;
 
+                    break;
+                }
+            }
+        }
 
-  public void removeEditableColumn(int col)
-  {
-    if (activeRow == -1)
-    {
-      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        if (activeRes == null)
+        {
+            activeRes = new Vector();
+        }
 
-      for (int j = 0; j < aa.length; j++)
-      {
-        if (aa[j].editable)
+        if (!activeRes.contains(String.valueOf(col)))
         {
-          activeRow = j;
-          break;
+            activeRes.addElement(String.valueOf(col));
         }
-      }
-    }
 
-    if (activeRes != null && activeRes.contains(String.valueOf(col)))
-    {
-      activeRes.removeElement(String.valueOf(col));
+        repaint();
     }
-    repaint();
-  }
-
 
-  public void addEditableColumn(int col)
-  {
-    if (activeRow == -1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void actionPerformed(ActionEvent evt)
     {
-      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        Annotation[] anot = aa[activeRow].annotations;
 
-      for (int j = 0; j < aa.length; j++)
-      {
-        if (aa[j].editable)
+        if (evt.getActionCommand().equals(REMOVE))
         {
-          activeRow = j;
-          break;
+            for (int i = 0; i < activeRes.size(); i++)
+            {
+                anot[Integer.parseInt(activeRes.get(i).toString())] = null;
+                anot[Integer.parseInt(activeRes.get(i).toString())] = null;
+            }
         }
-      }
-    }
-
-    if (activeRes == null)
-      activeRes = new Vector();
+        else if (evt.getActionCommand().equals(LABEL))
+        {
+            String label = JOptionPane.showInputDialog(this, "Enter Label ",
+                    "Enter label", JOptionPane.QUESTION_MESSAGE);
 
-    if (!activeRes.contains(String.valueOf(col)))
-      activeRes.addElement(String.valueOf(col));
+            if (label == null)
+            {
+                return;
+            }
 
-    repaint();
-  }
+            if ((label.length() > 0) && !aa[activeRow].hasText)
+            {
+                aa[activeRow].hasText = true;
+            }
 
-  public void actionPerformed(ActionEvent evt)
-  {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    Annotation[] anot = aa[activeRow].annotations;
+            for (int i = 0; i < activeRes.size(); i++)
+            {
+                int index = Integer.parseInt(activeRes.get(i).toString());
 
-    if (evt.getActionCommand().equals(REMOVE))
-    {
-      for (int i = 0; i < activeRes.size(); i++)
-      {
-        anot[Integer.parseInt(activeRes.get(i).toString())] = null;
-        anot[Integer.parseInt(activeRes.get(i).toString())] = null;
-      }
-    }
-    else if (evt.getActionCommand().equals(LABEL))
-    {
-      String label = JOptionPane.showInputDialog(this, "Enter Label ",
-                                                 "Enter label",
-                                                 JOptionPane.QUESTION_MESSAGE);
+                if (anot[index] == null)
+                {
+                    anot[index] = new Annotation(label, "", ' ', 0);
+                }
 
-      if (label == null)
-        return;
+                anot[index].displayCharacter = label;
+            }
+        }
+        else if (evt.getActionCommand().equals(COLOUR))
+        {
+            Color col = JColorChooser.showDialog(this,
+                    "Choose foreground colour", Color.black);
 
-      if ( (label.length() > 0) && !aa[activeRow].hasText)
-      {
-        aa[activeRow].hasText = true;
-      }
+            for (int i = 0; i < activeRes.size(); i++)
+            {
+                int index = Integer.parseInt(activeRes.get(i).toString());
 
-      for (int i = 0; i < activeRes.size(); i++)
-      {
-        int index = Integer.parseInt(activeRes.get(i).toString());
+                if (anot[index] == null)
+                {
+                    anot[index] = new Annotation("", "", ' ', 0);
+                }
 
-        if (anot[index] == null)
-        {
-          anot[index] = new Annotation(label, "", ' ', 0);
+                anot[index].colour = col;
+            }
         }
-        anot[index].displayCharacter = label;
-      }
-    }
-    else if (evt.getActionCommand().equals(COLOUR))
-    {
-      Color col = JColorChooser.showDialog(this,
-                                           "Choose foreground colour",
-                                           Color.black);
-
-      for (int i = 0; i < activeRes.size(); i++)
-      {
-        int index = Integer.parseInt(activeRes.get(i).toString());
-
-        if (anot[index] == null)
+        else // HELIX OR SHEET
         {
-          anot[index] = new Annotation("", "", ' ', 0);
-        }
+            char type = 0;
+            String symbol = "\u03B1";
 
-        anot[index].colour = col;
-      }
-    }
-    else // HELIX OR SHEET
-    {
-      char type = 0;
-      String symbol = "\u03B1";
-
-      if (evt.getActionCommand().equals(HELIX))
-      {
-        type = 'H';
-      }
-      else if (evt.getActionCommand().equals(SHEET))
-      {
-        type = 'E';
-        symbol = "\u03B2";
-      }
-
-      if (!aa[activeRow].hasIcons)
-      {
-        aa[activeRow].hasIcons = true;
-      }
-
-      String label = JOptionPane.showInputDialog(
-          "Enter a label for the structure?",
-          symbol);
-
-      if (label == null)
-        return;
-
-      if ( (label.length() > 0) && !aa[activeRow].hasText)
-      {
-        aa[activeRow].hasText = true;
-      }
+            if (evt.getActionCommand().equals(HELIX))
+            {
+                type = 'H';
+            }
+            else if (evt.getActionCommand().equals(SHEET))
+            {
+                type = 'E';
+                symbol = "\u03B2";
+            }
 
-      for (int i = 0; i < activeRes.size(); i++)
-      {
-        int index = Integer.parseInt(activeRes.get(i).toString());
+            if (!aa[activeRow].hasIcons)
+            {
+                aa[activeRow].hasIcons = true;
+            }
 
-        if (anot[index] == null)
-        {
-          anot[index] = new Annotation(label, "", type, 0);
-        }
+            String label = JOptionPane.showInputDialog("Enter a label for the structure?",
+                    symbol);
 
-        anot[index].secondaryStructure = type;
-        anot[index].displayCharacter = label;
-      }
-    }
+            if (label == null)
+            {
+                return;
+            }
 
-    adjustPanelHeight();
-    activeRes = null;
-    repaint();
+            if ((label.length() > 0) && !aa[activeRow].hasText)
+            {
+                aa[activeRow].hasText = true;
+            }
 
-    return;
-  }
+            for (int i = 0; i < activeRes.size(); i++)
+            {
+                int index = Integer.parseInt(activeRes.get(i).toString());
 
-  public void mousePressed(MouseEvent evt)
-  {
-    int height = 0;
-    activeRow = -1;
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+                if (anot[index] == null)
+                {
+                    anot[index] = new Annotation(label, "", type, 0);
+                }
 
-    for (int i = 0; i < aa.length; i++)
-    {
-      height += aa[i].height;
+                anot[index].secondaryStructure = type;
+                anot[index].displayCharacter = label;
+            }
+        }
 
-      if (evt.getY() < height)
-      {
-        if (aa[i].editable)
-           activeRow = i;
-         else
-           activeRes = null;
+        adjustPanelHeight();
+        activeRes = null;
+        repaint();
 
-        break;
-      }
+        return;
     }
 
-
-    if (SwingUtilities.isRightMouseButton(evt))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
     {
-      if (activeRes == null)
-      {
-        return;
-      }
-
-
-      JPopupMenu pop = new JPopupMenu("Structure type");
-      JMenuItem item = new JMenuItem(HELIX);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(SHEET);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(LABEL);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(COLOUR);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(REMOVE);
-      item.addActionListener(this);
-      pop.add(item);
-      pop.show(this, evt.getX(), evt.getY());
-
-      return;
-    }
+        int height = 0;
+        activeRow = -1;
 
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    if (aa == null)
-    {
-      return;
-    }
+        for (int i = 0; i < aa.length; i++)
+        {
+            height += aa[i].height;
 
+            if (evt.getY() < height)
+            {
+                if (aa[i].editable)
+                {
+                    activeRow = i;
+                }
+                else
+                {
+                    activeRes = null;
+                }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+                break;
+            }
+        }
 
-    if (evt.isControlDown() || evt.isAltDown())
-    {
-      addEditableColumn(res);
-    }
-    else if (evt.isShiftDown())
-    {
-      if (activeRes == null)
-      {
-        activeRes = new Vector();
-      }
-      else
-      {
-        int start = Integer.parseInt(activeRes.get(activeRes.size() -
-            1).toString());
-        int end = res;
-
-        if (end < start)
+        if (SwingUtilities.isRightMouseButton(evt))
         {
-          int temp = end;
-          end = start;
-          start = temp;
+            if (activeRes == null)
+            {
+                return;
+            }
+
+            JPopupMenu pop = new JPopupMenu("Structure type");
+            JMenuItem item = new JMenuItem(HELIX);
+            item.addActionListener(this);
+            pop.add(item);
+            item = new JMenuItem(SHEET);
+            item.addActionListener(this);
+            pop.add(item);
+            item = new JMenuItem(LABEL);
+            item.addActionListener(this);
+            pop.add(item);
+            item = new JMenuItem(COLOUR);
+            item.addActionListener(this);
+            pop.add(item);
+            item = new JMenuItem(REMOVE);
+            item.addActionListener(this);
+            pop.add(item);
+            pop.show(this, evt.getX(), evt.getY());
+
+            return;
         }
 
-        for (int n = start; n <= end; n++)
+        if (aa == null)
         {
-          addEditableColumn(n);
+            return;
         }
-      }
-    }
-    else
-    {
-      activeRes = new Vector();
-      activeRes.addElement(String.valueOf(res));
-    }
-
-    repaint();
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {
-  }
 
-  public void mouseExited(MouseEvent evt)
-  {
-  }
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-  public void mouseDragged(MouseEvent evt)
-  {
-  }
+        if (evt.isControlDown() || evt.isAltDown())
+        {
+            addEditableColumn(res);
+        }
+        else if (evt.isShiftDown())
+        {
+            if (activeRes == null)
+            {
+                activeRes = new Vector();
+            }
+            else
+            {
+                int start = Integer.parseInt(activeRes.get(activeRes.size() -
+                            1).toString());
+                int end = res;
+
+                if (end < start)
+                {
+                    int temp = end;
+                    end = start;
+                    start = temp;
+                }
+
+                for (int n = start; n <= end; n++)
+                {
+                    addEditableColumn(n);
+                }
+            }
+        }
+        else
+        {
+            activeRes = new Vector();
+            activeRes.addElement(String.valueOf(res));
+        }
 
-  public void mouseMoved(MouseEvent evt)
-  {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        repaint();
+    }
 
-    if (aa == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
     {
-      return;
     }
 
-    int row = -1;
-    int height = 0;
-
-    for (int i = 0; i < aa.length; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
     {
-      if (aa[i].visible)
-      {
-        height += aa[i].height;
-      }
-
-      if (evt.getY() < height)
-      {
-        row = i;
-
-        break;
-      }
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
-    if ( (row > -1) && (res < aa[row].annotations.length) &&
-        (aa[row].annotations[res] != null))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
     {
-      this.setToolTipText(aa[row].annotations[res].description);
-
-      StringBuffer text = new StringBuffer("Sequence position " +
-                                           (res + 1) + "  " +
-                                           aa[row].annotations[res].description);
-      ap.alignFrame.statusBar.setText(text.toString());
     }
-  }
 
-  public void mouseClicked(MouseEvent evt)
-  {
-  }
-
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    if (fastPaint)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
     {
-      g.drawImage(image, 0, 0, this);
-      fastPaint = false;
-
-      return;
     }
 
-    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
+    {
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
-                              BufferedImage.TYPE_INT_RGB);
-    gg = (Graphics2D) image.getGraphics();
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
+        if (aa == null)
+        {
+            return;
+        }
 
-    gg.setFont(av.getFont());
-    fm = gg.getFontMetrics();
+        int row = -1;
+        int height = 0;
 
-    drawComponent(gg, av.startRes, av.endRes + 1);
-    g.drawImage(image, 0, 0, this);
-  }
+        for (int i = 0; i < aa.length; i++)
+        {
+            if (aa[i].visible)
+            {
+                height += aa[i].height;
+            }
 
-  public void fastPaint(int horizontal)
-  {
-    if ( (horizontal == 0) ||
-        (av.alignment.getAlignmentAnnotation() == null) ||
-        (av.alignment.getAlignmentAnnotation().length < 1))
-    {
-      repaint();
+            if (evt.getY() < height)
+            {
+                row = i;
 
-      return;
-    }
+                break;
+            }
+        }
 
-    gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    int sr = av.startRes;
-    int er = av.endRes + 1;
-    int transX = 0;
+        if ((row > -1) && (res < aa[row].annotations.length) &&
+                (aa[row].annotations[res] != null))
+        {
+            this.setToolTipText(aa[row].annotations[res].description);
 
-    if (horizontal > 0) // scrollbar pulled right, image to the left
-    {
-      transX = (er - sr - horizontal) * av.charWidth;
-      sr = er - horizontal;
+            StringBuffer text = new StringBuffer("Sequence position " +
+                    (res + 1) + "  " + aa[row].annotations[res].description);
+            ap.alignFrame.statusBar.setText(text.toString());
+        }
     }
-    else if (horizontal < 0)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
     {
-      er = sr - horizontal;
     }
 
-    gg.translate(transX, 0);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
+    {
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
 
-    drawComponent(gg, sr, er);
+        if (fastPaint)
+        {
+            g.drawImage(image, 0, 0, this);
+            fastPaint = false;
 
-    gg.translate( -transX, 0);
+            return;
+        }
 
-    fastPaint = true;
-    repaint();
-  }
+        imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
-  public void drawComponent(Graphics2D g, int startRes, int endRes)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+                BufferedImage.TYPE_INT_RGB);
+        gg = (Graphics2D) image.getGraphics();
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
 
-    if ( (av.alignment.getAlignmentAnnotation() == null) ||
-        (av.alignment.getAlignmentAnnotation().length < 1))
-    {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, getWidth(), getHeight());
-      g.setColor(Color.black);
-      g.drawString("Alignment has no annotations", 20, 15);
+        gg.setFont(av.getFont());
 
-      return;
+        drawComponent(gg, av.startRes, av.endRes + 1);
+        g.drawImage(image, 0, 0, this);
     }
 
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
-    int j;
-    int x = 0;
-    int y = 0;
-    char[] lastSS = new char[aa.length];
-    int[] lastSSX = new int[aa.length];
-    int iconOffset = av.charHeight / 2;
-    boolean validRes = false;
-
-    //\u03B2 \u03B1
-    for (int i = 0; i < aa.length; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param horizontal DOCUMENT ME!
+     */
+    public void fastPaint(int horizontal)
     {
-      AlignmentAnnotation row = aa[i];
+        if ((horizontal == 0) ||
+                (av.alignment.getAlignmentAnnotation() == null) ||
+                (av.alignment.getAlignmentAnnotation().length < 1))
+        {
+            repaint();
 
-      if (!row.visible)
-      {
-        continue;
-      }
+            return;
+        }
 
-      if (row.isGraph)
-      {
-        // this is so that we draw the characters below the graph
-        y += row.height;
+        gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
 
-        if (row.hasText)
-        {
-          y -= av.charHeight;
-        }
-      }
-
-      if (row.hasText)
-      {
-        iconOffset = av.charHeight / 2;
-      }
-      else
-      {
-        iconOffset = 0;
-      }
-
-      for (j = startRes; j < endRes; j++)
-      {
-        if ( (row.annotations.length <= j) ||
-            (row.annotations[j] == null))
+        int sr = av.startRes;
+        int er = av.endRes + 1;
+        int transX = 0;
+
+        if (horizontal > 0) // scrollbar pulled right, image to the left
         {
-          validRes = false;
+            transX = (er - sr - horizontal) * av.charWidth;
+            sr = er - horizontal;
         }
-        else
+        else if (horizontal < 0)
         {
-          validRes = true;
+            er = sr - horizontal;
         }
 
-        x = (j - startRes) * av.charWidth;
+        gg.translate(transX, 0);
 
-        if (activeRow == i)
-        {
-          g.setColor(Color.red);
+        drawComponent(gg, sr, er);
 
-          if (activeRes != null)
-          {
-            for (int n = 0; n < activeRes.size(); n++)
-            {
-              int v = Integer.parseInt(activeRes.get(n).toString());
+        gg.translate(-transX, 0);
 
-              if (v == j)
-              {
-                g.fillRect( (j - startRes) * av.charWidth, y,
-                           av.charWidth, row.height);
-              }
-            }
-          }
-        }
+        fastPaint = true;
+        repaint();
+    }
 
-        if (validRes &&
-            (row.annotations[j].displayCharacter.length() > 0))
-        {
-          int charOffset = (av.charWidth -
-                            fm.charWidth(row.annotations[j].displayCharacter.
-                                         charAt(
-                                             0))) / 2;
-          g.setColor(row.annotations[j].colour);
-
-          if (j == 0)
-          {
-              g.drawString(row.annotations[j].displayCharacter,
-                           x, y + iconOffset + 2);
-          }
-          else if (
-                   ( (row.annotations[j - 1] == null) ||
-                    (row.annotations[j].displayCharacter != row.annotations[j -
-                     1].displayCharacter)))
-          {
-            g.drawString(row.annotations[j].displayCharacter, x,
-                         y + iconOffset + 2);
-          }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param startRes DOCUMENT ME!
+     * @param endRes DOCUMENT ME!
+     */
+    public void drawComponent(Graphics2D g, int startRes, int endRes)
+    {
+      if(fm==null)
+        fm = g.getFontMetrics();
 
-        }
+        g.setColor(Color.white);
+        g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
-        if (row.hasIcons)
+        if ((av.alignment.getAlignmentAnnotation() == null) ||
+                (av.alignment.getAlignmentAnnotation().length < 1))
         {
-          if (!validRes ||
-              (row.annotations[j].secondaryStructure != lastSS[i]))
-          {
-            switch (lastSS[i])
-            {
-              case 'H':
-                g.setColor(HELIX_COLOUR);
-                g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                                x - lastSSX[i], 7, 8, 8);
+            g.setColor(Color.white);
+            g.fillRect(0, 0, getWidth(), getHeight());
+            g.setColor(Color.black);
+            g.drawString("Alignment has no annotations", 20, 15);
 
-                break;
+            return;
+        }
 
-              case 'E':
-                g.setColor(SHEET_COLOUR);
-                g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                           x - lastSSX[i] - 4, 7);
-                g.fillPolygon(new int[]
-                              {x - 4, x - 4, x},
-                              new int[]
-                              {
-                              y + iconOffset, y + 14 + iconOffset,
-                              y + 8 + iconOffset
-                }, 3);
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-                break;
+        int j;
+        int x = 0;
+        int y = 0;
+        char[] lastSS = new char[aa.length];
+        int[] lastSSX = new int[aa.length];
+        int iconOffset = av.charHeight / 2;
+        boolean validRes = false;
 
-              case 'C':
-                break;
+        //\u03B2 \u03B1
+        for (int i = 0; i < aa.length; i++)
+        {
+            AlignmentAnnotation row = aa[i];
 
-              default:
-                g.setColor(Color.gray);
-                g.fillRect(lastSSX[i], y + 6 + iconOffset,
-                           x - lastSSX[i], 2);
+            if (!row.visible)
+            {
+                continue;
+            }
 
-                break;
+            if (row.isGraph)
+            {
+                // this is so that we draw the characters below the graph
+                y += row.height;
+
+                if (row.hasText)
+                {
+                    y -= av.charHeight;
+                }
             }
 
-            if (validRes)
+            if (row.hasText)
             {
-              lastSS[i] = row.annotations[j].secondaryStructure;
+                iconOffset = av.charHeight / 2;
             }
             else
             {
-              lastSS[i] = ' ';
+                iconOffset = 0;
             }
 
-            lastSSX[i] = x;
-          }
-        }
-
-        if (validRes && row.isGraph)
-        {
-          g.setColor(new Color(0, 0, 180));
-
-          int height = (int) ( (row.annotations[j].value / row.graphMax) *
-                              GRAPH_HEIGHT);
-
-          if (row.windowLength > 1)
-          {
-            int total = 0;
-
-            for (int i2 = j - (row.windowLength / 2);
-                 i2 < (j + (row.windowLength / 2)); i2++)
+            for (j = startRes; j < endRes; j++)
             {
-              if ( (i2 < 0) || (i2 >= av.alignment.getWidth()))
-              {
-                continue;
-              }
+                if ((row.annotations.length <= j) ||
+                        (row.annotations[j] == null))
+                {
+                    validRes = false;
+                }
+                else
+                {
+                    validRes = true;
+                }
+
+                x = (j - startRes) * av.charWidth;
+
+                if (activeRow == i)
+                {
+                    g.setColor(Color.red);
+
+                    if (activeRes != null)
+                    {
+                        for (int n = 0; n < activeRes.size(); n++)
+                        {
+                            int v = Integer.parseInt(activeRes.get(n).toString());
+
+                            if (v == j)
+                            {
+                                g.fillRect((j - startRes) * av.charWidth, y,
+                                    av.charWidth, row.height);
+                            }
+                        }
+                    }
+                }
+
+                if (validRes &&
+                        (row.annotations[j].displayCharacter.length() > 0))
+                {
+                    int charOffset = (av.charWidth -
+                        fm.charWidth(row.annotations[j].displayCharacter.charAt(
+                                0))) / 2;
+                    g.setColor(row.annotations[j].colour);
+
+                    if (j == 0)
+                    {
+                        g.drawString(row.annotations[j].displayCharacter, x+charOffset,
+                            y + iconOffset + 2);
+                    }
+                    else if (((row.annotations[j - 1] == null) ||
+                            (row.annotations[j].displayCharacter != row.annotations[j -
+                            1].displayCharacter)))
+                    {
+                        g.drawString(row.annotations[j].displayCharacter, x+charOffset,
+                            y + iconOffset + 2);
+                    }
+                }
+
+                if (row.hasIcons)
+                {
+                    if (!validRes ||
+                            (row.annotations[j].secondaryStructure != lastSS[i]))
+                    {
+                        switch (lastSS[i])
+                        {
+                        case 'H':
+                            g.setColor(HELIX_COLOUR);
+                            g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
+                                x - lastSSX[i], 7, 8, 8);
 
-              total += row.annotations[i2].value;
+                            break;
+
+                        case 'E':
+                            g.setColor(SHEET_COLOUR);
+                            g.fillRect(lastSSX[i], y + 4 + iconOffset,
+                                x - lastSSX[i] - 4, 7);
+                            g.fillPolygon(new int[] { x - 4, x - 4, x },
+                                new int[]
+                                {
+                                    y + iconOffset, y + 14 + iconOffset,
+                                    y + 8 + iconOffset
+                                }, 3);
+
+                            break;
+
+                        case 'C':
+                            break;
+
+                        default:
+                            g.setColor(Color.gray);
+                            g.fillRect(lastSSX[i], y + 6 + iconOffset,
+                                x - lastSSX[i], 2);
+
+                            break;
+                        }
+
+                        if (validRes)
+                        {
+                            lastSS[i] = row.annotations[j].secondaryStructure;
+                        }
+                        else
+                        {
+                            lastSS[i] = ' ';
+                        }
+
+                        lastSSX[i] = x;
+                    }
+                }
+
+                if (validRes && row.isGraph)
+                {
+                    g.setColor(new Color(0, 0, 180));
+
+                    int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);
+
+                    if (row.windowLength > 1)
+                    {
+                        int total = 0;
+
+                        for (int i2 = j - (row.windowLength / 2);
+                                i2 < (j + (row.windowLength / 2)); i2++)
+                        {
+                            if ((i2 < 0) || (i2 >= av.alignment.getWidth()))
+                            {
+                                continue;
+                            }
+
+                            total += row.annotations[i2].value;
+                        }
+
+                        total /= row.windowLength;
+                        height = (int) ((total / row.graphMax) * GRAPH_HEIGHT);
+                    }
+
+                    g.setColor(row.annotations[j].colour);
+                    g.fillRect(x, y - height, av.charWidth, height);
+                }
             }
 
-            total /= row.windowLength;
-            height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);
-          }
+            x += av.charWidth;
 
-          g.setColor(row.annotations[j].colour);
-          g.fillRect(x, y - height, av.charWidth, height);
-        }
-      }
+            if (row.hasIcons)
+            {
+                switch (lastSS[i])
+                {
+                case 'H':
+                    g.setColor(HELIX_COLOUR);
+                    g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
+                        x - lastSSX[i], 7, 8, 8);
+
+                    break;
+
+                case 'E':
+                    g.setColor(SHEET_COLOUR);
+                    g.fillRect(lastSSX[i], y + 4 + iconOffset,
+                        x - lastSSX[i] - 4, 7);
+                    g.fillPolygon(new int[] { x - 4, x - 4, x },
+                        new int[]
+                        {
+                            y + iconOffset, y + 14 + iconOffset,
+                            y + 7 + iconOffset
+                        }, 3);
+
+                    break;
+
+                case 'C':
+                    break;
+
+                default:
+                    g.setColor(Color.gray);
+                    g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
+
+                    break;
+                }
+            }
 
-      x += av.charWidth;
+            if (row.isGraph && row.hasText)
+            {
+                y += av.charHeight;
+            }
 
-      if (row.hasIcons)
-      {
-        switch (lastSS[i])
-        {
-          case 'H':
-            g.setColor(HELIX_COLOUR);
-            g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                            x - lastSSX[i], 7, 8, 8);
-
-            break;
-
-          case 'E':
-            g.setColor(SHEET_COLOUR);
-            g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                       x - lastSSX[i] - 4, 7);
-            g.fillPolygon(new int[]
-                          {x - 4, x - 4, x},
-                          new int[]
-                          {
-                          y + iconOffset, y + 14 + iconOffset,
-                          y + 7 + iconOffset
-            }, 3);
-
-            break;
-
-          case 'C':
-            break;
-
-          default:
-            g.setColor(Color.gray);
-            g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-
-            break;
+            if (!row.isGraph)
+            {
+                y += aa[i].height;
+            }
         }
-      }
-
-      if (row.isGraph && row.hasText)
-      {
-        y += av.charHeight;
-      }
-
-      if (!row.isGraph)
-      {
-        y += aa[i].height;
-      }
     }
-  }
 
-  // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, width, y);
-    g.setColor(new Color(0, 0, 180));
+    // used by overview window
+    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)
+    {
+        g.setColor(Color.white);
+        g.fillRect(0, 0, width, y);
+        g.setColor(new Color(0, 0, 180));
 
-    int x = 0;
+        int x = 0;
 
-    for (int j = 0; j < aa.annotations.length; j++)
-    {
-      g.setColor(new Color(0, 0, 180));
+        for (int j = 0; j < aa.annotations.length; j++)
+        {
+            g.setColor(new Color(0, 0, 180));
 
-      int height = (int) ( (aa.annotations[j].value / aa.graphMax) *
-                          GRAPH_HEIGHT);
-      g.fillRect(x, y - height, av.charWidth, height);
-      x += av.charWidth;
+            int height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+            g.fillRect(x, y - height, av.charWidth, height);
+            x += av.charWidth;
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index 2116d50..356dd1c 100755
--- a/src/jalview/gui/ColumnSelection.java
+++ b/src/jalview/gui/ColumnSelection.java
@@ -20,93 +20,150 @@ package jalview.gui;
 
 import java.util.*;
 
+
 /**
  * NOTE: Columns are zero based.
  */
 public class ColumnSelection
 {
-  Vector selected = new Vector();
-
-  public void addElement(int col)
-  {
-    if(!selected.contains(new Integer(col)))
-      selected.addElement(new Integer(col));
-  }
-
-  public void clear()
-  {
-    selected.removeAllElements();
-  }
-
-  public void removeElement(int col)
-  {
-    Integer colInt = new Integer(col);
-    if (selected.contains(colInt))
+    Vector selected = new Vector();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     */
+    public void addElement(int col)
     {
-      selected.removeElement(colInt);
+        if (!selected.contains(new Integer(col)))
+        {
+            selected.addElement(new Integer(col));
+        }
     }
-  }
-
-  public boolean contains(int col)
-  {
-    return selected.contains(new Integer(col));
-  }
 
-  public int columnAt(int i)
-  {
-    return ( (Integer) selected.elementAt(i)).intValue();
-  }
+    /**
+     * DOCUMENT ME!
+     */
+    public void clear()
+    {
+        selected.removeAllElements();
+    }
 
-  public int size()
-  {
-    return selected.size();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     */
+    public void removeElement(int col)
+    {
+        Integer colInt = new Integer(col);
 
-  public int getMax()
-  {
-    int max = -1;
+        if (selected.contains(colInt))
+        {
+            selected.removeElement(colInt);
+        }
+    }
 
-    for (int i = 0; i < selected.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean contains(int col)
     {
-      if (columnAt(i) > max)
-      {
-        max = columnAt(i);
-      }
+        return selected.contains(new Integer(col));
     }
 
-    return max;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int columnAt(int i)
+    {
+        return ((Integer) selected.elementAt(i)).intValue();
+    }
 
-  public int getMin()
-  {
-    int min = 1000000000;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int size()
+    {
+        return selected.size();
+    }
 
-    for (int i = 0; i < selected.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMax()
     {
-      if (columnAt(i) < min)
-      {
-        min = columnAt(i);
-      }
+        int max = -1;
+
+        for (int i = 0; i < selected.size(); i++)
+        {
+            if (columnAt(i) > max)
+            {
+                max = columnAt(i);
+            }
+        }
+
+        return max;
     }
 
-    return min;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMin()
+    {
+        int min = 1000000000;
+
+        for (int i = 0; i < selected.size(); i++)
+        {
+            if (columnAt(i) < min)
+            {
+                min = columnAt(i);
+            }
+        }
 
-  public Vector asVector()
-  {
-    return selected;
-  }
+        return min;
+    }
 
-  public void compensateForEdit(int start, int change)
-  {
-    for (int i = 0; i < size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector asVector()
     {
-      int temp = columnAt(i);
+        return selected;
+    }
 
-      if (temp >= start)
-      {
-        selected.setElementAt(new Integer(temp - change), i);
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param change DOCUMENT ME!
+     */
+    public void compensateForEdit(int start, int change)
+    {
+        for (int i = 0; i < size(); i++)
+        {
+            int temp = columnAt(i);
+
+            if (temp >= start)
+            {
+                selected.setElementAt(new Integer(temp - change), i);
+            }
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 175a609..9e0dca4 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -18,113 +18,153 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
 import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
 
-public class CutAndPasteTransfer
-    extends GCutAndPasteTransfer
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
-  public void setForInput()
-  {
-    getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
-  }
-
-  public String getText()
-  {
-    return textarea.getText();
-  }
-
-  public void setText(String text)
-  {
-    textarea.setText(text);
-  }
-
-  public void copyItem_actionPerformed(ActionEvent e)
-  {
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    c.setContents(new StringSelection(textarea.getText()), null);
-  }
-
-  public void pasteMenu_actionPerformed(ActionEvent e)
-  {
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    Transferable contents = c.getContents(this);
-
-    if (contents == null)
+    /**
+     * DOCUMENT ME!
+     */
+    public void setForInput()
     {
-      return;
+        getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
     }
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getText()
     {
-      textarea.setText( (String) contents.getTransferData(
-          DataFlavor.stringFlavor));
+        return textarea.getText();
     }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    String format = IdentifyFile.Identify(getText(), "Paste");
-    SequenceI[] sequences = null;
 
-    if (FormatAdapter.formats.contains(format))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void setText(String text)
     {
-      sequences = FormatAdapter.readFile(getText(), "Paste", format);
+        textarea.setText(text);
     }
 
-    if (sequences != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void copyItem_actionPerformed(ActionEvent e)
     {
-      AlignFrame af = new AlignFrame(new Alignment(sequences));
-      af.currentFileFormat = format;
-      Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
-                               AlignFrame.NEW_WINDOW_WIDTH,
-                               AlignFrame.NEW_WINDOW_HEIGHT);
-      af.statusBar.setText("Successfully pasted alignment file");
-
-      try
-      {
-        af.setMaximum(Preferences.showFullscreen);
-      }
-      catch (Exception ex)
-      {
-      }
-
-      try
-      {
-        this.setClosed(true);
-      }
-      catch (Exception ex)
-      {
-      }
+        Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+        c.setContents(new StringSelection(textarea.getText()), null);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pasteMenu_actionPerformed(ActionEvent e)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Couldn't read the pasted text.\n" +
-                                            "Formats currently supported are\n" +
-                                            "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",
-                                            "Error parsing text",
-                                            JOptionPane.WARNING_MESSAGE);
+        Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+        Transferable contents = c.getContents(this);
+
+        if (contents == null)
+        {
+            return;
+        }
+
+        try
+        {
+            textarea.setText((String) contents.getTransferData(
+                    DataFlavor.stringFlavor));
+        }
+        catch (Exception ex)
+        {
+        }
     }
-  }
 
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ok_actionPerformed(ActionEvent e)
     {
-      this.setClosed(true);
+        String format = IdentifyFile.Identify(getText(), "Paste");
+        SequenceI[] sequences = null;
+
+        if (FormatAdapter.formats.contains(format))
+        {
+            sequences = FormatAdapter.readFile(getText(), "Paste", format);
+        }
+
+        if (sequences != null)
+        {
+            AlignFrame af = new AlignFrame(new Alignment(sequences));
+            af.currentFileFormat = format;
+            Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
+                AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+            af.statusBar.setText("Successfully pasted alignment file");
+
+            try
+            {
+                af.setMaximum(Preferences.showFullscreen);
+            }
+            catch (Exception ex)
+            {
+            }
+
+            try
+            {
+                this.setClosed(true);
+            }
+            catch (Exception ex)
+            {
+            }
+        }
+        else
+        {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Couldn't read the pasted text.\n" +
+                "Formats currently supported are\n" +
+                "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",
+                "Error parsing text", JOptionPane.WARNING_MESSAGE);
+        }
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void cancel_actionPerformed(ActionEvent e)
     {
+        try
+        {
+            this.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 2a1979e..6a6ba2f 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -18,453 +18,573 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
 import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-import jalview.datamodel.*;
-import jalview.io.*;
 
-public class Desktop
-    extends jalview.jbgui.GDesktop implements DropTargetListener
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Desktop extends jalview.jbgui.GDesktop
+    implements DropTargetListener
 {
-  public static JDesktopPane desktop;
-  static int openFrameCount = 0;
-  static final int xOffset = 30;
-  static final int yOffset = 30;
-
-  public Desktop()
-  {
-    Image image = null;
-
-    try
+    /** DOCUMENT ME!! */
+    public static JDesktopPane desktop;
+    static int openFrameCount = 0;
+    static final int xOffset = 30;
+    static final int yOffset = 30;
+
+    /**
+     * Creates a new Desktop object.
+     */
+    public Desktop()
     {
-      java.net.URL url = getClass().getResource("/images/logo.gif");
+        Image image = null;
+
+        try
+        {
+            java.net.URL url = getClass().getResource("/images/logo.gif");
 
-      if (url != null)
-      {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+            if (url != null)
+            {
+                image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
 
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        mt.waitForID(0);
-        setIconImage(image);
-      }
-    }
-    catch (Exception ex)
-    {
-    }
+                MediaTracker mt = new MediaTracker(this);
+                mt.addImage(image, 0);
+                mt.waitForID(0);
+               // setIconImage(image);
+            }
+        }
+        catch (Exception ex)
+        {
+        }
 
-    setTitle("Jalview 2005");
-    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-    desktop = new JDesktopPane();
-    desktop.setBackground(Color.white);
-    setContentPane(desktop);
-    desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+        setTitle("Jalview 2005");
+        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+        desktop = new JDesktopPane();
+        desktop.setBackground(Color.white);
+        setContentPane(desktop);
+        desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
 
-    // This line prevents Windows Look&Feel resizing all new windows to maximum
-    // if previous window was maximised
-    desktop.setDesktopManager(new DefaultDesktopManager());
+        // This line prevents Windows Look&Feel resizing all new windows to maximum
+        // if previous window was maximised
+        desktop.setDesktopManager(new DefaultDesktopManager());
 
-    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-    String x = jalview.bin.Cache.getProperty("SCREEN_X");
-    String y = jalview.bin.Cache.getProperty("SCREEN_Y");
-    String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
-    String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
+        Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+        String x = jalview.bin.Cache.getProperty("SCREEN_X");
+        String y = jalview.bin.Cache.getProperty("SCREEN_Y");
+        String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
+        String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
 
-    if ( (x != null) && (y != null) && (width != null) && (height != null))
-    {
-      setBounds(Integer.parseInt(x), Integer.parseInt(y),
+        if ((x != null) && (y != null) && (width != null) && (height != null))
+        {
+            setBounds(Integer.parseInt(x), Integer.parseInt(y),
                 Integer.parseInt(width), Integer.parseInt(height));
-    }
-    else
-    {
-      setBounds( (int) (screenSize.width - 900) / 2,
+        }
+        else
+        {
+            setBounds((int) (screenSize.width - 900) / 2,
                 (int) (screenSize.height - 650) / 2, 900, 650);
-    }
+        }
 
-    this.addWindowListener(new WindowAdapter()
-    {
-      public void windowClosing(WindowEvent evt)
-      {
-        quit();
-      }
-    });
-    setVisible(true);
-
-    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
-
-    /////////Add a splashscreen on startup
-    /////////Add a splashscreen on startup
-    JInternalFrame frame = new JInternalFrame();
-
-    SplashScreen splash = new SplashScreen(frame, image);
-    frame.setContentPane(splash);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    addInternalFrame(frame, "", 750, 160, false);
-    frame.setLocation( (int) ( (getWidth() - 750) / 2),
-                      (int) ( (getHeight() - 160) / 2));
-  }
-
-  public static void addInternalFrame(final JInternalFrame frame,
-                                      String title, int w, int h)
-  {
-    addInternalFrame(frame, title, w, h, true);
-  }
-
-  public static void addInternalFrame(final JInternalFrame frame,
-                                      String title, int w, int h,
-                                      boolean resizable)
-  {
-    desktop.add(frame);
-    openFrameCount++;
-
-    try
-    {
-      frame.setSelected(true);
+        this.addWindowListener(new WindowAdapter()
+            {
+                public void windowClosing(WindowEvent evt)
+                {
+                    quit();
+                }
+            });
+
+        this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+
+        /////////Add a splashscreen on startup
+        /////////Add a splashscreen on startup
+        JInternalFrame frame = new JInternalFrame();
+
+        SplashScreen splash = new SplashScreen(frame, image);
+        frame.setContentPane(splash);
+        frame.setLayer(JLayeredPane.PALETTE_LAYER);
+        addInternalFrame(frame, "", 750, 160, false);
+        frame.setLocation((int) ((getWidth() - 750) / 2),
+            (int) ((getHeight() - 160) / 2));
     }
-    catch (java.beans.PropertyVetoException e)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param frame DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     * @param w DOCUMENT ME!
+     * @param h DOCUMENT ME!
+     */
+    public static void addInternalFrame(final JInternalFrame frame,
+        String title, int w, int h)
     {
+        addInternalFrame(frame, title, w, h, true);
     }
 
-    frame.setTitle(title);
-    frame.setSize(w, h);
-    frame.setClosable(true);
-    frame.setResizable(resizable);
-    frame.setMaximizable(resizable);
-    frame.setIconifiable(resizable);
-    frame.setFrameIcon(null);
-    frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);
-    frame.toFront();
-
-    final JMenuItem menuItem = new JMenuItem(title);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param frame DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     * @param w DOCUMENT ME!
+     * @param h DOCUMENT ME!
+     * @param resizable DOCUMENT ME!
+     */
+    public static void addInternalFrame(final JInternalFrame frame,
+        String title, int w, int h, boolean resizable)
     {
-      public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
-      {
-        openFrameCount--;
-        windowMenu.remove(menuItem);
-      }
-      ;
-    });
-
-    menuItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
+        desktop.add(frame);
+        openFrameCount++;
+
         try
         {
-          frame.setSelected(true);
-          frame.setIcon(false);
+            frame.setSelected(true);
         }
-        catch (java.beans.PropertyVetoException ex)
+        catch (java.beans.PropertyVetoException e)
         {
         }
 
-        ;
-      }
-    });
-
-    frame.setVisible(true);
-    windowMenu.add(menuItem);
-  }
-
-  public void dragEnter(DropTargetDragEvent evt)
-  {
-  }
-
-  public void dragExit(DropTargetEvent evt)
-  {
-  }
-
-  public void dragOver(DropTargetDragEvent evt)
-  {
-  }
+        frame.setTitle(title);
+        frame.setSize(w, h);
+        frame.setClosable(true);
+        frame.setResizable(resizable);
+        frame.setMaximizable(resizable);
+        frame.setIconifiable(resizable);
+        frame.setFrameIcon(null);
+        frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);
+        frame.toFront();
+
+        final JMenuItem menuItem = new JMenuItem(title);
+        frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+                public void internalFrameClosed(
+                    javax.swing.event.InternalFrameEvent evt)
+                {
+                    openFrameCount--;
+                    windowMenu.remove(menuItem);
+                }
+                ;
+            });
+
+        menuItem.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    try
+                    {
+                        frame.setSelected(true);
+                        frame.setIcon(false);
+                    }
+                    catch (java.beans.PropertyVetoException ex)
+                    {
+                    }
+
+                    ;
+                }
+            });
+
+        frame.setVisible(true);
+        windowMenu.add(menuItem);
+    }
 
-  public void dropActionChanged(DropTargetDragEvent evt)
-  {
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void dragEnter(DropTargetDragEvent evt)
+    {
+    }
 
-  public void drop(DropTargetDropEvent evt)
-  {
-    Transferable t = evt.getTransferable();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void dragExit(DropTargetEvent evt)
+    {
+    }
 
-    if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void dragOver(DropTargetDragEvent evt)
     {
-      return;
     }
 
-    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void dropActionChanged(DropTargetDragEvent evt)
+    {
+    }
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void drop(DropTargetDropEvent evt)
     {
-      java.util.List files = (java.util.List) t.getTransferData(DataFlavor.
-          javaFileListFlavor);
+        Transferable t = evt.getTransferable();
 
-      for (int i = 0; i < files.size(); i++)
-      {
-        String file = files.get(i).toString();
-        String protocol = "File";
+        if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+        {
+            return;
+        }
+
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 
-        if (file.endsWith(".jar"))
+        try
         {
-          Jalview2XML.LoadJalviewAlign(file);
+            java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+
+            for (int i = 0; i < files.size(); i++)
+            {
+                String file = files.get(i).toString();
+                String protocol = "File";
+                String format = null;
+
+                if (file.endsWith(".jar"))
+                {
+                  format = "Jalview";
+
+                }
+                else
+                {
+                    format = jalview.io.IdentifyFile.Identify(file,
+                            protocol);
+                }
+                LoadFile(file, protocol, format);
+            }
         }
-        else
+        catch (Exception ex)
         {
-          String format = jalview.io.IdentifyFile.Identify(file,
-              protocol);
-          LoadFile(file, protocol, format);
+            ex.printStackTrace();
         }
-      }
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
     {
-      ex.printStackTrace();
-    }
-  }
-
-  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"),
-        new String[]
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"),
+                new String[]
+                {
+                    "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+                    "jar"
+                },
+                new String[]
+                {
+                    "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+                }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Open local file");
+        chooser.setToolTipText("Open");
+
+        int value = chooser.showOpenDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
         {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "jar"
-    },
-        new String[]
-        {
-        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-    }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Open local file");
-    chooser.setToolTipText("Open");
-
-    int value = chooser.showOpenDialog(this);
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+
+            String format = null;
+            if (chooser.getSelectedFormat().equals("Jalview"))
+            {
+              format = "Jalview";
+            }
+            else
+            {
+                format = IdentifyFile.Identify(choice, "File");
+            }
+
+            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+            LoadFile(choice, "File", format);
+        }
+    }
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     * @param protocol DOCUMENT ME!
+     * @param format DOCUMENT ME!
+     */
+    public void LoadFile(String file, String protocol, String format)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
-
-      if (chooser.getSelectedFormat().equals("Jalview"))
-      {
-        jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");
-        Jalview2XML.LoadJalviewAlign(choice);
-      }
-      else
-      {
-        String format = IdentifyFile.Identify(choice, "File");
-        jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
-        LoadFile(choice, "File", format);
-      }
+        LoadingThread loader = new LoadingThread(file, protocol, format);
+        loader.start();
     }
-  }
-
-  public void LoadFile(String file, String protocol, String format)
-  {
-    LoadingThread loader = new LoadingThread(file, protocol, format);
-    loader.start();
-  }
-
-  public void inputURLMenuItem_actionPerformed(ActionEvent e)
-  {
-    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,
-        "Enter url of input file", "Input alignment from URL",
-        JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")
-        .toString();
-
-    if (url == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     * @param protocol DOCUMENT ME!
+     * @param format DOCUMENT ME!
+     */
+    public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, String format)
     {
-      return;
-    }
+        LoadingThread loader = new LoadingThread(file, protocol, format);
+        loader.start();
+
+        while (loader.isAlive())
+        {
+          try
+          {
+            Thread.sleep(50);
+          }
+          catch (Exception ex)
+          {}
+        }
 
-    String format = IdentifyFile.Identify(url, "URL");
+      return loader.af;
+    }
 
-    if (format.equals("URL NOT FOUND"))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void inputURLMenuItem_actionPerformed(ActionEvent e)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Couldn't locate " + url,
-                                            "URL not found",
-                                            JOptionPane.WARNING_MESSAGE);
+        String url = JOptionPane.showInternalInputDialog(Desktop.desktop,
+                "Enter url of input file", "Input alignment from URL",
+                JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")
+                                .toString();
+
+        if (url == null)
+        {
+            return;
+        }
+
+        if (url.trim().toLowerCase().endsWith(".jar"))
+        {
+               jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
+               Jalview2XML.LoadJalviewAlign(url);
+        }
+        else
+        {
 
-      return;
+          String format = IdentifyFile.Identify(url, "URL");
+
+          if (format.equals("URL NOT FOUND"))
+          {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                  "Couldn't locate " + url,
+                                                  "URL not found",
+                                                  JOptionPane.WARNING_MESSAGE);
+
+            return;
+          }
+
+          LoadFile(url, "URL", format);
+        }
     }
 
-    LoadFile(url, "URL", format);
-  }
-
-  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    cap.setForInput();
-    Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
-  }
-
-  /*
-   * Exit the program
-   */
-  public void quit()
-  {
-    if (jalview.bin.Jalview.applet != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
     {
-      jalview.bin.Jalview.applet.destroy();
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
+        cap.setForInput();
+        Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
     }
-    else
+
+    /*
+     * Exit the program
+     */
+    public void quit()
     {
-      jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x +
-                                    "");
-      jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y +
-                                    "");
-      jalview.bin.Cache.setProperty("SCREEN_WIDTH",
-                                    getWidth() + "");
-      jalview.bin.Cache.setProperty("SCREEN_HEIGHT",
-                                      getHeight() + "");
-      System.exit(0);
+        jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
+        jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
+        jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
+        jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+        System.exit(0);
     }
-  }
-
-  public void aboutMenuItem_actionPerformed(ActionEvent e)
-  {
-    JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                          "JalView 2005 version " +
-                                          jalview.bin.Cache.VERSION +
-                                          "; last updated: " +
-                                          jalview.bin.Cache.BUILD_DATE +
-                                          "\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
-                                          "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
-                                          "\nFor all issues relating to Jalview, email help@jalview.org" +
-                                          "\n\nIf  you use JalView, please cite:" +
-                                          "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
-                                          "\nBioinformatics,  2004 12;426-7.",
-                                          "About Jalview",
-                                          JOptionPane.INFORMATION_MESSAGE);
-  }
-
-  public void documentationMenuItem_actionPerformed(ActionEvent e)
-  {
-    try
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void aboutMenuItem_actionPerformed(ActionEvent e)
     {
-      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-      java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
-      javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
-      javax.help.HelpBroker hb = hs.createHelpBroker();
-      hb.setLocation(new Point(200, 50));
-      hb.setSize(new Dimension(800, 700));
-      hb.setCurrentID("home");
-      hb.setDisplayed(true);
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            "JalView 2005 version " + jalview.bin.Cache.VERSION +
+            "; last updated: " + jalview.bin.Cache.BUILD_DATE +
+            "\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
+            "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
+            "\nFor all issues relating to Jalview, email help@jalview.org" +
+            "\n\nIf  you use JalView, please cite:" +
+            "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
+            "\nBioinformatics,  2004 12;426-7.", "About Jalview",
+            JOptionPane.INFORMATION_MESSAGE);
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void documentationMenuItem_actionPerformed(ActionEvent e)
     {
-      ex.printStackTrace();
+        try
+        {
+            ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+            java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+            javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+            javax.help.HelpBroker hb = hs.createHelpBroker();
+            hb.setLocation(new Point(200, 50));
+            hb.setSize(new Dimension(800, 700));
+            hb.setCurrentID("home");
+            hb.setDisplayed(true);
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
     }
-  }
 
-  protected void preferences_actionPerformed(ActionEvent e)
-  {
-    Preferences pref = new Preferences();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void preferences_actionPerformed(ActionEvent e)
+    {
+        new Preferences();
+    }
 
-  public void saveState_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"jar"},
-        new String[]
-        {"Jalview Project"}, "Jalview Project");
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveState_actionPerformed(ActionEvent e)
+    {
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"), new String[] { "jar" },
+                new String[] { "Jalview Project" }, "Jalview Project");
 
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save State");
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save State");
 
-    int value = chooser.showSaveDialog(this);
+        int value = chooser.showSaveDialog(this);
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      java.io.File choice = chooser.getSelectedFile();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-      Jalview2XML.SaveState(choice);
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            java.io.File choice = chooser.getSelectedFile();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+            Jalview2XML.SaveState(choice);
+        }
     }
-  }
-
-  public void loadState_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"jar"},
-        new String[]
-        {"Jalview Project"}, "Jalview Project");
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Restore state");
-
-    int value = chooser.showOpenDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void loadState_actionPerformed(ActionEvent e)
     {
-      String choice = chooser.getSelectedFile().getAbsolutePath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
-      Jalview2XML.LoadJalviewAlign(choice);
-    }
-  }
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"), new String[] { "jar" },
+                new String[] { "Jalview Project" }, "Jalview Project");
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Restore state");
 
-  class LoadingThread
-      extends Thread
-  {
-    String file;
-    String protocol;
-    String format;
+        int value = chooser.showOpenDialog(this);
 
-    public LoadingThread(String file, String protocol, String format)
-    {
-      this.file = file;
-      this.protocol = protocol;
-      this.format = format;
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            String choice = chooser.getSelectedFile().getAbsolutePath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+            Jalview2XML.LoadJalviewAlign(choice);
+        }
     }
 
-    public void run()
+    class LoadingThread extends Thread
     {
-      SequenceI[] sequences = null;
+        String file;
+        String protocol;
+        String format;
+        AlignFrame af;
 
-      if (FormatAdapter.formats.contains(format))
-      {
-        sequences = FormatAdapter.readFile(file, protocol, format);
-      }
-
-      if ( (sequences != null) && (sequences.length > 0))
-      {
-        AlignFrame af = new AlignFrame(new Alignment(sequences));
-        addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
-                         AlignFrame.NEW_WINDOW_HEIGHT);
-        af.currentFileFormat = format;
-        af.statusBar.setText("Successfully loaded file " + file);
-
-        try
+        public LoadingThread(String file, String protocol, String format)
         {
-          af.setMaximum(Preferences.showFullscreen);
+            this.file = file;
+            this.protocol = protocol;
+            this.format = format;
         }
-        catch (Exception ex)
+
+        public void run()
         {
+            SequenceI[] sequences = null;
+
+            if(format.equalsIgnoreCase("Jalview"))
+            {
+              Jalview2XML.LoadJalviewAlign(file);
+            }
+            else
+            {
+              if (FormatAdapter.formats.contains(format))
+              {
+                sequences = FormatAdapter.readFile(file, protocol, format);
+              }
+
+              if ( (sequences != null) && (sequences.length > 0))
+              {
+                af = new AlignFrame(new Alignment(sequences));
+                addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
+                                 AlignFrame.NEW_WINDOW_HEIGHT);
+                af.currentFileFormat = format;
+                af.statusBar.setText("Successfully loaded file " + file);
+
+                try
+                {
+                  af.setMaximum(Preferences.showFullscreen);
+                }
+                catch (Exception ex)
+                {
+                }
+              }
+              else
+              {
+                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    "Couldn't open file.\n" +
+                    "Formats currently supported are\n" +
+                    "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!
+                    , "Error loading file", JOptionPane.WARNING_MESSAGE);
+              }
+            }
         }
-      }
-      else
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                              "Couldn't open file.\n" +
-                                              "Formats currently supported are\n" +
-                                              "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!
-                                              , "Error loading file",
-                                              JOptionPane.WARNING_MESSAGE);
-      }
     }
-  }
 }
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 1de32a5..8a94a89 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -18,93 +18,120 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
 
 import java.awt.*;
 
-import jalview.datamodel.*;
+import java.util.*;
+
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class FeatureRenderer
 {
-  AlignViewport av;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-
-  public FeatureRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
-  {
-    Vector features = seq.getSequenceFeatures();
-    Enumeration e = features.elements();
-
-    while (e.hasMoreElements())
+    AlignViewport av;
+    SequenceGroup currentSequenceGroup = null;
+    SequenceGroup[] allGroups = null;
+    Color resBoxColour;
+    Graphics graphics;
+
+    /**
+     * Creates a new FeatureRenderer object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public FeatureRenderer(AlignViewport av)
     {
-      SequenceFeature sf = (SequenceFeature) e.nextElement();
-
-      if (sf.getStart() > seq.getEnd())
-      {
-        continue;
-      }
-
-      int fstart = seq.findIndex(sf.getStart()) - 1;
-      int fend = seq.findIndex(sf.getEnd()) - 1;
+        this.av = av;
+    }
 
-      if ( ( (fstart <= end) && (fend >= start)))
-      {
-        if (fstart < start)
-        { // fix for if the feature we have starts before the sequence start,
-          fstart = start; // but the feature end is still valid!!
-        }
-        if(fend >=end)
-          fend = end;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param sg DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
+        int start, int end, int x1, int y1, int width, int height)
+    {
+        Vector features = seq.getSequenceFeatures();
+        Enumeration e = features.elements();
 
-        if (fstart == fend)
-        {
-          g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width,
-                          height, 4, 4);
-          g.setColor(Color.white);
-
-          char s = seq.getSequence().charAt(fstart);
-          FontMetrics fm = g.getFontMetrics();
-          int charOffset = (width - fm.charWidth(s)) / 2;
-          int pady = height / 5;
-          g.drawString(String.valueOf(s),
-                       charOffset + x1 + (width * (fstart - start)),
-                       (y1 + height) - pady);
-        }
-        else
+        while (e.hasMoreElements())
         {
-          for (int i = fstart; i <= fend; i++)
-          {
-            char s = seq.getSequence().charAt(i);
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
 
-            if (jalview.util.Comparison.isGap(s))
+            if (sf.getStart() > seq.getEnd())
             {
-              continue;
+                continue;
             }
 
-            g.setColor(Color.blue);
-            g.fillRect( (i - start) * width, y1, width, height);
-
-            g.setColor(Color.white);
+            int fstart = seq.findIndex(sf.getStart()) - 1;
+            int fend = seq.findIndex(sf.getEnd()) - 1;
 
-            FontMetrics fm = g.getFontMetrics();
-            int charOffset = (width - fm.charWidth(s)) / 2;
-            int pady = height / 5;
-            g.drawString(String.valueOf(s),
-                         charOffset + x1 + (width * (i - start)),
-                         (y1 + height) - pady);
-          }
+            if (((fstart <= end) && (fend >= start)))
+            {
+                if (fstart < start)
+                { // fix for if the feature we have starts before the sequence start,
+                    fstart = start; // but the feature end is still valid!!
+                }
+
+                if (fend >= end)
+                {
+                    fend = end;
+                }
+
+                if (fstart == fend)
+                {
+                    g.setColor(Color.red);
+                    g.fillRoundRect((fstart - start) * width, y1, width,
+                        height, 4, 4);
+                    g.setColor(Color.white);
+
+                    char s = seq.getSequence().charAt(fstart);
+                    FontMetrics fm = g.getFontMetrics();
+                    int charOffset = (width - fm.charWidth(s)) / 2;
+                    int pady = height / 5;
+                    g.drawString(String.valueOf(s),
+                        charOffset + x1 + (width * (fstart - start)),
+                        (y1 + height) - pady);
+                }
+                else
+                {
+                    for (int i = fstart; i <= fend; i++)
+                    {
+                        char s = seq.getSequence().charAt(i);
+
+                        if (jalview.util.Comparison.isGap(s))
+                        {
+                            continue;
+                        }
+
+                        g.setColor(Color.blue);
+                        g.fillRect((i - start) * width, y1, width, height);
+
+                        g.setColor(Color.white);
+
+                        FontMetrics fm = g.getFontMetrics();
+                        int charOffset = (width - fm.charWidth(s)) / 2;
+                        int pady = height / 5;
+                        g.drawString(String.valueOf(s),
+                            charOffset + x1 + (width * (i - start)),
+                            (y1 + height) - pady);
+                    }
+                }
+            }
         }
-      }
     }
-  }
 }
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 71a52e9..1aceb80 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -18,318 +18,362 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
+import java.util.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
 
-public class Finder
-    extends GFinder
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder extends GFinder
 {
-  AlignViewport av;
-  AlignmentPanel ap;
-  JInternalFrame frame;
-  SuperGroup searchGroup;
-  Vector searchResults;
-  int seqIndex = 0;
-  int resIndex = 0;
-
-  public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
-  {
-    this.av = av;
-    this.ap = ap;
-    frame = f;
-
-    // all a big pain, but we need to wait until the frame is visible before the textfield can
-    // obtain the focus/////////////////////////
-    frame.addInternalFrameListener(new InternalFrameAdapter()
-    {
-      public void internalFrameOpened(InternalFrameEvent evt)
-      {
-        SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            textfield.requestFocus();
-          }
-        });
-      }
-
-      public void internalFrameClosing(InternalFrameEvent evt)
-      {
-        cancel_actionPerformed(null);
-      }
-    });
-  }
-
-  public void textfield_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findNext_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findAll_actionPerformed(ActionEvent e)
-  {
-    resIndex = 0;
-    seqIndex = 0;
-    doSearch(true);
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try
+    AlignViewport av;
+    AlignmentPanel ap;
+    JInternalFrame frame;
+    SuperGroup searchGroup;
+    Vector searchResults;
+    int seqIndex = 0;
+    int resIndex = 0;
+
+    /**
+     * Creates a new Finder object.
+     *
+     * @param av DOCUMENT ME!
+     * @param ap DOCUMENT ME!
+     * @param f DOCUMENT ME!
+     */
+    public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
     {
-      // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      ap.highlightSearchResults(null);
-      ap.idPanel.highlightSearchResults(null);
-
-      // frame.setClosed(true);
+        this.av = av;
+        this.ap = ap;
+        frame = f;
+
+        // all a big pain, but we need to wait until the frame is visible before the textfield can
+        // obtain the focus/////////////////////////
+        frame.addInternalFrameListener(new InternalFrameAdapter()
+            {
+                public void internalFrameOpened(InternalFrameEvent evt)
+                {
+                    SwingUtilities.invokeLater(new Runnable()
+                        {
+                            public void run()
+                            {
+                                textfield.requestFocus();
+                            }
+                        });
+                }
+
+                /**
+                 * DOCUMENT ME!
+                 *
+                 * @param evt DOCUMENT ME!
+                 */
+                public void internalFrameClosing(InternalFrameEvent evt)
+                {
+                    cancel_actionPerformed(null);
+                }
+            });
     }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  public void createNewGroup_actionPerformed(ActionEvent e)
-  {
-    Color[] newColors = new Color[24];
 
-    for (int i = 0; i < 24; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void textfield_actionPerformed(ActionEvent e)
     {
-      newColors[i] = new Color(60, 160, 115);
+        doSearch(false);
     }
 
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-        newColors);
-    String searchString = textfield.getText();
-
-    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
-
-    for (int i = 0; i < searchResults.size(); i += 3)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findNext_actionPerformed(ActionEvent e)
     {
-      // its possible edits may have occurred since search was performed
-      // account for this here
-      SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(
-          searchResults.elementAt(i).toString()));
-      int startRes = seq.findIndex(Integer.parseInt(
-          searchResults.elementAt(i + 1).toString())) - 1;
-      int endRes = seq.findIndex(Integer.parseInt(
-          searchResults.elementAt(i + 2).toString())) - 1;
-
-      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,
-                                           false, startRes, endRes);
-      sg.addSequence(seq, false);
-      av.alignment.addGroup(sg);
-      searchGroup.addGroup(sg);
+        doSearch(false);
     }
 
-    ap.av.alignment.addSuperGroup(searchGroup);
-    ap.highlightSearchResults(null);
-  }
-
-  void doSearch(boolean findAll)
-  {
-    createNewGroup.setEnabled(false);
-
-    String searchString = textfield.getText().toUpperCase();
-
-    com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
-
-    searchResults = new Vector();
-
-    int[] allResults = null;
-
-    Sequence seq;
-    String item = null;
-    boolean found = false;
-
-    ////// is the searchString a residue number?
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findAll_actionPerformed(ActionEvent e)
     {
-      int res = Integer.parseInt(searchString);
-      found = true;
-
-      if (av.getSelectionGroup().getSize() > 0)
-      {
-        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
-      }
-      else
-      {
-        seq = (Sequence) av.getAlignment().getSequenceAt(0);
-      }
-
-      searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
-      searchResults.add(Integer.toString(seq.findIndex(res) - 1));
-      searchResults.add(Integer.toString(seq.findIndex(res) - 1));
+        resIndex = 0;
+        seqIndex = 0;
+        doSearch(true);
     }
-    catch (NumberFormatException ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void cancel_actionPerformed(ActionEvent e)
     {
-    }
+        try
+        {
+            // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+            ap.highlightSearchResults(null);
+            ap.idPanel.highlightSearchResults(null);
 
-    ///////////////////////////////////////////////
-    Color[] newColors = new Color[24];
+            // frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
+    }
 
-    for (int i = 0; i < 24; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void createNewGroup_actionPerformed(ActionEvent e)
     {
-      newColors[i] = new Color(60, 160, 115);
-    }
+        Color[] newColors = new Color[24];
 
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-        newColors);
+        for (int i = 0; i < 24; i++)
+        {
+            newColors[i] = new Color(60, 160, 115);
+        }
 
-    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
+        jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
+        String searchString = textfield.getText();
 
-    int end = av.alignment.getHeight();
+        searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
-    SequenceGroup selection = av.getSelectionGroup();
+        for (int i = 0; i < searchResults.size(); i += 3)
+        {
+            // its possible edits may have occurred since search was performed
+            // account for this here
+            SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(
+                        searchResults.elementAt(i).toString()));
+            int startRes = seq.findIndex(Integer.parseInt(
+                        searchResults.elementAt(i + 1).toString())) - 1;
+            int endRes = seq.findIndex(Integer.parseInt(
+                        searchResults.elementAt(i + 2).toString())) - 1;
+
+            SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,
+                    false, startRes, endRes);
+            sg.addSequence(seq, false);
+            av.alignment.addGroup(sg);
+            searchGroup.addGroup(sg);
+        }
 
-    if (selection != null)
-    {
-      if ( (selection.getSize() < 1) ||
-          ( (selection.getEndRes() - selection.getStartRes()) < 2))
-      {
-        selection = null;
-      }
+        ap.av.alignment.addSuperGroup(searchGroup);
+        ap.highlightSearchResults(null);
     }
 
-    while (!found && (seqIndex < end))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param findAll DOCUMENT ME!
+     */
+    void doSearch(boolean findAll)
     {
-      seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
+        createNewGroup.setEnabled(false);
 
-      if ( (selection != null) && !selection.sequences.contains(seq))
-      {
-        seqIndex++;
-        resIndex = 0;
+        String searchString = textfield.getText().toUpperCase();
 
-        continue;
-      }
+        com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
-      item = seq.getSequence().toUpperCase();
+        searchResults = new Vector();
 
-      if ( (selection != null) &&
-          (selection.getEndRes() < av.alignment.getWidth()))
-      {
-        item = item.substring(0, selection.getEndRes() + 1);
-      }
+        int[] allResults = null;
 
-      ///Shall we ignore gaps????
-      StringBuffer noGaps = new StringBuffer();
-      int insertCount = 0;
-      Vector spaces = new Vector();
+        Sequence seq;
+        String item = null;
+        boolean found = false;
 
-      for (int j = 0; j < item.length(); j++)
-      {
-        if (!jalview.util.Comparison.isGap(item.charAt(j)))
+        ////// is the searchString a residue number?
+        try
         {
-          noGaps.append(item.charAt(j));
-          spaces.add(new Integer(insertCount));
+            int res = Integer.parseInt(searchString);
+            found = true;
+
+            if (av.getSelectionGroup().getSize() > 0)
+            {
+                seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+            }
+            else
+            {
+                seq = (Sequence) av.getAlignment().getSequenceAt(0);
+            }
+
+            searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
+            searchResults.add(Integer.toString(seq.findIndex(res) - 1));
+            searchResults.add(Integer.toString(seq.findIndex(res) - 1));
         }
-        else
+        catch (NumberFormatException ex)
         {
-          insertCount++;
         }
-      }
 
-      for (int r = resIndex; r < noGaps.length(); r++)
-      {
-        if (regex.searchFrom(noGaps.toString(), r))
+        ///////////////////////////////////////////////
+        Color[] newColors = new Color[24];
+
+        for (int i = 0; i < 24; i++)
         {
-          resIndex = regex.matchedFrom();
-
-          if ( (selection != null) &&
-              ( (resIndex +
-                 Integer.parseInt(spaces.get(resIndex).toString())) <
-               selection.getStartRes()))
-          {
-            continue;
-          }
-
-          searchResults.add(Integer.toString(seqIndex));
-
-          int sres = seq.findPosition(resIndex +
-                                      Integer.parseInt(spaces.elementAt(
-              resIndex)
-              .toString()));
-          int eres = seq.findPosition(regex.matchedTo() - 1 +
-                                      Integer.parseInt(spaces.elementAt(regex.
-              matchedTo() -
-              1).toString()));
-
-          searchResults.addElement(sres + "");
-          searchResults.addElement(eres + "");
-
-          if (!findAll)
-          {
-            // thats enough, break and display the result
-            found = true;
-            resIndex++;
+            newColors[i] = new Color(60, 160, 115);
+        }
+
+        jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
 
-            break;
-          }
+        searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
-          r = resIndex;
+        int end = av.alignment.getHeight();
+
+        SequenceGroup selection = av.getSelectionGroup();
+
+        if (selection != null)
+        {
+            if ((selection.getSize() < 1) ||
+                    ((selection.getEndRes() - selection.getStartRes()) < 2))
+            {
+                selection = null;
+            }
         }
-      }
 
-      if (!found)
-      {
-        seqIndex++;
-        resIndex = 0;
-      }
-    }
+        while (!found && (seqIndex < end))
+        {
+            seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
+
+            if ((selection != null) && !selection.sequences.contains(seq))
+            {
+                seqIndex++;
+                resIndex = 0;
+
+                continue;
+            }
+
+            item = seq.getSequence().toUpperCase();
+
+            if ((selection != null) &&
+                    (selection.getEndRes() < av.alignment.getWidth()))
+            {
+                item = item.substring(0, selection.getEndRes() + 1);
+            }
+
+            ///Shall we ignore gaps????
+            StringBuffer noGaps = new StringBuffer();
+            int insertCount = 0;
+            Vector spaces = new Vector();
+
+            for (int j = 0; j < item.length(); j++)
+            {
+                if (!jalview.util.Comparison.isGap(item.charAt(j)))
+                {
+                    noGaps.append(item.charAt(j));
+                    spaces.add(new Integer(insertCount));
+                }
+                else
+                {
+                    insertCount++;
+                }
+            }
+
+            for (int r = resIndex; r < noGaps.length(); r++)
+            {
+                if (regex.searchFrom(noGaps.toString(), r))
+                {
+                    resIndex = regex.matchedFrom();
+
+                    if ((selection != null) &&
+                            ((resIndex +
+                            Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
+                    {
+                        continue;
+                    }
+
+                    searchResults.add(Integer.toString(seqIndex));
+
+                    int sres = seq.findPosition(resIndex +
+                            Integer.parseInt(spaces.elementAt(resIndex)
+                                                   .toString()));
+                    int eres = seq.findPosition(regex.matchedTo() - 1 +
+                            Integer.parseInt(spaces.elementAt(regex.matchedTo() -
+                                    1).toString()));
+
+                    searchResults.addElement(sres + "");
+                    searchResults.addElement(eres + "");
+
+                    if (!findAll)
+                    {
+                        // thats enough, break and display the result
+                        found = true;
+                        resIndex++;
+
+                        break;
+                    }
+
+                    r = resIndex;
+                }
+            }
+
+            if (!found)
+            {
+                seqIndex++;
+                resIndex = 0;
+            }
+        }
 
-    Vector idMatch = new Vector();
+        Vector idMatch = new Vector();
 
-    for (int id = 0; id < av.alignment.getHeight(); id++)
-    {
-      if (regex.search(av.alignment.getSequenceAt(id).getName()))
-      {
-        idMatch.add(av.alignment.getSequenceAt(id));
-      }
-    }
+        for (int id = 0; id < av.alignment.getHeight(); id++)
+        {
+            if (regex.search(av.alignment.getSequenceAt(id).getName()))
+            {
+                idMatch.add(av.alignment.getSequenceAt(id));
+            }
+        }
 
-    if ( (searchResults.size() == 0) && (idMatch.size() > 0))
-    {
-      ap.idPanel.highlightSearchResults(idMatch);
-    }
+        if ((searchResults.size() == 0) && (idMatch.size() > 0))
+        {
+            ap.idPanel.highlightSearchResults(idMatch);
+        }
 
-    if (searchResults.size() > 0)
-    {
-      allResults = new int[searchResults.size()];
+        if (searchResults.size() > 0)
+        {
+            allResults = new int[searchResults.size()];
 
-      for (int i = 0; i < searchResults.size(); i++)
-      {
-        allResults[i] = Integer.parseInt(searchResults.get(i).toString());
-      }
+            for (int i = 0; i < searchResults.size(); i++)
+            {
+                allResults[i] = Integer.parseInt(searchResults.get(i).toString());
+            }
 
-      createNewGroup.setEnabled(true);
-    }
-    else
-    {
-      JOptionPane.showInternalMessageDialog(this, "Finished searching",
-                                            null,
-                                            JOptionPane.INFORMATION_MESSAGE);
-      resIndex = 0;
-      seqIndex = 0;
-    }
+            createNewGroup.setEnabled(true);
+        }
+        else
+        {
+            JOptionPane.showInternalMessageDialog(this, "Finished searching",
+                null, JOptionPane.INFORMATION_MESSAGE);
+            resIndex = 0;
+            seqIndex = 0;
+        }
 
-    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-    ap.highlightSearchResults(allResults);
+        // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+        ap.highlightSearchResults(allResults);
 
-    if (findAll)
-    {
-      String message = (searchResults.size() / 3) + " matches found.";
-      JOptionPane.showInternalMessageDialog(this, message, null,
-                                            JOptionPane.INFORMATION_MESSAGE);
+        if (findAll)
+        {
+            String message = (searchResults.size() / 3) + " matches found.";
+            JOptionPane.showInternalMessageDialog(this, message, null,
+                JOptionPane.INFORMATION_MESSAGE);
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index b911d7d..527bf5d 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -18,132 +18,177 @@
  */
 package jalview.gui;
 
+import jalview.bin.*;
+
+import jalview.jbgui.*;
+
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-import jalview.bin.*;
-import jalview.jbgui.*;
 
-public class FontChooser
-    extends GFontChooser
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FontChooser extends GFontChooser
 {
-  AlignmentPanel ap;
-  Font oldFont;
-  boolean init = true;
-  JInternalFrame frame;
-
-  public FontChooser(AlignmentPanel ap)
-  {
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Change Font", 480, 100, false);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-
-    this.ap = ap;
+    AlignmentPanel ap;
+    Font oldFont;
+    boolean init = true;
+    JInternalFrame frame;
+
+    /**
+     * Creates a new FontChooser object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public FontChooser(AlignmentPanel ap)
+    {
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "Change Font", 480, 100, false);
+        frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
-    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
-        .getAvailableFontFamilyNames();
+        this.ap = ap;
 
-    for (int i = 0; i < fonts.length; i++)
-    {
-      fontName.addItem(fonts[i]);
-    }
+        String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+                                                     .getAvailableFontFamilyNames();
 
-    for (int i = 1; i < 31; i++)
-    {
-      fontSize.addItem(i + "");
-    }
+        for (int i = 0; i < fonts.length; i++)
+        {
+            fontName.addItem(fonts[i]);
+        }
 
-    fontStyle.addItem("plain");
-    fontStyle.addItem("bold");
-    fontStyle.addItem("italic");
+        for (int i = 1; i < 31; i++)
+        {
+            fontSize.addItem(i + "");
+        }
 
-    oldFont = ap.av.getFont();
-    fontName.setSelectedItem(oldFont.getName());
-    fontSize.setSelectedItem(oldFont.getSize() + "");
-    fontStyle.setSelectedIndex(oldFont.getStyle());
+        fontStyle.addItem("plain");
+        fontStyle.addItem("bold");
+        fontStyle.addItem("italic");
 
-    init = false;
-  }
+        oldFont = ap.av.getFont();
+        fontName.setSelectedItem(oldFont.getName());
+        fontSize.setSelectedItem(oldFont.getSize() + "");
+        fontStyle.setSelectedIndex(oldFont.getStyle());
 
-  protected void ok_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      frame.setClosed(true);
+        init = false;
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void ok_actionPerformed(ActionEvent e)
     {
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
+
+        if (ap.getOverviewPanel() != null)
+        {
+            ap.getOverviewPanel().updateOverviewImage();
+        }
     }
 
-    if (ap.getOverviewPanel() != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cancel_actionPerformed(ActionEvent e)
     {
-      ap.getOverviewPanel().updateOverviewImage();
+        ap.av.setFont(oldFont);
+        ap.repaint();
+        fontName.setSelectedItem(oldFont.getName());
+        fontSize.setSelectedItem(oldFont.getSize() + "");
+        fontStyle.setSelectedIndex(oldFont.getStyle());
+
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
     }
-  }
 
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-    ap.av.setFont(oldFont);
-    ap.repaint();
-    fontName.setSelectedItem(oldFont.getName());
-    fontSize.setSelectedItem(oldFont.getSize() + "");
-    fontStyle.setSelectedIndex(oldFont.getStyle());
-
-    try
+    /**
+     * DOCUMENT ME!
+     */
+    void changeFont()
     {
-      frame.setClosed(true);
+        Font newFont = new Font(fontName.getSelectedItem().toString(),
+                fontStyle.getSelectedIndex(),
+                Integer.parseInt(fontSize.getSelectedItem().toString()));
+        ap.av.setFont(newFont);
+        ap.fontChanged();
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void fontName_actionPerformed(ActionEvent e)
     {
+        if (init)
+        {
+            return;
+        }
+
+        changeFont();
     }
-  }
-
-  void changeFont()
-  {
-    Font newFont = new Font(fontName.getSelectedItem().toString(),
-                            fontStyle.getSelectedIndex(),
-                            Integer.parseInt(fontSize.getSelectedItem().
-                                             toString()));
-    ap.av.setFont(newFont);
-    ap.fontChanged();
-  }
-
-  protected void fontName_actionPerformed(ActionEvent e)
-  {
-    if (init)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void fontSize_actionPerformed(ActionEvent e)
     {
-      return;
-    }
+        if (init)
+        {
+            return;
+        }
 
-    changeFont();
-  }
+        changeFont();
+    }
 
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-    if (init)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void fontStyle_actionPerformed(ActionEvent e)
     {
-      return;
-    }
+        if (init)
+        {
+            return;
+        }
 
-    changeFont();
-  }
+        changeFont();
+    }
 
-  protected void fontStyle_actionPerformed(ActionEvent e)
-  {
-    if (init)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void defaultButton_actionPerformed(ActionEvent e)
     {
-      return;
+        Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
+        Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex() + "");
+        Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
     }
-
-    changeFont();
-  }
-
-  public void defaultButton_actionPerformed(ActionEvent e)
-  {
-    Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
-    Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex() + "");
-    Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
-  }
 }
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index b38fd21..9581ccc 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -18,240 +18,278 @@
  */
 package jalview.gui;
 
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
 import java.awt.*;
 import java.awt.image.*;
+
 import javax.swing.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
 
-public class IdCanvas
-    extends JPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas extends JPanel
 {
-  protected AlignViewport av;
-  protected boolean showScores = true;
-  protected int maxIdLength = -1;
-  protected String maxIdStr = null;
-  BufferedImage image;
-  Graphics2D gg;
-  int imgHeight = 0;
-  boolean fastPaint = false;
-  java.util.Vector searchResults;
-
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(new BorderLayout());
-    this.av = av;
-    PaintRefresher.Register(this, av.alignment);
-  }
-
-  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
-                           int ypos)
-  {
-    int charHeight = av.getCharHeight();
-
-    if ( (searchResults != null) && searchResults.contains(s))
+    protected AlignViewport av;
+    protected boolean showScores = true;
+    protected int maxIdLength = -1;
+    protected String maxIdStr = null;
+    BufferedImage image;
+    Graphics2D gg;
+    int imgHeight = 0;
+    boolean fastPaint = false;
+    java.util.Vector searchResults;
+
+    /**
+     * Creates a new IdCanvas object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public IdCanvas(AlignViewport av)
     {
-      gg.setColor(Color.black);
-      gg.fillRect(0,
-                  AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
-                  getWidth(), charHeight);
-      gg.setColor(Color.white);
-    }
-    else if ( (av.getSelectionGroup() != null) &&
-             av.getSelectionGroup().sequences.contains(s))
-    {
-      gg.setColor(Color.lightGray);
-      gg.fillRect(0,
-                  AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
-                  getWidth(), charHeight);
-      gg.setColor(Color.white);
-    }
-    else
-    {
-      gg.setColor(s.getColor());
-      gg.fillRect(0,
-                  AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
-                  getWidth(), charHeight);
-      gg.setColor(Color.black);
+        setLayout(new BorderLayout());
+        this.av = av;
+        PaintRefresher.Register(this, av.alignment);
     }
 
-    String string = s.getName();
-
-    if (av.getShowFullId())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gg DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     * @param i DOCUMENT ME!
+     * @param starty DOCUMENT ME!
+     * @param ypos DOCUMENT ME!
+     */
+    public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+        int ypos)
     {
-      string = s.getDisplayId();
-    }
+        int charHeight = av.charHeight;
 
-    gg.drawString(string, 0,
-                  (AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +
-                   charHeight) - (charHeight / 5));
-  }
-
-  public void fastPaint(int vertical)
-  {
-    if (gg == null)
-    {
-      repaint();
-      return;
-    }
+        if ((searchResults != null) && searchResults.contains(s))
+        {
+            gg.setColor(Color.black);
+            gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+                charHeight);
+            gg.setColor(Color.white);
+        }
+        else if ((av.getSelectionGroup() != null) &&
+                av.getSelectionGroup().sequences.contains(s))
+        {
+            gg.setColor(Color.lightGray);
+            gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+                charHeight);
+            gg.setColor(Color.white);
+        }
+        else
+        {
+            gg.setColor(s.getColor());
+            gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+                charHeight);
+            gg.setColor(Color.black);
+        }
 
-    gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+        String string = s.getName();
 
-    int ss = av.startSeq;
-    int es = av.endSeq;
-    int transY = 0;
+        if (av.getShowFullId())
+        {
+            string = s.getDisplayId();
+        }
 
-    if (vertical > 0) // scroll down
-    {
-      ss = es - vertical;
-
-      if (ss < av.startSeq)
-      { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
-      }
-      else
-      {
-        transY = imgHeight - (vertical * av.charHeight);
-      }
+        gg.drawString(string, 0,
+            (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
     }
-    else if (vertical < 0)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param vertical DOCUMENT ME!
+     */
+    public void fastPaint(int vertical)
     {
-      es = ss - vertical;
+        if (gg == null)
+        {
+            repaint();
 
-      if (es > av.endSeq)
-      {
-        es = av.endSeq;
-      }
-    }
+            return;
+        }
 
-    gg.translate(0, transY);
+        gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
 
-    drawIds(ss, es);
+        int ss = av.startSeq;
+        int es = av.endSeq;
+        int transY = 0;
 
-    gg.translate(0, -transY);
+        if (vertical > 0) // scroll down
+        {
+            ss = es - vertical;
+
+            if (ss < av.startSeq)
+            { // ie scrolling too fast, more than a page at a time
+                ss = av.startSeq;
+            }
+            else
+            {
+                transY = imgHeight - (vertical * av.charHeight);
+            }
+        }
+        else if (vertical < 0)
+        {
+            es = ss - vertical;
 
-    fastPaint = true;
-    repaint();
-  }
+            if (es > av.endSeq)
+            {
+                es = av.endSeq;
+            }
+        }
 
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+        gg.translate(0, transY);
 
-    if (fastPaint)
-    {
-      fastPaint = false;
-      g.drawImage(image, 0, 0, this);
+        drawIds(ss, es);
 
-      return;
-    }
+        gg.translate(0, -transY);
 
-    imgHeight = getHeight();
-    imgHeight -= (imgHeight % av.charHeight);
+        fastPaint = true;
+        repaint();
+    }
 
-    if (imgHeight < 1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      return;
-    }
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
 
-    image = new BufferedImage(getWidth(), imgHeight,
-                              BufferedImage.TYPE_INT_RGB);
-    gg = (Graphics2D) image.getGraphics();
+        if (fastPaint)
+        {
+            fastPaint = false;
+            g.drawImage(image, 0, 0, this);
 
-    //Fill in the background
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, getWidth(), imgHeight);
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
+            return;
+        }
 
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
-    gg.setFont(italic);
+        imgHeight = getHeight();
+        imgHeight -= (imgHeight % av.charHeight);
 
-    drawIds(av.getStartSeq(), av.endSeq);
+        if (imgHeight < 1)
+        {
+            return;
+        }
 
-    g.drawImage(image, 0, 0, this);
-  }
+        image = new BufferedImage(getWidth(), imgHeight,
+                BufferedImage.TYPE_INT_RGB);
+        gg = (Graphics2D) image.getGraphics();
 
-  void drawIds(int starty, int endy)
-  {
+        //Fill in the background
+        gg.setColor(Color.white);
+        gg.fillRect(0, 0, getWidth(), imgHeight);
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
 
-    Color currentColor = Color.white;
-    Color currentTextColor = Color.black;
+        Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                av.getFont().getSize());
+        gg.setFont(italic);
 
-    if (av.getWrapAlignment())
-    {
-      int rowSize = av.getEndRes() - av.getStartRes();
-
-      // Draw the rest of the panels
-      for (int ypos = 2 * av.charHeight, row = av.startRes;
-           (ypos <= getHeight()) && (row < av.alignment.getWidth());
-           ypos += av.chunkHeight, row += rowSize)
-      {
-        for (int i = starty; i < av.alignment.getHeight(); i++)
-        {
-          SequenceI s = av.alignment.getSequenceAt(i);
-          drawIdString(gg, s, i, 0, ypos);
-        }
-      }
+        drawIds(av.getStartSeq(), av.endSeq);
+
+        g.drawImage(image, 0, 0, this);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param starty DOCUMENT ME!
+     * @param endy DOCUMENT ME!
+     */
+    void drawIds(int starty, int endy)
     {
-      //Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        // Selected sequence colours
-        if ( (searchResults != null) &&
-            searchResults.contains(av.alignment.getSequenceAt(i)))
-        {
-          gg.setColor(Color.black);
-          currentColor = Color.black;
-          currentTextColor = Color.white;
-        }
-        else if ( (av.getSelectionGroup() != null) &&
-                 av.getSelectionGroup().sequences.contains(
-                     av.alignment.getSequenceAt(i)))
+        Color currentColor = Color.white;
+        Color currentTextColor = Color.black;
+
+        if (av.getWrapAlignment())
         {
-          currentColor = Color.lightGray;
-          currentTextColor = Color.black;
+            int rowSize = av.getEndRes() - av.getStartRes();
+
+            // Draw the rest of the panels
+            for (int ypos = 2 * av.charHeight, row = av.startRes;
+                    (ypos <= getHeight()) && (row < av.alignment.getWidth());
+                    ypos += av.chunkHeight, row += rowSize)
+            {
+                for (int i = starty; i < av.alignment.getHeight(); i++)
+                {
+                    SequenceI s = av.alignment.getSequenceAt(i);
+                    drawIdString(gg, s, i, 0, ypos);
+                }
+            }
         }
         else
         {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
-          currentTextColor = Color.black;
-        }
-
-        gg.setColor(currentColor);
-
-        gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                    getWidth(), av.charHeight);
-
-        gg.setColor(currentTextColor);
-
-        String string = av.alignment.getSequenceAt(i).getName();
-
-        if (av.getShowFullId())
-        {
-          string = av.alignment.getSequenceAt(i).getDisplayId();
+            //Now draw the id strings
+            for (int i = starty; i < endy; i++)
+            {
+                // Selected sequence colours
+                if ((searchResults != null) &&
+                        searchResults.contains(av.alignment.getSequenceAt(i)))
+                {
+                    gg.setColor(Color.black);
+                    currentColor = Color.black;
+                    currentTextColor = Color.white;
+                }
+                else if ((av.getSelectionGroup() != null) &&
+                        av.getSelectionGroup().sequences.contains(
+                            av.alignment.getSequenceAt(i)))
+                {
+                    currentColor = Color.lightGray;
+                    currentTextColor = Color.black;
+                }
+                else
+                {
+                    currentColor = av.alignment.getSequenceAt(i).getColor();
+                    currentTextColor = Color.black;
+                }
+
+                gg.setColor(currentColor);
+
+                gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
+                    av.charHeight);
+
+                gg.setColor(currentTextColor);
+
+                String string = av.alignment.getSequenceAt(i).getName();
+
+                if (av.getShowFullId())
+                {
+                    string = av.alignment.getSequenceAt(i).getDisplayId();
+                }
+
+                gg.drawString(string, 0,
+                    (((i - starty) * av.charHeight) + av.charHeight) -
+                    (av.charHeight / 5));
+            }
+
+            // add a border
+            gg.setColor(Color.white);
+            gg.fillRect(getWidth() - 4, 0, 4, getHeight());
         }
-
-        gg.drawString(string, 0,
-                      (AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +
-                       av.charHeight) - (av.charHeight / 5));
-      }
-
-      // add a border
-      gg.setColor(Color.white);
-      gg.fillRect(getWidth() - 4, 0, 4, getHeight());
     }
-  }
 
-  public void setHighlighted(java.util.Vector found)
-  {
-    searchResults = found;
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param found DOCUMENT ME!
+     */
+    public void setHighlighted(java.util.Vector found)
+    {
+        searchResults = found;
+        repaint();
+    }
 }
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 3dd7b5b..310276c 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -18,316 +18,380 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.*;
+
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-import jalview.datamodel.*;
 
-public class IdPanel
-    extends JPanel implements MouseListener,
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdPanel extends JPanel implements MouseListener,
     MouseMotionListener
 {
-  protected IdCanvas idCanvas;
-  protected AlignViewport av;
-  protected AlignmentPanel alignPanel;
-  ScrollThread scrollThread = null;
-  int offy;
-  int width;
-  int lastid = -1;
-  boolean mouseDragging = false;
-
-  public IdPanel(AlignViewport av, AlignmentPanel parent)
-  {
-    this.av = av;
-    alignPanel = parent;
-    idCanvas = new IdCanvas(av);
-    setLayout(new BorderLayout());
-    add(idCanvas, BorderLayout.CENTER);
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public void mouseMoved(MouseEvent e)
-  {
-  }
-
-  public void mouseDragged(MouseEvent e)
-  {
-    mouseDragging = true;
-
-    int y = e.getY();
-
-    if (av.getWrapAlignment())
+    protected IdCanvas idCanvas;
+    protected AlignViewport av;
+    protected AlignmentPanel alignPanel;
+    ScrollThread scrollThread = null;
+    int offy;
+    int width;
+    int lastid = -1;
+    boolean mouseDragging = false;
+
+    /**
+     * Creates a new IdPanel object.
+     *
+     * @param av DOCUMENT ME!
+     * @param parent DOCUMENT ME!
+     */
+    public IdPanel(AlignViewport av, AlignmentPanel parent)
     {
-      y -= (2 * av.charHeight);
+        this.av = av;
+        alignPanel = parent;
+        idCanvas = new IdCanvas(av);
+        setLayout(new BorderLayout());
+        add(idCanvas, BorderLayout.CENTER);
+        addMouseListener(this);
+        addMouseMotionListener(this);
     }
 
-    int seq = av.getIndex(y);
-
-    if (seq < 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent e)
     {
-      return;
     }
 
-    if (seq < lastid)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent e)
     {
-      selectSeqs(lastid - 1, seq);
-    }
-    else if (seq > lastid)
-    {
-      selectSeqs(lastid + 1, seq);
-    }
+        mouseDragging = true;
 
-    lastid = seq;
-    alignPanel.repaint();
-  }
+        int y = e.getY();
 
-  public void mouseClicked(MouseEvent e)
-  {
-    if (e.getClickCount() == 2)
-    {
-      int y = e.getY();
-
-      if (av.getWrapAlignment())
-      {
-        y -= (2 * av.charHeight);
-      }
-
-      int seq = av.getIndex(y);
-      String id = av.getAlignment().getSequenceAt(seq).getName();
-
-      try
-      {
-        jalview.util.BrowserLauncher.openURL(
-            "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:" +
-            id + "]+-vn+2");
-      }
-      catch (Exception ex)
-      {
-        // TODO: JBPNote : state dependent error message for real browserLaunch problems rather than unix misconfiguration.
-        System.err.println(ex.getMessage() +
-                           "\nUnixers: Try adding this jalview.browser property line \n" +
-                           "in your jalview.properties file (/usr/local/bin/firefox is an exanmple browser path):\n" +
-                           "jalview.browser=/usr/local/bin/firefox\n");
-
-        //ex.printStackTrace();
-      }
-    }
-  }
+        if (av.getWrapAlignment())
+        {
+            y -= (2 * av.charHeight);
+        }
 
-  public void mouseEntered(MouseEvent e)
-  {
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
-    }
-  }
+        int seq = av.getIndex(y);
 
-  public void mouseExited(MouseEvent e)
-  {
-    if (av.getWrapAlignment())
-    {
-      return;
-    }
+        if (seq < 0)
+        {
+            return;
+        }
 
-    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
-    {
-      scrollThread = new ScrollThread(true);
+        if (seq < lastid)
+        {
+            selectSeqs(lastid - 1, seq);
+        }
+        else if (seq > lastid)
+        {
+            selectSeqs(lastid + 1, seq);
+        }
+
+        lastid = seq;
+        alignPanel.repaint();
     }
 
-    if (mouseDragging && (e.getY() >= getHeight()) &&
-        (av.alignment.getHeight() > av.getEndSeq()))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent e)
     {
-      scrollThread = new ScrollThread(false);
+        if (e.getClickCount() == 2)
+        {
+            int y = e.getY();
+
+            if (av.getWrapAlignment())
+            {
+                y -= (2 * av.charHeight);
+            }
+
+            int seq = av.getIndex(y);
+            String id = av.getAlignment().getSequenceAt(seq).getName();
+
+            try
+            {
+                jalview.util.BrowserLauncher.openURL(
+                    "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:" +
+                    id + "]+-vn+2");
+            }
+            catch (Exception ex)
+            {
+                // TODO: JBPNote : state dependent error message for real browserLaunch problems rather than unix misconfiguration.
+                System.err.println(ex.getMessage() +
+                    "\nUnixers: Try adding this jalview.browser property line \n" +
+                    "in your jalview.properties file (/usr/local/bin/firefox is an exanmple browser path):\n" +
+                    "jalview.browser=/usr/local/bin/firefox\n");
+
+                //ex.printStackTrace();
+            }
+        }
     }
-  }
 
-  public void mousePressed(MouseEvent e)
-  {
-    if (e.getClickCount() == 2)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent e)
     {
-      return;
+        if (scrollThread != null)
+        {
+            scrollThread.running = false;
+        }
     }
 
-    int y = e.getY();
-
-    if (av.getWrapAlignment())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent e)
     {
-      y -= (2 * av.charHeight);
-    }
+        if (av.getWrapAlignment())
+        {
+            return;
+        }
 
-    int seq = av.getIndex(y);
+        if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+        {
+            scrollThread = new ScrollThread(true);
+        }
 
-    if (seq == -1)
-    {
-      return;
+        if (mouseDragging && (e.getY() >= getHeight()) &&
+                (av.alignment.getHeight() > av.getEndSeq()))
+        {
+            scrollThread = new ScrollThread(false);
+        }
     }
 
-    if (javax.swing.SwingUtilities.isRightMouseButton(e))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent e)
     {
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-          (Sequence) av.getAlignment().getSequenceAt(seq));
-      pop.show(this, e.getX(), y);
+        if (e.getClickCount() == 2)
+        {
+            return;
+        }
 
-      return;
-    }
+        int y = e.getY();
 
-    if (!e.isControlDown() && !e.isShiftDown() &&
-        (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))
-    {
-      SequenceGroup selection = new SequenceGroup();
-      SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(
-          seq));
-      selection.setStartRes(0);
-      selection.setEndRes(av.alignment.getWidth() - 1);
+        if (av.getWrapAlignment())
+        {
+            y -= (2 * av.charHeight);
+        }
 
-      for (int i = 0; i < sg.getSize(); i++)
-      {
-        selection.addSequence(sg.getSequenceAt(i), true);
-      }
+        int seq = av.getIndex(y);
 
-      av.setSelectionGroup(selection);
+        if (seq == -1)
+        {
+            return;
+        }
 
-      return;
-    }
+        if (javax.swing.SwingUtilities.isRightMouseButton(e))
+        {
+            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
+                    (Sequence) av.getAlignment().getSequenceAt(seq));
+            pop.show(this, e.getX(), y);
 
-    if ( (av.getSelectionGroup() == null) ||
-        (!e.isControlDown() && (av.getSelectionGroup() != null)))
-    {
-      av.setSelectionGroup(new SequenceGroup());
-    }
+            return;
+        }
 
-    av.getSelectionGroup().setStartRes(0);
-    av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+        if (!e.isControlDown() && !e.isShiftDown() &&
+                (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))
+        {
+            SequenceGroup selection = new SequenceGroup();
+            SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(
+                        seq));
+            selection.setStartRes(0);
+            selection.setEndRes(av.alignment.getWidth() - 1);
 
-    if (e.isShiftDown() && (lastid != -1))
-    {
-      selectSeqs(lastid, seq);
-    }
-    else
-    {
-      selectSeq(seq);
-    }
+            for (int i = 0; i < sg.getSize(); i++)
+            {
+                selection.addSequence(sg.getSequenceAt(i), true);
+            }
 
-    alignPanel.repaint();
-  }
+            av.setSelectionGroup(selection);
 
-  void selectSeq(int seq)
-  {
-    lastid = seq;
+            return;
+        }
 
-    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq, true);
-  }
+        if ((av.getSelectionGroup() == null) ||
+                (!e.isControlDown() && (av.getSelectionGroup() != null)))
+        {
+            av.setSelectionGroup(new SequenceGroup());
+        }
 
-  void selectSeqs(int start, int end)
-  {
-    lastid = start;
+        av.getSelectionGroup().setStartRes(0);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
 
-    if (end < start)
-    {
-      int tmp = start;
-      start = end;
-      end = tmp;
-      lastid = end;
-    }
+        if (e.isShiftDown() && (lastid != -1))
+        {
+            selectSeqs(lastid, seq);
+        }
+        else
+        {
+            selectSeq(seq);
+        }
 
-    for (int i = start; i <= end; i++)
-    {
-      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), true);
+        alignPanel.repaint();
     }
-  }
 
-  public void mouseReleased(MouseEvent e)
-  {
-    if (scrollThread != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    void selectSeq(int seq)
     {
-      scrollThread.running = false;
-    }
-
-    mouseDragging = false;
-    PaintRefresher.Refresh(av.alignment);
-  }
-
-  public void highlightSearchResults(java.util.Vector found)
-  {
-    idCanvas.setHighlighted(found);
+        lastid = seq;
 
-    if (found == null)
-    {
-      return;
+        SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+        av.getSelectionGroup().addOrRemove(pickedSeq, true);
     }
 
-    int index = av.alignment.findIndex( (SequenceI) found.get(0));
-
-    // do we need to scroll the panel?
-    if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    void selectSeqs(int start, int end)
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
-    }
-  }
+        lastid = start;
 
-  // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
-  {
-    boolean running = false;
-    boolean up = true;
+        if (end < start)
+        {
+            int tmp = start;
+            start = end;
+            end = tmp;
+            lastid = end;
+        }
 
-    public ScrollThread(boolean up)
-    {
-      this.up = up;
-      start();
+        for (int i = start; i <= end; i++)
+        {
+            av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+                true);
+        }
     }
 
-    public void stopScrolling()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent e)
     {
-      running = false;
+        if (scrollThread != null)
+        {
+            scrollThread.running = false;
+        }
+
+        mouseDragging = false;
+        PaintRefresher.Refresh(av.alignment);
     }
 
-    public void run()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param found DOCUMENT ME!
+     */
+    public void highlightSearchResults(java.util.Vector found)
     {
-      running = true;
+        idCanvas.setHighlighted(found);
 
-      while (running)
-      {
-        if (alignPanel.scrollUp(up))
+        if (found == null)
         {
-          // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
-
-          if (!up)
-          {
-            seq = av.getEndSeq();
-          }
+            return;
+        }
 
-          if (seq < lastid)
-          {
-            selectSeqs(lastid - 1, seq);
-          }
-          else if (seq > lastid)
-          {
-            selectSeqs(lastid + 1, seq);
-          }
+        int index = av.alignment.findIndex((SequenceI) found.get(0));
 
-          lastid = seq;
-        }
-        else
+        // do we need to scroll the panel?
+        if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
         {
-          running = false;
+            alignPanel.setScrollValues(av.getStartRes(), index);
         }
+    }
 
-        alignPanel.repaint();
+    // this class allows scrolling off the bottom of the visible alignment
+    class ScrollThread extends Thread
+    {
+        boolean running = false;
+        boolean up = true;
+
+        public ScrollThread(boolean up)
+        {
+            this.up = up;
+            start();
+        }
 
-        try
+        public void stopScrolling()
         {
-          Thread.sleep(100);
+            running = false;
         }
-        catch (Exception ex)
+
+        public void run()
         {
+            running = true;
+
+            while (running)
+            {
+                if (alignPanel.scrollUp(up))
+                {
+                    // scroll was ok, so add new sequence to selection
+                    int seq = av.getStartSeq();
+
+                    if (!up)
+                    {
+                        seq = av.getEndSeq();
+                    }
+
+                    if (seq < lastid)
+                    {
+                        selectSeqs(lastid - 1, seq);
+                    }
+                    else if (seq > lastid)
+                    {
+                        selectSeqs(lastid + 1, seq);
+                    }
+
+                    lastid = seq;
+                }
+                else
+                {
+                    running = false;
+                }
+
+                alignPanel.repaint();
+
+                try
+                {
+                    Thread.sleep(100);
+                }
+                catch (Exception ex)
+                {
+                }
+            }
         }
-      }
     }
-  }
 }
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 5599a6d..1fc524a 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -20,91 +20,143 @@ package jalview.gui;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-public class IdwidthAdjuster
-    extends JPanel implements MouseListener,
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdwidthAdjuster extends JPanel implements MouseListener,
     MouseMotionListener
 {
-  boolean active = false;
-  int oldX = 0;
-  Image image;
-  AlignmentPanel ap;
+    boolean active = false;
+    int oldX = 0;
+    Image image;
+    AlignmentPanel ap;
+
+    /**
+     * Creates a new IdwidthAdjuster object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public IdwidthAdjuster(AlignmentPanel ap)
+    {
+        this.ap = ap;
 
-  public IdwidthAdjuster(AlignmentPanel ap)
-  {
-    this.ap = ap;
+        java.net.URL url = getClass().getResource("/images/idwidth.gif");
 
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
+        if (url != null)
+        {
+            image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+        }
 
-    if (url != null)
+        addMouseListener(this);
+        addMouseMotionListener(this);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
     {
-      image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+        oldX = evt.getX();
     }
 
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    oldX = evt.getX();
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {
-    active = true;
-    repaint();
-  }
-
-  public void mouseExited(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    active = true;
-
-    Dimension d = ap.idPanel.idCanvas.getPreferredSize();
-    int dif = evt.getX() - oldX;
-
-    if ( ( (d.width + dif) > 20) || (dif > 0))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
     {
-      ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,
-          d.height));
-      ap.repaint();
+        active = false;
+        repaint();
     }
 
-    oldX = evt.getX();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
+    {
+        active = true;
+        repaint();
+    }
 
-  public void mouseMoved(MouseEvent evt)
-  {
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
+    {
+        active = false;
+        repaint();
+    }
 
-  public void mouseClicked(MouseEvent evt)
-  {
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
+    {
+        active = true;
+
+        Dimension d = ap.idPanel.idCanvas.getPreferredSize();
+        int dif = evt.getX() - oldX;
+
+        if (((d.width + dif) > 20) || (dif > 0))
+        {
+            ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,
+                    d.height));
+            ap.repaint();
+        }
+
+        oldX = evt.getX();
+    }
 
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
+    {
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
+    {
+    }
 
-    if (active)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      if (image != null)
-      {
-        g.drawImage(image, getWidth() - 20, 2, this);
-      }
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
+
+        if (active)
+        {
+            if (image != null)
+            {
+                g.drawImage(image, getWidth() - 20, 2, this);
+            }
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index bdd255c..ee96baa 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -18,761 +18,778 @@
  */
 package jalview.gui;
 
+import jalview.binding.*;
+
+import jalview.io.*;
+
+import jalview.schemes.*;
+
 import java.io.*;
+
 import java.net.*;
+
 import java.util.*;
 import java.util.jar.*;
 
 import javax.swing.*;
 
-import jalview.binding.*;
-import jalview.io.*;
-import jalview.schemes.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class Jalview2XML
 {
-  // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
-  public static void SaveState(File statefile)
-  {
-    long creation = System.currentTimeMillis();
-    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
-    if (frames == null)
-    {
-      return;
-    }
-
-    try
+    // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
+    public static void SaveState(File statefile)
     {
-      FileOutputStream fos = new FileOutputStream(statefile);
-      JarOutputStream jout = new JarOutputStream(fos);
+        long creation = System.currentTimeMillis();
+        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
-      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-      ////////////////////////////////////////////////////
-      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-          "UTF-8"));
-
-      Vector shortNames = new Vector();
-      int treeCount=1;
-
-      //REVERSE ORDER
-      for (int i = frames.length - 1; i > -1; i--)
-      {
-        if (frames[i] instanceof AlignFrame)
+        if (frames == null)
         {
-          AlignFrame af = (AlignFrame) frames[i];
+            return;
+        }
 
-          String shortName = af.getTitle();
+        try
+        {
+            FileOutputStream fos = new FileOutputStream(statefile);
+            JarOutputStream jout = new JarOutputStream(fos);
 
-          if (shortName.indexOf(File.separatorChar) > -1)
-          {
-            shortName = shortName.substring(shortName.lastIndexOf(
-                File.separatorChar) + 1);
-          }
+            //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+            ////////////////////////////////////////////////////
+            PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+                        "UTF-8"));
 
-          int count = 1;
+            Vector shortNames = new Vector();
 
-          while (shortNames.contains(shortName))
-          {
-            if (shortName.endsWith("_" + (count - 1)))
+            //REVERSE ORDER
+            for (int i = frames.length - 1; i > -1; i--)
             {
-              shortName = shortName.substring(0,
-                                              shortName.lastIndexOf("_"));
-            }
+                if (frames[i] instanceof AlignFrame)
+                {
+                    AlignFrame af = (AlignFrame) frames[i];
 
-            shortName = shortName.concat("_" + count);
-            count++;
-          }
+                    String shortName = af.getTitle();
 
-          shortNames.addElement(shortName);
+                    if (shortName.indexOf(File.separatorChar) > -1)
+                    {
+                        shortName = shortName.substring(shortName.lastIndexOf(
+                                    File.separatorChar) + 1);
+                    }
 
-          if (!shortName.endsWith(".xml"))
-          {
-            shortName = shortName + ".xml";
-          }
+                    int count = 1;
 
-          SaveState(af, creation, shortName, jout, out);
-        }
-      }
+                    while (shortNames.contains(shortName))
+                    {
+                        if (shortName.endsWith("_" + (count - 1)))
+                        {
+                            shortName = shortName.substring(0,
+                                    shortName.lastIndexOf("_"));
+                        }
 
-      out.close();
-      jout.close();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
+                        shortName = shortName.concat("_" + count);
+                        count++;
+                    }
 
+                    shortNames.addElement(shortName);
 
-  // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-  public static void SaveAlignment(AlignFrame af, String jarFile, String fileName)
-  {
-    try
-    {
-      FileOutputStream fos = new FileOutputStream(jarFile);
-      JarOutputStream jout = new JarOutputStream(fos);
+                    if (!shortName.endsWith(".xml"))
+                    {
+                        shortName = shortName + ".xml";
+                    }
 
-      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-      ////////////////////////////////////////////////////
-      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-          "UTF-8"));
+                    SaveState(af, creation, shortName, jout, out);
+                }
+            }
 
-      SaveState(af, System.currentTimeMillis(), fileName, jout, out);
-      out.close();
-      jout.close();
-    }
-    catch (Exception ex)
-    {
+            out.close();
+            jout.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
     }
-  }
 
-  public static void SaveState(AlignFrame af, long timeStamp,
-                               String fileName, JarOutputStream jout,
-                               PrintWriter out)
-  {
-    Vector seqids = new Vector();
-    Vector userColours = new Vector();
+    // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+    public static void SaveAlignment(AlignFrame af, String jarFile,
+        String fileName)
+    {
+        try
+        {
+            FileOutputStream fos = new FileOutputStream(jarFile);
+            JarOutputStream jout = new JarOutputStream(fos);
 
-    AlignViewport av = af.viewport;
+            //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+            ////////////////////////////////////////////////////
+            PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+                        "UTF-8"));
 
-    JalviewModel object = new JalviewModel();
-    object.setVamsasModel(new VamsasModel());
+            SaveState(af, System.currentTimeMillis(), fileName, jout, out);
+            out.close();
+            jout.close();
+        }
+        catch (Exception ex)
+        {
+        }
+    }
 
-    object.setCreationDate(new java.util.Date(timeStamp));
-    object.setVersion(jalview.bin.Cache.VERSION);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param af DOCUMENT ME!
+     * @param timeStamp DOCUMENT ME!
+     * @param fileName DOCUMENT ME!
+     * @param jout DOCUMENT ME!
+     * @param out DOCUMENT ME!
+     */
+    public static void SaveState(AlignFrame af, long timeStamp,
+        String fileName, JarOutputStream jout, PrintWriter out)
+    {
+        Vector seqids = new Vector();
+        Vector userColours = new Vector();
 
-    jalview.datamodel.AlignmentI jal = af.viewport.alignment;
+        AlignViewport av = af.viewport;
 
-    SequenceSet vamsasSet = new SequenceSet();
-    Sequence vamsasSeq;
-    JalviewModelSequence jms = new JalviewModelSequence();
+        JalviewModel object = new JalviewModel();
+        object.setVamsasModel(new VamsasModel());
 
-    vamsasSet.setGapChar(jal.getGapCharacter() + "");
+        object.setCreationDate(new java.util.Date(timeStamp));
+        object.setVersion(jalview.bin.Cache.VERSION);
 
-    JSeq jseq;
+        jalview.datamodel.AlignmentI jal = af.viewport.alignment;
 
-    //SAVE SEQUENCES
-    int id = 0;
+        SequenceSet vamsasSet = new SequenceSet();
+        Sequence vamsasSeq;
+        JalviewModelSequence jms = new JalviewModelSequence();
 
-    for (int i = 0; i < jal.getHeight(); i++)
-    {
-      seqids.add(jal.getSequenceAt(i));
+        vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
-      vamsasSeq = new Sequence();
-      vamsasSeq.setId(id + "");
-      vamsasSeq.setName(jal.getSequenceAt(i).getName());
-      vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
+        JSeq jseq;
 
-      jseq = new JSeq();
-      jseq.setStart(jal.getSequenceAt(i).getStart());
-      jseq.setEnd(jal.getSequenceAt(i).getEnd());
+        //SAVE SEQUENCES
+        int id = 0;
 
-      jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
+        for (int i = 0; i < jal.getHeight(); i++)
+        {
+            seqids.add(jal.getSequenceAt(i));
 
-      jseq.setId(id);
+            vamsasSeq = new Sequence();
+            vamsasSeq.setId(id + "");
+            vamsasSeq.setName(jal.getSequenceAt(i).getName());
+            vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
 
-      jms.addJSeq(jseq);
-      vamsasSet.addSequence(vamsasSeq);
-      id++;
-    }
+            jseq = new JSeq();
+            jseq.setStart(jal.getSequenceAt(i).getStart());
+            jseq.setEnd(jal.getSequenceAt(i).getEnd());
 
-    //SAVE TREES
-    ///////////////////////////////////
-    if (af.viewport.currentTree != null)
-    {
-      // FIND ANY ASSOCIATED TREES
-      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-      for(int t=0; t<frames.length; t++)
-      {
-        if (frames[t] instanceof TreePanel)
-        {
-          TreePanel tp = (TreePanel) frames[t];
-          if(tp.treeCanvas.av.alignment==jal)
-          {
-            Tree tree = new Tree();
-            tree.setTitle(tp.getTitle());
-            tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
-            tree.setNewick(tp.getTree().toString());
-            tree.setThreshold(tp.treeCanvas.threshold);
-
-            tree.setFitToWindow(tp.fitToWindow.getState());
-            tree.setFontSize(tp.treeCanvas.fontSize);
-            tree.setMarkUnlinked( tp.placeholdersMenu.getState() );
-            tree.setShowBootstrap( tp.bootstrapMenu.getState() );
-            tree.setShowDistances( tp.distanceMenu.getState() );
-
-            tree.setHeight(tp.getHeight());
-            tree.setWidth(tp.getWidth());
-            tree.setXpos(tp.getX());
-            tree.setYpos(tp.getY());
-
-            jms.addTree(tree);
-          }
-        }
-      }
-    }
+            jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
 
-    //SAVE ANNOTATIONS
-    if (jal.getAlignmentAnnotation() != null)
-    {
-      jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+            jseq.setId(id);
 
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (aa[i].label.equals("Quality") ||
-            aa[i].label.equals("Conservation") ||
-            aa[i].label.equals("Consensus"))
-        {
-          continue;
+            jms.addJSeq(jseq);
+            vamsasSet.addSequence(vamsasSeq);
+            id++;
         }
 
-        Annotation an = new Annotation();
-        an.setDescription(aa[i].description);
-        an.setGraph(aa[i].isGraph);
-        an.setLabel(aa[i].label);
+        //SAVE TREES
+        ///////////////////////////////////
+        if (af.viewport.currentTree != null)
+        {
+            // FIND ANY ASSOCIATED TREES
+            JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
-        AnnotationElement ae;
+            for (int t = 0; t < frames.length; t++)
+            {
+                if (frames[t] instanceof TreePanel)
+                {
+                    TreePanel tp = (TreePanel) frames[t];
+
+                    if (tp.treeCanvas.av.alignment == jal)
+                    {
+                        Tree tree = new Tree();
+                        tree.setTitle(tp.getTitle());
+                        tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
+                        tree.setNewick(tp.getTree().toString());
+                        tree.setThreshold(tp.treeCanvas.threshold);
+
+                        tree.setFitToWindow(tp.fitToWindow.getState());
+                        tree.setFontSize(tp.treeCanvas.fontSize);
+                        tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+                        tree.setShowBootstrap(tp.bootstrapMenu.getState());
+                        tree.setShowDistances(tp.distanceMenu.getState());
+
+                        tree.setHeight(tp.getHeight());
+                        tree.setWidth(tp.getWidth());
+                        tree.setXpos(tp.getX());
+                        tree.setYpos(tp.getY());
+
+                        jms.addTree(tree);
+                    }
+                }
+            }
+        }
 
-        for (int a = 0; a < aa[i].annotations.length; a++)
+        //SAVE ANNOTATIONS
+        if (jal.getAlignmentAnnotation() != null)
         {
-          if ( (aa[i] == null) || (aa[i].annotations[a] == null))
-          {
-            continue;
-          }
-
-          ae = new AnnotationElement();
-          ae.setDescription(aa[i].annotations[a].description);
-          ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
-          ae.setValue(aa[i].annotations[a].value);
-          ae.setPosition(a);
-          ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
-                                   "");
-          an.addAnnotationElement(ae);
-        }
+            jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 
-        vamsasSet.addAnnotation(an);
-      }
-    }
+            for (int i = 0; i < aa.length; i++)
+            {
+                if (aa[i].label.equals("Quality") ||
+                        aa[i].label.equals("Conservation") ||
+                        aa[i].label.equals("Consensus"))
+                {
+                    continue;
+                }
+
+                Annotation an = new Annotation();
+                an.setDescription(aa[i].description);
+                an.setGraph(aa[i].isGraph);
+                an.setLabel(aa[i].label);
+
+                AnnotationElement ae;
+
+                for (int a = 0; a < aa[i].annotations.length; a++)
+                {
+                    if ((aa[i] == null) || (aa[i].annotations[a] == null))
+                    {
+                        continue;
+                    }
+
+                    ae = new AnnotationElement();
+                    ae.setDescription(aa[i].annotations[a].description);
+                    ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+                    ae.setValue(aa[i].annotations[a].value);
+                    ae.setPosition(a);
+                    ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
+                        "");
+                    an.addAnnotationElement(ae);
+                }
+
+                vamsasSet.addAnnotation(an);
+            }
+        }
 
-    //SAVE GROUPS
-    if (jal.getGroups() != null)
-    {
-      JGroup[] groups = new JGroup[jal.getGroups().size()];
+        //SAVE GROUPS
+        if (jal.getGroups() != null)
+        {
+            JGroup[] groups = new JGroup[jal.getGroups().size()];
 
-      for (int i = 0; i < groups.length; i++)
-      {
-        groups[i] = new JGroup();
+            for (int i = 0; i < groups.length; i++)
+            {
+                groups[i] = new JGroup();
+
+                jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
+                                                                                          .elementAt(i);
+                groups[i].setStart(sg.getStartRes());
+                groups[i].setEnd(sg.getEndRes());
+                groups[i].setName(sg.getName());
+
+                if (sg.cs instanceof ConservationColourScheme)
+                {
+                    groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc);
+                }
+
+                if (sg.cs instanceof ResidueColourScheme)
+                {
+                    groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());
+                }
+                else if (sg.cs instanceof ScoreColourScheme)
+                {
+                    groups[i].setPidThreshold(((ScoreColourScheme) sg.cs).getThreshold());
+                }
+
+                if (sg.cs instanceof jalview.schemes.UserColourScheme)
+                {
+                    groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+                            jms));
+                }
+                else
+                {
+                    groups[i].setColour(ColourSchemeProperty.getColourName(
+                            sg.cs));
+                }
+
+                groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
+                groups[i].setDisplayBoxes(sg.getDisplayBoxes());
+                groups[i].setDisplayText(sg.getDisplayText());
+                groups[i].setColourText(sg.getColourText());
+
+                for (int s = 0; s < sg.getSize(); s++)
+                {
+                    jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
+                    int index = seqids.indexOf(seq);
+                    groups[i].addSeq(index);
+                }
+            }
 
-        jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
-            jal.getGroups()
-            .elementAt(i);
-        groups[i].setStart(sg.getStartRes());
-        groups[i].setEnd(sg.getEndRes());
-        groups[i].setName(sg.getName());
+            jms.setJGroup(groups);
+        }
 
-        if (sg.cs instanceof ConservationColourScheme)
+        ///////////SAVE VIEWPORT
+        Viewport view = new Viewport();
+        view.setTitle(af.getTitle());
+        view.setXpos(af.getX());
+        view.setYpos(af.getY());
+        view.setWidth(af.getWidth());
+        view.setHeight(af.getHeight());
+        view.setStartRes(av.startRes);
+        view.setStartSeq(av.startSeq);
+
+        if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
         {
-          groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);
+            view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
+                    userColours, jms));
         }
-
-        if (sg.cs instanceof ResidueColourScheme)
+        else
         {
-          groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).
-                                    getThreshold());
+            view.setBgColour(ColourSchemeProperty.getColourName(
+                    av.getGlobalColourScheme()));
         }
-        else if (sg.cs instanceof ScoreColourScheme)
+
+        ColourSchemeI cs = av.getGlobalColourScheme();
+
+        if (cs instanceof ConservationColourScheme)
         {
-          groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
+            view.setConsThreshold(((ConservationColourScheme) cs).inc);
         }
 
-        if (sg.cs instanceof jalview.schemes.UserColourScheme)
+        if (cs instanceof ResidueColourScheme)
         {
-          groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
-                                                  jms));
+            view.setPidThreshold(((ResidueColourScheme) cs).getThreshold());
         }
-        else
+        else if (cs instanceof ScoreColourScheme)
         {
-          groups[i].setColour(ColourSchemeProperty.getColourName(
-              sg.cs));
+            view.setPidThreshold(((ScoreColourScheme) cs).getThreshold());
         }
 
-        groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
-        groups[i].setDisplayBoxes(sg.getDisplayBoxes());
-        groups[i].setDisplayText(sg.getDisplayText());
-        groups[i].setColourText(sg.getColourText());
+        view.setConservationSelected(av.getConservationSelected());
+        view.setPidSelected(av.getAbovePIDThreshold());
+        view.setFontName(av.font.getFontName());
+        view.setFontSize(av.font.getSize());
+        view.setFontStyle(av.font.getStyle());
+        view.setRenderGaps(av.renderGaps);
+        view.setShowAnnotation(av.getShowAnnotation());
+        view.setShowBoxes(av.getShowBoxes());
+        view.setShowColourText(av.getColourText());
+        view.setShowConservation(av.showConservation);
+        view.setShowFullId(av.getShowFullId());
+        view.setShowIdentity(av.showIdentity);
+        view.setShowQuality(av.showQuality);
+        view.setShowSequenceFeatures(av.showSequenceFeatures);
+        view.setShowText(av.getShowText());
+        view.setWrapAlignment(av.getWrapAlignment());
+
+        jms.addViewport(view);
+
+        object.setJalviewModelSequence(jms);
+        object.getVamsasModel().addSequenceSet(vamsasSet);
+
+        try
+        {
+            if (!fileName.endsWith(".xml"))
+            {
+                fileName = fileName + ".xml";
+            }
 
-        for (int s = 0; s < sg.getSize(); s++)
+            JarEntry entry = new JarEntry(fileName);
+            jout.putNextEntry(entry);
+
+            object.marshal(out);
+        }
+        catch (Exception ex)
         {
-          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.
-              getSequenceAt(s);
-          int index = seqids.indexOf(seq);
-          groups[i].addSeq(index);
+            ex.printStackTrace();
         }
-      }
-
-      jms.setJGroup(groups);
     }
 
-    ///////////SAVE VIEWPORT
-    Viewport view = new Viewport();
-    view.setTitle(af.getTitle());
-    view.setXpos(af.getX());
-    view.setYpos(af.getY());
-    view.setWidth(af.getWidth());
-    view.setHeight(af.getHeight());
-    view.setStartRes(av.startRes);
-    view.setStartSeq(av.startSeq);
-
-    if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
-    {
-      view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
-                                           userColours, jms));
-    }
-    else
+    static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+        Vector userColours, JalviewModelSequence jms)
     {
-      view.setBgColour(ColourSchemeProperty.getColourName(
-          av.getGlobalColourScheme()));
-    }
-
-    ColourSchemeI cs = av.getGlobalColourScheme();
+        String id = null;
+        jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 
-    if (cs instanceof ConservationColourScheme)
-    {
-      view.setConsThreshold( ( (ConservationColourScheme) cs).inc);
-    }
+        if (!userColours.contains(ucs))
+        {
+            userColours.add(ucs);
 
-    if (cs instanceof ResidueColourScheme)
-    {
-      view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
-    }
+            java.awt.Color[] colours = ucs.getColours();
+            jalview.binding.UserColours uc = new jalview.binding.UserColours();
+            jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
 
-    view.setConservationSelected(av.getConservationSelected());
-    view.setPidSelected(av.getAbovePIDThreshold());
-    view.setFontName(av.font.getFontName());
-    view.setFontSize(av.font.getSize());
-    view.setFontStyle(av.font.getStyle());
-    view.setRenderGaps(av.renderGaps);
-    view.setShowAnnotation(av.getShowAnnotation());
-    view.setShowBoxes(av.getShowBoxes());
-    view.setShowColourText(av.getColourText());
-    view.setShowConservation(av.showConservation);
-    view.setShowFullId(av.getShowFullId());
-    view.setShowIdentity(av.showIdentity);
-    view.setShowQuality(av.showQuality);
-    view.setShowSequenceFeatures(av.showSequenceFeatures);
-    view.setShowText(av.getShowText());
-    view.setWrapAlignment(av.getWrapAlignment());
-
-    jms.addViewport(view);
-
-    object.setJalviewModelSequence(jms);
-    object.getVamsasModel().addSequenceSet(vamsasSet);
-
-    try
-    {
-      if (!fileName.endsWith(".xml"))
-      {
-        fileName = fileName + ".xml";
-      }
+            for (int i = 0; i < colours.length; i++)
+            {
+                jalview.binding.Colour col = new jalview.binding.Colour();
+                col.setRGB(jalview.util.Format.getHexString(colours[i]));
+                jbucs.addColour(col);
+            }
 
-      JarEntry entry = new JarEntry(fileName);
-      jout.putNextEntry(entry);
+            id = "ucs" + userColours.indexOf(ucs);
+            uc.setId(id);
+            uc.setUserColourScheme(jbucs);
+            jms.addUserColours(uc);
+        }
 
-      object.marshal(out);
+        return id;
     }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
-                                    Vector userColours,
-                                    JalviewModelSequence jms)
-  {
-    String id = null;
-    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
-        cs;
 
-    if (!userColours.contains(ucs))
+    static jalview.schemes.UserColourScheme GetUserColourScheme(
+        JalviewModelSequence jms, String id)
     {
-      userColours.add(ucs);
-
-      java.awt.Color[] colours = ucs.getColours();
-      jalview.binding.UserColours uc = new jalview.binding.UserColours();
-      jalview.binding.UserColourScheme jbucs = new jalview.binding.
-          UserColourScheme();
-
-      for (int i = 0; i < colours.length; i++)
-      {
-        jalview.binding.Colour col = new jalview.binding.Colour();
-        col.setRGB(jalview.util.Format.getHexString(colours[i]));
-        jbucs.addColour(col);
-      }
-
-      id = "ucs" + userColours.indexOf(ucs);
-      uc.setId(id);
-      uc.setUserColourScheme(jbucs);
-      jms.addUserColours(uc);
-    }
-
-    return id;
-  }
+        UserColours[] uc = jms.getUserColours();
+        UserColours colours = null;
 
-  static jalview.schemes.UserColourScheme GetUserColourScheme(
-      JalviewModelSequence jms, String id)
-  {
-    UserColours[] uc = jms.getUserColours();
-    UserColours colours = null;
+        for (int i = 0; i < uc.length; i++)
+        {
+            if (uc[i].getId().equals(id))
+            {
+                colours = uc[i];
 
-    for (int i = 0; i < uc.length; i++)
-    {
-      if (uc[i].getId().equals(id))
-      {
-        colours = uc[i];
+                break;
+            }
+        }
 
-        break;
-      }
-    }
+        int csize = colours.getUserColourScheme().getColourCount();
+        java.awt.Color[] newColours = new java.awt.Color[csize];
 
-    int csize = colours.getUserColourScheme().getColourCount();
-    java.awt.Color[] newColours = new java.awt.Color[csize];
+        for (int i = 0; i < csize; i++)
+        {
+            newColours[i] = new java.awt.Color(Integer.parseInt(
+                        colours.getUserColourScheme().getColour(i).getRGB(), 16));
+        }
 
-    for (int i = 0; i < csize; i++)
-    {
-      newColours[i] = new java.awt.Color(Integer.parseInt(
-          colours.getUserColourScheme().getColour(i).getRGB(), 16));
+        return new jalview.schemes.UserColourScheme(newColours);
     }
 
-    return new jalview.schemes.UserColourScheme(newColours);
-  }
-
-  public static void LoadJalviewAlign(String file)
-  {
-    JalviewModel object = new JalviewModel();
-
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     */
+    public static AlignFrame LoadJalviewAlign(String file)
     {
-      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
-      URL url = null;
+        JalviewModel object = new JalviewModel();
+        jalview.gui.AlignFrame af = null;
 
-      if (file.startsWith("http://"))
-      {
-        url = new URL(file);
-      }
+        try
+        {
+            //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+            URL url = null;
 
-      JarInputStream jin = null;
-      JarEntry jarentry = null;
-      int entryCount = 1;
+            if (file.startsWith("http://"))
+            {
+                url = new URL(file);
+            }
 
-      do
-      {
-        if (url != null)
-        {
-          jin = new JarInputStream(url.openStream());
+            JarInputStream jin = null;
+            JarEntry jarentry = null;
+            int entryCount = 1;
+
+            do
+            {
+                if (url != null)
+                {
+                    jin = new JarInputStream(url.openStream());
+                }
+                else
+                {
+                    jin = new JarInputStream(new FileInputStream(file));
+                }
+
+                for (int i = 0; i < entryCount; i++)
+                {
+                    jarentry = jin.getNextJarEntry();
+                }
+
+                if (jarentry != null)
+                {
+                    InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+                    object = (JalviewModel) object.unmarshal(in);
+                    af = LoadFromObject(object);
+                    entryCount++;
+                }
+            }
+            while (jarentry != null);
         }
-        else
+        catch (Exception ex)
         {
-          jin = new JarInputStream(new FileInputStream(file));
-        }
+            System.err.println("Exception whilst loading jalview XML file : " +
+                ex + "\n");
+             JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                      "Couldn't locate " + file,
+                                      "URL not found",
+                                      JOptionPane.WARNING_MESSAGE);
 
-        for (int i = 0; i < entryCount; i++)
-        {
-          jarentry = jin.getNextJarEntry();
         }
 
-        if (jarentry != null)
-        {
-          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-          object = (JalviewModel) object.unmarshal(in);
-          LoadFromObject(object);
-          entryCount++;
-        }
-      }
-      while (jarentry != null);
+        return af;
     }
-    catch (Exception ex)
+
+    static AlignFrame LoadFromObject(JalviewModel object)
     {
-      System.err.println("Exception whilst loading jalview XML file : " +
-                         ex + "\n");
-      ex.printStackTrace();
+        Vector seqids = new Vector();
+        SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+        Sequence[] vamsasSeq = vamsasSet.getSequence();
 
-      return;
-    }
-  }
+        JalviewModelSequence jms = object.getJalviewModelSequence();
 
-  static void LoadFromObject(JalviewModel object)
-  {
-    Vector seqids = new Vector();
-    SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
-    Sequence[] vamsasSeq = vamsasSet.getSequence();
+        //////////////////////////////////
+        //LOAD SEQUENCES
+        jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
+        JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 
-    JalviewModelSequence jms = object.getJalviewModelSequence();
+        for (int i = 0; i < vamsasSeq.length; i++)
+        {
+            jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+                    vamsasSeq[i].getSequence());
 
-    //////////////////////////////////
-    //LOAD SEQUENCES
-    jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[
-        vamsasSeq.length];
-    JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+            jseqs[i].setStart(JSEQ[i].getStart());
+            jseqs[i].setEnd(JSEQ[i].getEnd());
+            jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
+            seqids.add(jseqs[i]);
+        }
 
-    for (int i = 0; i < vamsasSeq.length; i++)
-    {
-      jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
-                                                vamsasSeq[i].getSequence());
+        /////////////////////////////////
+        jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 
-      jseqs[i].setStart(JSEQ[i].getStart());
-      jseqs[i].setEnd(JSEQ[i].getEnd());
-      jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
-      seqids.add(jseqs[i]);
-    }
+        /////////////////////////////////
+        //////////////////////////////////
+        //LOAD ANNOTATIONS
+        if (vamsasSet.getAnnotation() != null)
+        {
+            Annotation[] an = vamsasSet.getAnnotation();
 
-    /////////////////////////////////
-    jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+            for (int i = 0; i < an.length; i++)
+            {
+                AnnotationElement[] ae = an[i].getAnnotationElement();
+                jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
+
+                for (int aa = 0; aa < ae.length; aa++)
+                {
+                    anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
+                            ae[aa].getDescription(),
+                            ae[aa].getSecondaryStructure().charAt(0),
+                            ae[aa].getValue());
+                }
+
+                jalview.datamodel.AlignmentAnnotation jaa = null;
+
+                if (an[i].getGraph())
+                {
+                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                            an[i].getDescription(), anot, 0, 0, 1);
+                }
+                else
+                {
+                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                            an[i].getDescription(), anot);
+                }
+
+                al.addAnnotation(jaa);
+            }
+        }
 
-    /////////////////////////////////
-    //////////////////////////////////
-    //LOAD ANNOTATIONS
-    if (vamsasSet.getAnnotation() != null)
-    {
-      Annotation[] an = vamsasSet.getAnnotation();
+        /////////////////////////////////
+        // LOAD VIEWPORT
+        Viewport[] views = jms.getViewport();
+        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 
-      for (int i = 0; i < an.length; i++)
-      {
-        AnnotationElement[] ae = an[i].getAnnotationElement();
-        jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
-            al.getWidth()];
+        AlignFrame af = new AlignFrame(al);
 
-        for (int aa = 0; aa < ae.length; aa++)
+        //  af.changeColour() );
+        /////////////////////////
+        //LOAD GROUPS
+        if (jms.getJGroupCount() > 0)
         {
-          anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
-              getDisplayCharacter(),
-              ae[aa].getDescription(),
-              ae[aa].getSecondaryStructure().charAt(0),
-              ae[aa].getValue());
-        }
+            JGroup[] groups = jms.getJGroup();
 
-        jalview.datamodel.AlignmentAnnotation jaa = null;
+            for (int i = 0; i < groups.length; i++)
+            {
+                ColourSchemeI cs = null;
+
+                if (groups[i].getColour() != null)
+                {
+                    if (groups[i].getColour().startsWith("ucs"))
+                    {
+                        cs = GetUserColourScheme(jms, groups[i].getColour());
+                    }
+                    else
+                    {
+                        cs = ColourSchemeProperty.getColour(al,
+                                groups[i].getColour());
+                    }
+
+                    if (cs instanceof ResidueColourScheme)
+                    {
+                        ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+                    }
+                    else if (cs instanceof ScoreColourScheme)
+                    {
+                        ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+                    }
+                }
+
+                Vector seqs = new Vector();
+                int[] ids = groups[i].getSeq();
+
+                for (int s = 0; s < ids.length; s++)
+                {
+                    seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
+                            ids[s]));
+                }
+
+                jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
+                        groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+                        groups[i].getDisplayText(), groups[i].getColourText(),
+                        groups[i].getStart(), groups[i].getEnd());
+
+                sg.setOutlineColour(new java.awt.Color(
+                        groups[i].getOutlineColour()));
+
+                if (groups[i].getConsThreshold() != 0)
+                {
+                    jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
+                            ResidueProperties.propHash, 3, sg.sequences, 0,
+                            sg.getWidth() - 1);
+                    c.calculate();
+                    c.verdict(false, 25);
+                    cs = new ConservationColourScheme(c, cs);
+                    sg.cs = cs;
+                }
+
+                al.addGroup(sg);
+            }
+        }
 
-        if (an[i].getGraph())
+        Desktop.addInternalFrame(af, view.getTitle(),
+            AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+        af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+            view.getHeight());
+        af.viewport.setStartRes(view.getStartRes());
+        af.viewport.setStartSeq(view.getStartSeq());
+        af.viewport.showConservation = view.getShowConservation();
+        af.viewport.showQuality = view.getShowQuality();
+        af.viewport.showIdentity = view.getShowIdentity();
+        af.viewport.setAbovePIDThreshold(view.getPidSelected());
+        af.abovePIDThreshold.setSelected(view.getPidSelected());
+        af.viewport.setColourText(view.getShowColourText());
+        af.colourTextMenuItem.setSelected(view.getShowColourText());
+        af.viewport.setConservationSelected(view.getConservationSelected());
+        af.conservationMenuItem.setSelected(view.getConservationSelected());
+
+        af.viewport.setShowFullId(view.getShowFullId());
+        af.fullSeqId.setSelected(view.getShowFullId());
+
+        af.viewport.setFont(new java.awt.Font(view.getFontName(),
+                view.getFontStyle(), view.getFontSize()));
+        af.alignPanel.fontChanged();
+
+        af.viewport.setRenderGaps(view.getRenderGaps());
+        af.renderGapsMenuItem.setSelected(view.getRenderGaps());
+
+        af.viewport.setWrapAlignment(view.getWrapAlignment());
+        af.wrapMenuItem.setSelected(view.getWrapAlignment());
+
+        if (view.getWrapAlignment())
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-              an[i].getDescription(), anot, 0, 0, 1);
+            af.alignPanel.setWrapAlignment(view.getWrapAlignment());
         }
         else
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-              an[i].getDescription(), anot);
+            af.annotationPanelMenuItem.setState(view.getShowAnnotation());
+            af.viewport.setShowAnnotation(view.getShowAnnotation());
+            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
         }
 
-        al.addAnnotation(jaa);
-      }
-    }
-
-    /////////////////////////////////
-    // LOAD VIEWPORT
-    Viewport[] views = jms.getViewport();
-    Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
-
-    AlignFrame af = new AlignFrame(al);
+        af.viewport.setShowBoxes(view.getShowBoxes());
+        af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
+        af.viewport.setShowText(view.getShowText());
+        af.viewTextMenuItem.setSelected(view.getShowText());
 
-    //  af.changeColour() );
-    /////////////////////////
-    //LOAD GROUPS
-    if (jms.getJGroupCount() > 0)
-    {
-      JGroup[] groups = jms.getJGroup();
-
-      for (int i = 0; i < groups.length; i++)
-      {
         ColourSchemeI cs = null;
 
-        if (groups[i].getColour() != null)
+        if (view.getBgColour() != null)
         {
-          if (groups[i].getColour().startsWith("ucs"))
-          {
-            cs = GetUserColourScheme(jms, groups[i].getColour());
-          }
-          else
-          {
-            cs = ColourSchemeProperty.getColour(al,
-                                                groups[i].getColour());
-          }
-
-          if (cs instanceof ResidueColourScheme)
-          {
-            ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
-          }
-          else if (cs instanceof ScoreColourScheme)
-          {
-            ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
-          }
-        }
+            if (view.getBgColour().startsWith("ucs"))
+            {
+                cs = GetUserColourScheme(jms, view.getBgColour());
+            }
+            else
+            {
+                cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+            }
 
-        Vector seqs = new Vector();
-        int[] ids = groups[i].getSeq();
+            if (cs instanceof ConservationColourScheme)
+            {
+                ((ConservationColourScheme) cs).inc = view.getConsThreshold();
+            }
 
-        for (int s = 0; s < ids.length; s++)
-        {
-          seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(
-              ids[s]));
+            if (cs instanceof ResidueColourScheme)
+            {
+                ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
+            }
+            else if (cs instanceof ScoreColourScheme)
+            {
+                ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
+            }
         }
 
-        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
-            SequenceGroup(seqs, groups[i].getName(),
-                          cs, groups[i].getDisplayBoxes(),
-                          groups[i].getDisplayText(), groups[i].getColourText(),
-                          groups[i].getStart(), groups[i].getEnd());
+        af.viewport.setGlobalColourScheme(cs);
 
-        sg.setOutlineColour(new java.awt.Color(
-            groups[i].getOutlineColour()));
+        af.viewport.setColourAppliesToAllGroups(false);
+        af.changeColour(af.viewport.getGlobalColourScheme());
+        af.viewport.setColourAppliesToAllGroups(true);
 
-
-        if (groups[i].getConsThreshold() != 0)
+        if (view.getShowSequenceFeatures())
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-              "All",
-              ResidueProperties.propHash, 3, sg.sequences, 0,
-              sg.getWidth() - 1);
-          c.calculate();
-          c.verdict(false, 25);
-          cs = new ConservationColourScheme(c, cs);
-          sg.cs = cs;
+            af.viewport.showSequenceFeatures = true;
+            af.sequenceFeatures.setSelected(true);
+            new SequenceFeatureFetcher(al, af.alignPanel);
+            al.featuresAdded = true;
         }
 
-        al.addGroup(sg);
-      }
-    }
-
-    Desktop.addInternalFrame(af, view.getTitle(),
-                             AlignFrame.NEW_WINDOW_WIDTH,
-                             AlignFrame.NEW_WINDOW_HEIGHT);
-    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
-                 view.getHeight());
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
-    af.viewport.showConservation = view.getShowConservation();
-    af.viewport.showQuality = view.getShowQuality();
-    af.viewport.showIdentity = view.getShowIdentity();
-    af.viewport.setAbovePIDThreshold(view.getPidSelected());
-    af.abovePIDThreshold.setSelected(view.getPidSelected());
-    af.viewport.setColourText(view.getShowColourText());
-    af.colourTextMenuItem.setSelected(view.getShowColourText());
-    af.viewport.setConservationSelected(view.getConservationSelected());
-    af.conservationMenuItem.setSelected(view.getConservationSelected());
-
-    af.viewport.setShowFullId(view.getShowFullId());
-    af.fullSeqId.setSelected(view.getShowFullId());
-
-    af.viewport.setFont(new java.awt.Font(view.getFontName(),
-                                          view.getFontStyle(), view.getFontSize()));
-    af.alignPanel.fontChanged();
-
-    af.viewport.setRenderGaps(view.getRenderGaps());
-    af.renderGapsMenuItem.setSelected(view.getRenderGaps());
-
-    af.viewport.setWrapAlignment(view.getWrapAlignment());
-    af.wrapMenuItem.setSelected(view.getWrapAlignment());
-
-    if (view.getWrapAlignment())
-    {
-      af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-    }
-    else
-    {
-      af.annotationPanelMenuItem.setState(view.getShowAnnotation());
-      af.viewport.setShowAnnotation(view.getShowAnnotation());
-      af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-    }
-
-    af.viewport.setShowBoxes(view.getShowBoxes());
-    af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
-    af.viewport.setShowText(view.getShowText());
-    af.viewTextMenuItem.setSelected(view.getShowText());
-
-    ColourSchemeI cs = null;
-
-    if (view.getBgColour() != null)
-    {
-      if (view.getBgColour().startsWith("ucs"))
-      {
-        cs = GetUserColourScheme(jms, view.getBgColour());
-      }
-      else
-      {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
-      }
-
-      if (cs instanceof ConservationColourScheme)
-      {
-        ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
-      }
-
-      if (cs instanceof ResidueColourScheme)
-      {
-        ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
-      }
-      else if (cs instanceof ScoreColourScheme)
-      {
-        ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
-      }
-    }
-
-    af.viewport.setGlobalColourScheme(cs);
-
-    af.viewport.setColourAppliesToAllGroups(false);
-    af.changeColour(af.viewport.getGlobalColourScheme());
-    af.viewport.setColourAppliesToAllGroups(true);
-
-    if (view.getShowSequenceFeatures())
-    {
-      af.viewport.showSequenceFeatures = true;
-      af.sequenceFeatures.setSelected(true);
-      new SequenceFeatureFetcher(al, af.alignPanel);
-       al.featuresAdded = true;
-    }
-
-    //LOAD TREES
-    ///////////////////////////////////////
-    if (jms.getTreeCount() > 0)
-    {
-      try
-      {
-        for(int t = 0; t<jms.getTreeCount(); t++)
+        //LOAD TREES
+        ///////////////////////////////////////
+        if (jms.getTreeCount() > 0)
         {
-          Tree tree = jms.getTree(t);
-
-          TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
-                  tree.getNewick()), tree.getTitle());
-
-          tp.setBounds( tree.getXpos(),
-                        tree.getYpos(),
-                        tree.getWidth(),
-                        tree.getHeight());
-
-          tp.fitToWindow.setState(tree.getFitToWindow());
-          tp.fitToWindow_actionPerformed(null);
-          tp.treeCanvas.fontSize = tree.getFontSize();
-          tp.fontSize.setText("Font Size - "+tree.getFontSize());
-          tp.placeholdersMenu.setState(tree.getMarkUnlinked());
-          tp.placeholdersMenu_actionPerformed(null);
-          tp.bootstrapMenu.setState(tree.getShowBootstrap());
-          tp.bootstrapMenu_actionPerformed(null);
-          tp.distanceMenu.setState(tree.getShowDistances());
-          tp.distanceMenu_actionPerformed(null);
-          tp.treeCanvas.threshold = tree.getThreshold();
-          if(tree.getCurrentTree());
-             af.viewport.setCurrentTree(tp.getTree());
+            try
+            {
+                for (int t = 0; t < jms.getTreeCount(); t++)
+                {
+                    Tree tree = jms.getTree(t);
+
+                    TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
+                                tree.getNewick()), tree.getTitle());
+
+                    tp.setBounds(tree.getXpos(), tree.getYpos(),
+                        tree.getWidth(), tree.getHeight());
+
+                    tp.fitToWindow.setState(tree.getFitToWindow());
+                    tp.fitToWindow_actionPerformed(null);
+                    tp.treeCanvas.fontSize = tree.getFontSize();
+                    tp.fontSize.setText("Font Size - " + tree.getFontSize());
+                    tp.placeholdersMenu.setState(tree.getMarkUnlinked());
+                    tp.placeholdersMenu_actionPerformed(null);
+                    tp.bootstrapMenu.setState(tree.getShowBootstrap());
+                    tp.bootstrapMenu_actionPerformed(null);
+                    tp.distanceMenu.setState(tree.getShowDistances());
+                    tp.distanceMenu_actionPerformed(null);
+                    tp.treeCanvas.threshold = tree.getThreshold();
+
+                    if (tree.getCurrentTree())
+                      af.viewport.setCurrentTree(tp.getTree());
+                }
+            }
+            catch (Exception ex)
+            {
+                ex.printStackTrace();
+            }
         }
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+        return af;
     }
-  }
 }
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 244d884..62f8ca9 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -21,305 +21,346 @@ package jalview.gui;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
+
 import javax.swing.*;
 
-public class OverviewPanel
-    extends JPanel implements Runnable
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class OverviewPanel extends JPanel implements Runnable
 {
-  BufferedImage miniMe;
-  AlignViewport av;
-  AlignmentPanel ap;
-  float scalew = 1f;
-  float scaleh = 1f;
-  int width;
-  int sequencesHeight;
-  int graphHeight = 30;
-  int boxX = -1;
-  int boxY = -1;
-  int boxWidth = -1;
-  int boxHeight = -1;
-  boolean resizing = false;
-
-  public OverviewPanel(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    setLayout(null);
-
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.alignment.getWidth() /
-        (float) av.alignment.getHeight();
-
-    if (av.alignment.getWidth() > av.alignment.getHeight())
+    BufferedImage miniMe;
+    AlignViewport av;
+    AlignmentPanel ap;
+    float scalew = 1f;
+    float scaleh = 1f;
+    int width;
+    int sequencesHeight;
+    int graphHeight = 30;
+    int boxX = -1;
+    int boxY = -1;
+    int boxWidth = -1;
+    int boxHeight = -1;
+    boolean resizing = false;
+
+    /**
+     * Creates a new OverviewPanel object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public OverviewPanel(AlignmentPanel ap)
     {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
+        this.av = ap.av;
+        this.ap = ap;
+        setLayout(null);
 
-    addComponentListener(new ComponentAdapter()
-    {
-      public void componentResized(ComponentEvent evt)
-      {
-        if ( (getWidth() != width) ||
-            (getHeight() != (sequencesHeight + graphHeight)))
+        // scale the initial size of overviewpanel to shape of alignment
+        float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();
+
+        if (av.alignment.getWidth() > av.alignment.getHeight())
         {
-          updateOverviewImage();
+            // wider
+            width = 400;
+            sequencesHeight = (int) (400f / initialScale);
+        }
+        else
+        {
+            // taller
+            width = (int) (400f * initialScale);
+            sequencesHeight = 300;
+
+            if (width < 120)
+            {
+                width = 120;
+            }
         }
-      }
-    });
-
-    addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseDragged(MouseEvent evt)
-      {
-        doMouseDragged(evt);
-      }
-    });
 
-    addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      {
-        doMousePressed(evt);
-      }
-
-      public void mouseReleased(MouseEvent evt)
-      {
-        doMouseReleased(evt);
-      }
-    });
-
-    updateOverviewImage();
-  }
-
-  public void doMousePressed(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-
-    checkValid();
-    repaint();
-  }
-
-  public void doMouseReleased(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-
-    if (!resizing)
-    {
-      ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
+        addComponentListener(new ComponentAdapter()
+            {
+                public void componentResized(ComponentEvent evt)
+                {
+                    if ((getWidth() != width) ||
+                            (getHeight() != (sequencesHeight + graphHeight)))
+                    {
+                        updateOverviewImage();
+                    }
+                }
+            });
+
+        addMouseMotionListener(new MouseMotionAdapter()
+            {
+                public void mouseDragged(MouseEvent evt)
+                {
+                    doMouseDragged(evt);
+                }
+            });
+
+        addMouseListener(new MouseAdapter()
+            {
+                public void mousePressed(MouseEvent evt)
+                {
+                    doMousePressed(evt);
+                }
+
+                public void mouseReleased(MouseEvent evt)
+                {
+                    doMouseReleased(evt);
+                }
+            });
+
+        updateOverviewImage();
     }
-  }
 
-  public void doMouseDragged(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-
-    if (!resizing)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMousePressed(MouseEvent evt)
     {
-      ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
-    }
-  }
+        boxX = evt.getX();
+        boxY = evt.getY();
 
-  void checkValid()
-  {
-    if (boxY < 0)
-    {
-      boxY = 0;
+        checkValid();
+        repaint();
     }
 
-    if (boxY > (sequencesHeight - boxHeight))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseReleased(MouseEvent evt)
     {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
+        boxX = evt.getX();
+        boxY = evt.getY();
+        checkValid();
 
-    if (boxX < 0)
-    {
-      boxX = 0;
+        if (!resizing)
+        {
+            ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),
+                (int) (boxY / scaleh / av.getCharHeight()));
+        }
     }
 
-    if (boxX > (width - boxWidth))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseDragged(MouseEvent evt)
     {
-      boxX = width - boxWidth;
-    }
-  }
+        boxX = evt.getX();
+        boxY = evt.getY();
+        checkValid();
 
-  public void updateOverviewImage()
-  {
-    if (resizing)
-    {
-      return;
+        if (!resizing)
+        {
+            ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),
+                (int) (boxY / scaleh / av.getCharHeight()));
+        }
     }
 
-    resizing = true;
-
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     */
+    void checkValid()
+    {
+        if (boxY < 0)
+        {
+            boxY = 0;
+        }
 
-  public void run()
-  {
-    miniMe = null;
+        if (boxY > (sequencesHeight - boxHeight))
+        {
+            boxY = sequencesHeight - boxHeight + 1;
+        }
 
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight();
+        if (boxX < 0)
+        {
+            boxX = 0;
+        }
 
-    if ( (getWidth() > 0) && (getHeight() > 0))
-    {
-      width = getWidth();
-      sequencesHeight = getHeight() - graphHeight;
+        if (boxX > (width - boxWidth))
+        {
+            boxX = width - boxWidth;
+        }
     }
 
-    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
+    /**
+     * DOCUMENT ME!
+     */
+    public void updateOverviewImage()
+    {
+        if (resizing)
+        {
+            return;
+        }
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+        resizing = true;
 
-    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
-                               BufferedImage.TYPE_INT_RGB);
+        Thread thread = new Thread(this);
+        thread.start();
+        repaint();
+    }
 
-    Graphics mg = miniMe.getGraphics();
-    BufferedImage consensus = new BufferedImage(fullsizeWidth, 60,
-                                                BufferedImage.TYPE_3BYTE_BGR);
-    Graphics g = consensus.getGraphics();
-    ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);
-    mg.drawImage(consensus, 0, sequencesHeight, width,
-                 sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
+    {
+        miniMe = null;
 
-    boolean oldRenderGaps = av.renderGaps;
+        int alwidth = av.alignment.getWidth();
+        int alheight = av.alignment.getHeight();
 
-    try
-    {
-      // We'll have to draw the full size alignment in chunks, as an image of the
-      // whole alignment requires too much memory
-      // Max size depends on the font size, the following is a
-      // guess at a size which works
-      int maxSize = 2000 / av.getFont().getSize();
-      BufferedImage block;
-      int blockx = 0;
-      int blocky = 0;
-      int blockw = 0;
-      int blockh = 0;
-      int eRes = 0;
-      int eSeq = 0;
-
-      av.setRenderGaps(false);
-
-      for (int sRes = 0, chunkx = 0; sRes < alwidth;
-           sRes += maxSize, chunkx++)
-      {
-        eSeq = 0;
-        eRes += maxSize;
-
-        if (eRes > alwidth)
+        if ((getWidth() > 0) && (getHeight() > 0))
         {
-          eRes = alwidth;
+            width = getWidth();
+            sequencesHeight = getHeight() - graphHeight;
         }
 
-        for (int sSeq = 0, chunky = 0; sSeq < alheight;
-             sSeq += maxSize, chunky++)
-        {
-          eSeq += maxSize;
+        setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
-          if (eSeq > alheight)
-          {
-            eSeq = alheight;
-          }
+        int fullsizeWidth = alwidth * av.getCharWidth();
+        int fullsizeHeight = alheight * av.getCharHeight();
 
-          blocky = 0;
-          blockx = (int) ( (float) sRes / (float) alwidth * width);
+        scalew = (float) width / (float) fullsizeWidth;
+        scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
-          block = new BufferedImage( (eRes - sRes) * av.charWidth,
-                                    (eSeq - sSeq) * av.charHeight,
-                                    BufferedImage.TYPE_3BYTE_BGR);
-          g = block.getGraphics();
+        miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+                BufferedImage.TYPE_INT_RGB);
 
-          ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq,
-                                          sRes, sSeq, 0);
+        Graphics mg = miniMe.getGraphics();
+        BufferedImage consensus = new BufferedImage(fullsizeWidth, 60,
+                BufferedImage.TYPE_3BYTE_BGR);
+        Graphics g = consensus.getGraphics();
+        ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);
+        mg.drawImage(consensus, 0, sequencesHeight, width,
+            sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);
 
-          blockh = (int) ( (float) (eSeq - sSeq) / (float) alheight *
-                          sequencesHeight) +
-              1;
-          blockw = (int) ( (float) (eRes - sRes) / (float) alwidth * width) +
-              1;
+        boolean oldRenderGaps = av.renderGaps;
 
-          blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);
+        try
+        {
+            // We'll have to draw the full size alignment in chunks, as an image of the
+            // whole alignment requires too much memory
+            // Max size depends on the font size, the following is a
+            // guess at a size which works
+            int maxSize = 2000 / av.getFont().getSize();
+            BufferedImage block;
+            int blockx = 0;
+            int blocky = 0;
+            int blockw = 0;
+            int blockh = 0;
+            int eRes = 0;
+            int eSeq = 0;
+
+            av.setRenderGaps(false);
+
+            for (int sRes = 0, chunkx = 0; sRes < alwidth;
+                    sRes += maxSize, chunkx++)
+            {
+                eSeq = 0;
+                eRes += maxSize;
+
+                if (eRes > alwidth)
+                {
+                    eRes = alwidth;
+                }
+
+                for (int sSeq = 0, chunky = 0; sSeq < alheight;
+                        sSeq += maxSize, chunky++)
+                {
+                    eSeq += maxSize;
+
+                    if (eSeq > alheight)
+                    {
+                        eSeq = alheight;
+                    }
+
+                    blocky = 0;
+                    blockx = (int) ((float) sRes / (float) alwidth * width);
+
+                    block = new BufferedImage((eRes - sRes) * av.charWidth,
+                            (eSeq - sSeq) * av.charHeight,
+                            BufferedImage.TYPE_3BYTE_BGR);
+                    g = block.getGraphics();
+
+                    ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq,
+                        sRes, sSeq, 0);
+
+                    blockh = (int) ((float) (eSeq - sSeq) / (float) alheight * sequencesHeight) +
+                        1;
+                    blockw = (int) ((float) (eRes - sRes) / (float) alwidth * width) +
+                        1;
+
+                    blocky += (int) ((float) sSeq / (float) alheight * sequencesHeight);
+
+                    mg.drawImage(block, blockx, blocky, blockx + blockw,
+                        blocky + blockh, 0, 0, block.getWidth(),
+                        block.getHeight(), this);
+
+                    block = null;
+                }
+            }
+        }
+        catch (OutOfMemoryError error)
+        {
+            System.err.println(
+                "Out of memory when trying to calculate the overview window image!");
+        }
 
-          mg.drawImage(block, blockx, blocky, blockx + blockw,
-                       blocky + blockh, 0, 0, block.getWidth(),
-                       block.getHeight(), this);
+        av.setRenderGaps(oldRenderGaps);
+        resizing = false;
 
-          block = null;
-        }
-      }
-    }
-    catch (OutOfMemoryError error)
-    {
-      System.err.println(
-          "Out of memory when trying to calculate the overview window image!");
+        setBoxPosition();
     }
 
-    av.setRenderGaps(oldRenderGaps);
-    resizing = false;
-
-    setBoxPosition();
-  }
-
-  public void setBoxPosition()
-  {
-    boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);
-    boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);
-    boxWidth = (int) ( (av.getEndRes() - av.getStartRes() + 1) *
-                      av.getCharWidth() * scalew);
-    boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -
-        boxY;
-    repaint();
-  }
-
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-    g.setColor(Color.black);
-
-    if (resizing)
+    /**
+     * DOCUMENT ME!
+     */
+    public void setBoxPosition()
     {
-      g.setFont(new Font("Verdana", Font.BOLD, 15));
-      g.drawString("Recalculating", 5, sequencesHeight / 2);
-      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
+        boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);
+        boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);
+        boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth() * scalew);
+        boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -
+            boxY;
+        repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      if (miniMe != null)
-      {
-        g.drawImage(miniMe, 0, 0, this);
-      }
-
-      g.setColor(Color.red);
-      g.drawRect(boxX, boxY, boxWidth, boxHeight);
-      g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
+        g.setColor(Color.black);
+
+        if (resizing)
+        {
+            g.setFont(new Font("Verdana", Font.BOLD, 15));
+            g.drawString("Recalculating", 5, sequencesHeight / 2);
+            g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
+        }
+        else
+        {
+            if (miniMe != null)
+            {
+                g.drawImage(miniMe, 0, 0, this);
+            }
+
+            g.setColor(Color.red);
+            g.drawRect(boxX, boxY, boxWidth, boxHeight);
+            g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index ebde9cb..7bda65a 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -18,133 +18,168 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
-import jalview.jbgui.*;
 
-public class PCAPanel
-    extends GPCAPanel implements Runnable
-{
-  PCA pca;
-  int top;
-  RotatableCanvas rc;
-  AlignViewport av;
+import jalview.jbgui.*;
 
-  public PCAPanel(AlignViewport av, SequenceI[] s)
-  {
-    this.av = av;
+import java.awt.*;
+import java.awt.event.*;
 
-    if ( (av.getSelectionGroup() != null) &&
-        (av.getSelectionGroup().getSize() > 3))
-    {
-      s = new Sequence[av.getSelectionGroup().getSize()];
+import java.util.*;
 
-      for (int i = 0; i < s.length; i++)
-      {
-        s[i] = av.getSelectionGroup().getSequenceAt(i);
-      }
-    }
 
-    if (s == null)
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PCAPanel extends GPCAPanel implements Runnable
+{
+    PCA pca;
+    int top;
+    RotatableCanvas rc;
+    AlignViewport av;
+
+    /**
+     * Creates a new PCAPanel object.
+     *
+     * @param av DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     */
+    public PCAPanel(AlignViewport av, SequenceI[] s)
     {
-      s = new Sequence[av.getAlignment().getHeight()];
-
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)
-      {
-        s[i] = av.getAlignment().getSequenceAt(i);
-      }
+        this.av = av;
+
+        if ((av.getSelectionGroup() != null) &&
+                (av.getSelectionGroup().getSize() > 3))
+        {
+            s = new Sequence[av.getSelectionGroup().getSize()];
+
+            for (int i = 0; i < s.length; i++)
+            {
+                s[i] = av.getSelectionGroup().getSequenceAt(i);
+            }
+        }
+
+        if (s == null)
+        {
+            s = new Sequence[av.getAlignment().getHeight()];
+
+            for (int i = 0; i < av.getAlignment().getHeight(); i++)
+            {
+                s[i] = av.getAlignment().getSequenceAt(i);
+            }
+        }
+
+        //////////////////////This part was done in PCATHread originally. Is it too slow???
+        pca = new PCA(s);
+        pca.run();
+
+        // Now find the component coordinates
+        int ii = 0;
+
+        while ((ii < s.length) && (s[ii] != null))
+        {
+            ii++;
+        }
+
+        double[][] comps = new double[ii][ii];
+
+        for (int i = 0; i < ii; i++)
+        {
+            if (pca.getEigenvalue(i) > 1e-4)
+            {
+                comps[i] = pca.component(i);
+            }
+        }
+
+        //////////////////
+        xCombobox.setSelectedIndex(0);
+        yCombobox.setSelectedIndex(1);
+        zCombobox.setSelectedIndex(2);
+
+        top = pca.getM().rows - 1;
+
+        Vector points = new Vector();
+        float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+
+        for (int i = 0; i < pca.getM().rows; i++)
+        {
+            SequencePoint sp = new SequencePoint(s[i], scores[i]);
+            points.addElement(sp);
+        }
+
+        rc = new RotatableCanvas(av, points, pca.getM().rows);
+
+        //rc.printPoints();
+        add(rc, BorderLayout.CENTER);
     }
 
-    //////////////////////This part was done in PCATHread originally. Is it too slow???
-    pca = new PCA(s);
-    pca.run();
-
-    // Now find the component coordinates
-    int ii = 0;
-
-    while ( (ii < s.length) && (s[ii] != null))
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
     {
-      ii++;
+        // do stuff
     }
 
-    double[][] comps = new double[ii][ii];
-
-    for (int i = 0; i < ii; i++)
+    /**
+     * DOCUMENT ME!
+     */
+    void doDimensionChange()
     {
-      if (pca.getEigenvalue(i) > 1e-4)
-      {
-        comps[i] = pca.component(i);
-      }
+        if (top == 0)
+        {
+            return;
+        }
+
+        int dim1 = top - xCombobox.getSelectedIndex();
+        int dim2 = top - yCombobox.getSelectedIndex();
+        int dim3 = top - zCombobox.getSelectedIndex();
+
+        float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
+
+        for (int i = 0; i < pca.getM().rows; i++)
+        {
+            ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+        }
+
+        rc.img = null;
+        rc.rotmat.setIdentity();
+        rc.initAxes();
+        rc.paint(rc.getGraphics());
     }
 
-    //////////////////
-    xCombobox.setSelectedIndex(0);
-    yCombobox.setSelectedIndex(1);
-    zCombobox.setSelectedIndex(2);
-
-    top = pca.getM().rows - 1;
-
-    Vector points = new Vector();
-    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
-
-    for (int i = 0; i < pca.getM().rows; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void xCombobox_actionPerformed(ActionEvent e)
     {
-      SequencePoint sp = new SequencePoint(s[i], scores[i]);
-      points.addElement(sp);
+        doDimensionChange();
     }
 
-    rc = new RotatableCanvas(av, points, pca.getM().rows);
-
-    //rc.printPoints();
-    add(rc, BorderLayout.CENTER);
-  }
-
-  public void run()
-  {
-    // do stuff
-  }
-
-  void doDimensionChange()
-  {
-    if (top == 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void yCombobox_actionPerformed(ActionEvent e)
     {
-      return;
+        doDimensionChange();
     }
 
-    int dim1 = top - xCombobox.getSelectedIndex();
-    int dim2 = top - yCombobox.getSelectedIndex();
-    int dim3 = top - zCombobox.getSelectedIndex();
-
-    float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
-
-    for (int i = 0; i < pca.getM().rows; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void zCombobox_actionPerformed(ActionEvent e)
     {
-      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+        doDimensionChange();
     }
-
-    rc.img = null;
-    rc.rotmat.setIdentity();
-    rc.initAxes();
-    rc.paint(rc.getGraphics());
-  }
-
-  protected void xCombobox_actionPerformed(ActionEvent e)
-  {
-    doDimensionChange();
-  }
-
-  protected void yCombobox_actionPerformed(ActionEvent e)
-  {
-    doDimensionChange();
-  }
-
-  protected void zCombobox_actionPerformed(ActionEvent e)
-  {
-    doDimensionChange();
-  }
 }
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index e59ecd9..0fe4b85 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -16,53 +16,82 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.gui;
+
+import jalview.datamodel.*;
+
 import java.awt.*;
+
 import java.util.*;
-import jalview.datamodel.*;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class PaintRefresher
 {
-  static Hashtable components = new Hashtable();
+    static Hashtable components = new Hashtable();
 
-  public static void Register(Component comp, AlignmentI al)
-  {
-    if(components.containsKey(al))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param comp DOCUMENT ME!
+     * @param al DOCUMENT ME!
+     */
+    public static void Register(Component comp, AlignmentI al)
     {
-      Vector comps = (Vector)components.get(al);
-      comps.addElement(comp);
+        if (components.containsKey(al))
+        {
+            Vector comps = (Vector) components.get(al);
+            comps.addElement(comp);
+        }
+        else
+        {
+            Vector vcoms = new Vector();
+            vcoms.addElement(comp);
+            components.put(al, vcoms);
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param al DOCUMENT ME!
+     */
+    public static void Refresh(AlignmentI al)
     {
-      Vector vcoms = new Vector();
-      vcoms.addElement(comp);
-      components.put(al, vcoms);
+        Refresh(null, al);
     }
-  }
-
-  public static void Refresh(AlignmentI al)
-  {
-    Refresh(null, al);
-  }
 
-  public static void Refresh(Component c, AlignmentI al)
-  {
-    Component temp;
-    Vector coms = (Vector)components.get(al);
-    Enumeration e = coms.elements();
-    while( e.hasMoreElements() )
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     * @param al DOCUMENT ME!
+     */
+    public static void Refresh(Component c, AlignmentI al)
     {
-      temp = (Component)e.nextElement();
+        Component temp;
+        Vector coms = (Vector) components.get(al);
+        Enumeration e = coms.elements();
 
-      if(!temp.isValid())
-        coms.removeElement( temp );
-      else if( temp == c )
-        continue;
+        while (e.hasMoreElements())
+        {
+            temp = (Component) e.nextElement();
 
-      temp.repaint();
-    }
-
-  }
+            if (!temp.isValid())
+            {
+                coms.removeElement(temp);
+            }
+            else if (temp == c)
+            {
+                continue;
+            }
 
+            temp.repaint();
+        }
+    }
 }
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 69789b9..6509063 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -18,101 +18,118 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.event.*;
-
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
+
 import jalview.jbgui.*;
 
-public class PairwiseAlignPanel
-    extends GPairwiseAlignPanel
-{
-  Vector sequences = new Vector();
-  AlignViewport av;
+import java.awt.event.*;
 
-  public PairwiseAlignPanel(AlignViewport av)
-  {
-    super();
-    this.av = av;
+import java.util.*;
 
-    Vector selsubset = new Vector();
 
-    for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
+{
+    Vector sequences = new Vector();
+    AlignViewport av;
+
+    /**
+     * Creates a new PairwiseAlignPanel object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public PairwiseAlignPanel(AlignViewport av)
     {
-      if (av.getAlignment().getSequences().contains(av.getSelectionGroup()
-          .getSequenceAt(i)))
-      {
-        selsubset.add(av.getSelectionGroup().getSequenceAt(i));
-      }
-    }
-
-    float[][] scores = new float[selsubset.size()][selsubset.size()];
-    double totscore = 0;
-    int count = selsubset.size();
+        super();
+        this.av = av;
 
-    int acount = 0;
+        Vector selsubset = new Vector();
 
-    for (int i = 1; i < count; i++)
-    {
-      for (int j = 0; j < i; j++)
-      {
-        acount++;
-
-        AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),
-                                   (SequenceI) selsubset.elementAt(j), "pep");
-        as.calcScoreMatrix();
-        as.traceAlignment();
-        as.printAlignment();
-        scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
-        totscore = totscore + scores[i][j];
-
-        textarea.append(as.getOutput());
-        sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
-        sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
-      }
-    }
-
-    if (count > 2)
-    {
-      System.out.println(
-          "Pairwise alignment scaled similarity score matrix\n");
+        for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)
+        {
+            if (av.getAlignment().getSequences().contains(av.getSelectionGroup()
+                                                                .getSequenceAt(i)))
+            {
+                selsubset.add(av.getSelectionGroup().getSequenceAt(i));
+            }
+        }
 
-      for (int i = 0; i < count; i++)
-      {
-        jalview.util.Format.print(System.out, "%s \n",
-                                  ("" + i) + " " +
-                                  ( (SequenceI) selsubset.elementAt(i)).getName());
-      }
+        float[][] scores = new float[selsubset.size()][selsubset.size()];
+        double totscore = 0;
+        int count = selsubset.size();
 
-      System.out.println("\n");
+        int acount = 0;
 
-      for (int i = 0; i < count; i++)
-      {
-        for (int j = 0; j < i; j++)
+        for (int i = 1; i < count; i++)
         {
-          jalview.util.Format.print(System.out, "%7.3f",
-                                    scores[i][j] / totscore);
+            for (int j = 0; j < i; j++)
+            {
+                acount++;
+
+                AlignSeq as = new AlignSeq((SequenceI) selsubset.elementAt(i),
+                        (SequenceI) selsubset.elementAt(j), "pep");
+                as.calcScoreMatrix();
+                as.traceAlignment();
+                as.printAlignment();
+                scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+                totscore = totscore + scores[i][j];
+
+                textarea.append(as.getOutput());
+                sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
+                sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
+            }
         }
-      }
 
-      System.out.println("\n");
+        if (count > 2)
+        {
+            System.out.println(
+                "Pairwise alignment scaled similarity score matrix\n");
+
+            for (int i = 0; i < count; i++)
+            {
+                jalview.util.Format.print(System.out, "%s \n",
+                    ("" + i) + " " +
+                    ((SequenceI) selsubset.elementAt(i)).getName());
+            }
+
+            System.out.println("\n");
+
+            for (int i = 0; i < count; i++)
+            {
+                for (int j = 0; j < i; j++)
+                {
+                    jalview.util.Format.print(System.out, "%7.3f",
+                        scores[i][j] / totscore);
+                }
+            }
+
+            System.out.println("\n");
+        }
     }
-  }
-
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
-    Sequence[] seq = new Sequence[sequences.size()];
 
-    for (int i = 0; i < sequences.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void viewInEditorButton_actionPerformed(ActionEvent e)
     {
-      seq[i] = (Sequence) sequences.elementAt(i);
-    }
+        Sequence[] seq = new Sequence[sequences.size()];
 
-    AlignFrame af = new AlignFrame(new Alignment(seq));
-    Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-                             AlignFrame.NEW_WINDOW_WIDTH,
-                             AlignFrame.NEW_WINDOW_HEIGHT);
-  }
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            seq[i] = (Sequence) sequences.elementAt(i);
+        }
+
+        AlignFrame af = new AlignFrame(new Alignment(seq));
+        Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+            AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+    }
 }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 828bbe8..5ff9ad9 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -18,689 +18,842 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
 import MCview.*;
+
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
+
 import jalview.io.*;
+
 import jalview.schemes.*;
 
-public class PopupMenu
-    extends JPopupMenu
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PopupMenu extends JPopupMenu
 {
-  JMenu groupMenu = new JMenu();
-  JMenuItem groupName = new JMenuItem();
-  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new
-      JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-  protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
-  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-  AlignmentPanel ap;
-  JMenu sequenceMenu = new JMenu();
-  JMenuItem sequenceName = new JMenuItem();
-  Sequence sequence;
-  JMenuItem unGroupMenuItem = new JMenuItem();
-  JMenuItem pdbMenuItem = new JMenuItem();
-  JMenuItem outline = new JMenuItem();
-  JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
-  JMenu colourMenu = new JMenu();
-  JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
-  JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
-  JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-
-  public PopupMenu(AlignmentPanel ap, Sequence seq)
-  {
-    ///////////////////////////////////////////////////////////
-    // If this is activated from the sequence panel, the user may want to
-    // edit or annotate a particular residue. Therefore display the residue menu
-    //
-    // If from the IDPanel, we must display the sequence menu
-    //////////////////////////////////////////////////////////
-    this.ap = ap;
-    sequence = seq;
-
-    ButtonGroup colours = new ButtonGroup();
-    colours.add(noColourmenuItem);
-    colours.add(clustalColour);
-    colours.add(zappoColour);
-    colours.add(taylorColour);
-    colours.add(hydrophobicityColour);
-    colours.add(helixColour);
-    colours.add(strandColour);
-    colours.add(turnColour);
-    colours.add(buriedColour);
-    colours.add(abovePIDColour);
-    colours.add(userDefinedColour);
-    colours.add(PIDColour);
-    colours.add(BLOSUM62Colour);
-
-    try
-    {
-      jbInit();
+    JMenu groupMenu = new JMenu();
+    JMenuItem groupName = new JMenuItem();
+    protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+    protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+    protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+    protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+    JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+    protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+    AlignmentPanel ap;
+    JMenu sequenceMenu = new JMenu();
+    JMenuItem sequenceName = new JMenuItem();
+    Sequence sequence;
+    JMenuItem unGroupMenuItem = new JMenuItem();
+    JMenuItem pdbMenuItem = new JMenuItem();
+    JMenuItem outline = new JMenuItem();
+    JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+    JMenu colourMenu = new JMenu();
+    JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+    JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+    JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+
+    /**
+     * Creates a new PopupMenu object.
+     *
+     * @param ap DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    public PopupMenu(AlignmentPanel ap, Sequence seq)
+    {
+        ///////////////////////////////////////////////////////////
+        // If this is activated from the sequence panel, the user may want to
+        // edit or annotate a particular residue. Therefore display the residue menu
+        //
+        // If from the IDPanel, we must display the sequence menu
+        //////////////////////////////////////////////////////////
+        this.ap = ap;
+        sequence = seq;
+
+        ButtonGroup colours = new ButtonGroup();
+        colours.add(noColourmenuItem);
+        colours.add(clustalColour);
+        colours.add(zappoColour);
+        colours.add(taylorColour);
+        colours.add(hydrophobicityColour);
+        colours.add(helixColour);
+        colours.add(strandColour);
+        colours.add(turnColour);
+        colours.add(buriedColour);
+        colours.add(abovePIDColour);
+        colours.add(userDefinedColour);
+        colours.add(PIDColour);
+        colours.add(BLOSUM62Colour);
+
+        try
+        {
+            jbInit();
+        }
+        catch (Exception e)
+        {
+            e.printStackTrace();
+        }
+
+        if ((seq == null) || (seq.getPDBId() == null))
+        {
+            pdbMenuItem.setVisible(false);
+        }
+
+        SequenceGroup sg = ap.av.getSelectionGroup();
+
+        if (sg != null)
+        {
+            groupName.setText(sg.getName());
+
+            if (sg.cs instanceof ZappoColourScheme)
+            {
+                zappoColour.setSelected(true);
+            }
+            else if (sg.cs instanceof TaylorColourScheme)
+            {
+                taylorColour.setSelected(true);
+            }
+            else if (sg.cs instanceof PIDColourScheme)
+            {
+                PIDColour.setSelected(true);
+            }
+            else if (sg.cs instanceof Blosum62ColourScheme)
+            {
+                BLOSUM62Colour.setSelected(true);
+            }
+            else if (sg.cs instanceof UserColourScheme)
+            {
+                userDefinedColour.setSelected(true);
+            }
+            else if (sg.cs instanceof HydrophobicColourScheme)
+            {
+                hydrophobicityColour.setSelected(true);
+            }
+            else if (sg.cs instanceof HelixColourScheme)
+            {
+                helixColour.setSelected(true);
+            }
+            else if (sg.cs instanceof StrandColourScheme)
+            {
+                strandColour.setSelected(true);
+            }
+            else if (sg.cs instanceof TurnColourScheme)
+            {
+                turnColour.setSelected(true);
+            }
+            else if (sg.cs instanceof BuriedColourScheme)
+            {
+                buriedColour.setSelected(true);
+            }
+            else if (sg.cs instanceof ClustalxColourScheme)
+            {
+                clustalColour.setSelected(true);
+            }
+            else
+            {
+                noColourmenuItem.setSelected(true);
+            }
+
+            if (sg.cs instanceof ConservationColourScheme)
+            {
+                conservationMenuItem.setSelected(true);
+            }
+
+            showText.setSelected(sg.getDisplayText());
+            showColourText.setSelected(sg.getColourText());
+            showBoxes.setSelected(sg.getDisplayBoxes());
+        }
+
+        if (!ap.av.alignment.getGroups().contains(sg))
+        {
+            unGroupMenuItem.setVisible(false);
+        }
+        else
+        {
+            groupMenu.insertSeparator(3);
+        }
+
+        if (seq == null)
+        {
+            sequenceMenu.setVisible(false);
+        }
     }
-    catch (Exception e)
-    {
-      e.printStackTrace();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
+        groupMenu.setText("Group");
+        groupMenu.setText("Define");
+        groupName.setText("Name");
+        groupName.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    groupName_actionPerformed(e);
+                }
+            });
+        sequenceMenu.setText("Sequence");
+        sequenceName.setText("Edit name");
+        sequenceName.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    sequenceName_actionPerformed(e);
+                }
+            });
+        PIDColour.setFocusPainted(false);
+        unGroupMenuItem.setText("Remove Group");
+        unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    unGroupMenuItem_actionPerformed(e);
+                }
+            });
+        pdbMenuItem.setText("View PDB structure");
+        pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    pdbMenuItem_actionPerformed(e);
+                }
+            });
+        outline.setText("Border colour");
+        outline.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    outline_actionPerformed(e);
+                }
+            });
+        nucleotideMenuItem.setText("Nucleotide");
+        nucleotideMenuItem.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    nucleotideMenuItem_actionPerformed(e);
+                }
+            });
+        colourMenu.setText("Group Colour");
+        showBoxes.setText("Boxes");
+        showBoxes.setState(true);
+        showBoxes.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    showBoxes_actionPerformed(e);
+                }
+            });
+        showText.setText("Text");
+        showText.setState(true);
+        showText.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    showText_actionPerformed(e);
+                }
+            });
+        showColourText.setText("Colour Text");
+        showColourText.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    showColourText_actionPerformed(e);
+                }
+            });
+        add(groupMenu);
+        add(sequenceMenu);
+        groupMenu.add(groupName);
+        groupMenu.addSeparator();
+        groupMenu.add(unGroupMenuItem);
+        groupMenu.add(colourMenu);
+        groupMenu.addSeparator();
+        groupMenu.add(showBoxes);
+        groupMenu.add(showText);
+        groupMenu.add(showColourText);
+        groupMenu.addSeparator();
+        groupMenu.add(outline);
+        sequenceMenu.add(sequenceName);
+        sequenceMenu.add(pdbMenuItem);
+        colourMenu.add(noColourmenuItem);
+        colourMenu.add(clustalColour);
+        colourMenu.add(BLOSUM62Colour);
+        colourMenu.add(PIDColour);
+        colourMenu.add(zappoColour);
+        colourMenu.add(taylorColour);
+        colourMenu.add(hydrophobicityColour);
+        colourMenu.add(helixColour);
+        colourMenu.add(strandColour);
+        colourMenu.add(turnColour);
+        colourMenu.add(buriedColour);
+        colourMenu.add(nucleotideMenuItem);
+        colourMenu.add(userDefinedColour);
+        colourMenu.addSeparator();
+        colourMenu.add(abovePIDColour);
+        colourMenu.add(conservationMenuItem);
+        noColourmenuItem.setText("None");
+        noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    noColourmenuItem_actionPerformed(e);
+                }
+            });
+
+        clustalColour.setText("Clustalx colours");
+        clustalColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    clustalColour_actionPerformed(e);
+                }
+            });
+        zappoColour.setText("Zappo");
+        zappoColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    zappoColour_actionPerformed(e);
+                }
+            });
+        taylorColour.setText("Taylor");
+        taylorColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    taylorColour_actionPerformed(e);
+                }
+            });
+        hydrophobicityColour.setText("Hydrophobicity");
+        hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    hydrophobicityColour_actionPerformed(e);
+                }
+            });
+        helixColour.setText("Helix propensity");
+        helixColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    helixColour_actionPerformed(e);
+                }
+            });
+        strandColour.setText("Strand propensity");
+        strandColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    strandColour_actionPerformed(e);
+                }
+            });
+        turnColour.setText("Turn propensity");
+        turnColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    turnColour_actionPerformed(e);
+                }
+            });
+        buriedColour.setText("Buried Index");
+        buriedColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    buriedColour_actionPerformed(e);
+                }
+            });
+        abovePIDColour.setText("Above % Identity");
+        abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    abovePIDColour_actionPerformed(e);
+                }
+            });
+        userDefinedColour.setText("User Defined");
+        userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    userDefinedColour_actionPerformed(e);
+                }
+            });
+        PIDColour.setText("Percentage Identity");
+        PIDColour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    PIDColour_actionPerformed(e);
+                }
+            });
+        BLOSUM62Colour.setText("BLOSUM62");
+        BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    BLOSUM62Colour_actionPerformed(e);
+                }
+            });
+        conservationMenuItem.setText("Conservation");
+        conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    conservationMenuItem_actionPerformed(e);
+                }
+            });
     }
 
-    if(seq==null || seq.getPDBId()==null)
-      pdbMenuItem.setVisible(false);
+    /**
+     * DOCUMENT ME!
+     */
+    void refresh()
+    {
+        SequenceGroup sg = getGroup();
+        SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
 
-    SequenceGroup sg = ap.av.getSelectionGroup();
+        if (superG != null)
+        {
+            superG.setSuperGroupProperties(sg);
+        }
 
-    if (sg != null)
-    {
-      groupName.setText(sg.getName());
-
-      if (sg.cs instanceof ZappoColourScheme)
-      {
-        zappoColour.setSelected(true);
-      }
-      else if (sg.cs instanceof TaylorColourScheme)
-      {
-        taylorColour.setSelected(true);
-      }
-      else if (sg.cs instanceof PIDColourScheme)
-      {
-        PIDColour.setSelected(true);
-      }
-      else if (sg.cs instanceof Blosum62ColourScheme)
-      {
-        BLOSUM62Colour.setSelected(true);
-      }
-      else if (sg.cs instanceof UserColourScheme)
-      {
-        userDefinedColour.setSelected(true);
-      }
-      else if (sg.cs instanceof HydrophobicColourScheme)
-      {
-        hydrophobicityColour.setSelected(true);
-      }
-      else if (sg.cs instanceof HelixColourScheme)
-      {
-        helixColour.setSelected(true);
-      }
-      else if (sg.cs instanceof StrandColourScheme)
-      {
-        strandColour.setSelected(true);
-      }
-      else if (sg.cs instanceof TurnColourScheme)
-      {
-        turnColour.setSelected(true);
-      }
-      else if (sg.cs instanceof BuriedColourScheme)
-      {
-        buriedColour.setSelected(true);
-      }
-      else if (sg.cs instanceof ClustalxColourScheme)
-      {
-        clustalColour.setSelected(true);
-      }
-      else
-      {
-        noColourmenuItem.setSelected(true);
-      }
-
-      if (sg.cs instanceof ConservationColourScheme)
-      {
-        conservationMenuItem.setSelected(true);
-      }
-
-      showText.setSelected(sg.getDisplayText());
-      showColourText.setSelected(sg.getColourText());
-      showBoxes.setSelected(sg.getDisplayBoxes());
+        ap.seqPanel.repaint();
     }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
-    {
-      unGroupMenuItem.setVisible(false);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void clustalColour_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
+        sg.cs = new ClustalxColourScheme(sg.sequences,
+                ap.av.alignment.getWidth());
+        refresh();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void zappoColour_actionPerformed(ActionEvent e)
     {
-      groupMenu.insertSeparator(3);
+        getGroup().cs = new ZappoColourScheme();
+        refresh();
     }
 
-    if (seq == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void taylorColour_actionPerformed(ActionEvent e)
     {
-      sequenceMenu.setVisible(false);
+        getGroup().cs = new TaylorColourScheme();
+        refresh();
     }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    groupMenu.setText("Group");
-    groupMenu.setText("Define");
-    groupName.setText("Name");
-    groupName.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        groupName_actionPerformed(e);
-      }
-    });
-    sequenceMenu.setText("Sequence");
-    sequenceName.setText("Edit name");
-    sequenceName.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sequenceName_actionPerformed(e);
-      }
-    });
-    PIDColour.setFocusPainted(false);
-    unGroupMenuItem.setText("Remove Group");
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        unGroupMenuItem_actionPerformed(e);
-      }
-    });
-    pdbMenuItem.setText("View PDB structure");
-    pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pdbMenuItem_actionPerformed(e);
-      }
-    });
-    outline.setText("Border colour");
-    outline.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        outline_actionPerformed(e);
-      }
-    });
-    nucleotideMenuItem.setText("Nucleotide");
-    nucleotideMenuItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideMenuItem_actionPerformed(e);
-      }
-    });
-    colourMenu.setText("Group Colour");
-    showBoxes.setText("Boxes");
-    showBoxes.setState(true);
-    showBoxes.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        showBoxes_actionPerformed(e);
-      }
-    });
-    showText.setText("Text");
-    showText.setState(true);
-    showText.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        showText_actionPerformed(e);
-      }
-    });
-    showColourText.setText("Colour Text");
-    showColourText.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        showColourText_actionPerformed(e);
-      }
-    });
-    add(groupMenu);
-    add(sequenceMenu);
-    groupMenu.add(groupName);
-    groupMenu.addSeparator();
-    groupMenu.add(unGroupMenuItem);
-    groupMenu.add(colourMenu);
-    groupMenu.addSeparator();
-    groupMenu.add(showBoxes);
-    groupMenu.add(showText);
-    groupMenu.add(showColourText);
-    groupMenu.addSeparator();
-    groupMenu.add(outline);
-    sequenceMenu.add(sequenceName);
-    sequenceMenu.add(pdbMenuItem);
-    colourMenu.add(noColourmenuItem);
-    colourMenu.add(clustalColour);
-    colourMenu.add(BLOSUM62Colour);
-    colourMenu.add(PIDColour);
-    colourMenu.add(zappoColour);
-    colourMenu.add(taylorColour);
-    colourMenu.add(hydrophobicityColour);
-    colourMenu.add(helixColour);
-    colourMenu.add(strandColour);
-    colourMenu.add(turnColour);
-    colourMenu.add(buriedColour);
-    colourMenu.add(nucleotideMenuItem);
-    colourMenu.add(userDefinedColour);
-    colourMenu.addSeparator();
-    colourMenu.add(abovePIDColour);
-    colourMenu.add(conservationMenuItem);
-    noColourmenuItem.setText("None");
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        noColourmenuItem_actionPerformed(e);
-      }
-    });
-
-    clustalColour.setText("Clustalx colours");
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed(e);
-      }
-    });
-    zappoColour.setText("Zappo");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed(e);
-      }
-    });
-    taylorColour.setText("Taylor");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed(e);
-      }
-    });
-    hydrophobicityColour.setText("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
-    helixColour.setText("Helix propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed(e);
-      }
-    });
-    strandColour.setText("Strand propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed(e);
-      }
-    });
-    turnColour.setText("Turn propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed(e);
-      }
-    });
-    buriedColour.setText("Buried Index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed(e);
-      }
-    });
-    abovePIDColour.setText("Above % Identity");
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDColour_actionPerformed(e);
-      }
-    });
-    userDefinedColour.setText("User Defined");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
-    PIDColour.setText("Percentage Identity");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed(e);
-      }
-    });
-    BLOSUM62Colour.setText("BLOSUM62");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void hydrophobicityColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed(e);
-      }
-    });
-    conservationMenuItem.setText("Conservation");
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+        getGroup().cs = new HydrophobicColourScheme();
+        refresh();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void helixColour_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed(e);
-      }
-    });
-  }
-
-  void refresh()
-  {
-    SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
-    if (superG != null)
+        getGroup().cs = new HelixColourScheme();
+        refresh();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void strandColour_actionPerformed(ActionEvent e)
     {
-      superG.setSuperGroupProperties(sg);
+        getGroup().cs = new StrandColourScheme();
+        refresh();
     }
 
-    ap.seqPanel.repaint();
-  }
-
-  protected void clustalColour_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences,
-                                     ap.av.alignment.getWidth());
-    refresh();
-  }
-
-  protected void zappoColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new ZappoColourScheme();
-    refresh();
-  }
-
-  protected void taylorColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new TaylorColourScheme();
-    refresh();
-  }
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new HydrophobicColourScheme();
-    refresh();
-  }
-
-  protected void helixColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new HelixColourScheme();
-    refresh();
-  }
-
-  protected void strandColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new StrandColourScheme();
-    refresh();
-  }
-
-  protected void turnColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new TurnColourScheme();
-    refresh();
-  }
-
-  protected void buriedColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new BuriedColourScheme();
-    refresh();
-  }
-
-  public void nucleotideMenuItem_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new NucleotideColourScheme();
-    refresh();
-  }
-
-  protected void abovePIDColour_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-
-    if (abovePIDColour.isSelected())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void turnColour_actionPerformed(ActionEvent e)
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
-
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
-          getGroup().getName());
-
-      if (sg.cs instanceof ResidueColourScheme)
-      {
-        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-      }
-      else if (sg.cs instanceof ScoreColourScheme)
-      {
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-      }
-
-      SliderPanel.showPIDSlider();
+        getGroup().cs = new TurnColourScheme();
+        refresh();
     }
-    else // remove PIDColouring
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void buriedColour_actionPerformed(ActionEvent e)
     {
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-      rcs.setThreshold(0);
-      sg.cs = rcs;
+        getGroup().cs = new BuriedColourScheme();
+        refresh();
     }
 
-    refresh();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void nucleotideMenuItem_actionPerformed(ActionEvent e)
+    {
+        getGroup().cs = new NucleotideColourScheme();
+        refresh();
+    }
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    new UserDefinedColours(ap, getGroup());
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void abovePIDColour_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
+
+        if (abovePIDColour.isSelected())
+        {
+            sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                    ap.av.alignment.getWidth()));
+
+            int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+                    getGroup().getName());
+
+            if (sg.cs instanceof ResidueColourScheme)
+            {
+                ((ResidueColourScheme) sg.cs).setThreshold(threshold);
+            }
+            else if (sg.cs instanceof ScoreColourScheme)
+            {
+                ((ScoreColourScheme) sg.cs).setThreshold(threshold);
+            }
+
+            SliderPanel.showPIDSlider();
+        }
+        else // remove PIDColouring
+        {
+            ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
+            rcs.setThreshold(0);
+            sg.cs = rcs;
+        }
+
+        refresh();
+    }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-    sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                             ap.av.alignment.getWidth()));
-    refresh();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void userDefinedColour_actionPerformed(ActionEvent e)
+    {
+        new UserDefinedColours(ap, getGroup());
+    }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void PIDColour_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
+        sg.cs = new PIDColourScheme();
+        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                ap.av.alignment.getWidth()));
+        refresh();
+    }
 
-    sg.cs = new Blosum62ColourScheme();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                             ap.av.alignment.getWidth()));
+        sg.cs = new Blosum62ColourScheme();
 
-    refresh();
-  }
+        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                ap.av.alignment.getWidth()));
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = null;
-    refresh();
-  }
+        refresh();
+    }
 
-  protected void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void noColourmenuItem_actionPerformed(ActionEvent e)
+    {
+        getGroup().cs = null;
+        refresh();
+    }
 
-    if (conservationMenuItem.isSelected())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void conservationMenuItem_actionPerformed(ActionEvent e)
     {
-      Conservation c = new Conservation("Group",
-                                        ResidueProperties.propHash, 3,
-                                        sg.sequences, 0,
-                                        ap.av.alignment.getWidth());
+        SequenceGroup sg = getGroup();
 
-      c.calculate();
-      c.verdict(false, ap.av.ConsPercGaps);
+        if (conservationMenuItem.isSelected())
+        {
+            Conservation c = new Conservation("Group",
+                    ResidueProperties.propHash, 3, sg.sequences, 0,
+                    ap.av.alignment.getWidth());
 
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+            c.calculate();
+            c.verdict(false, ap.av.ConsPercGaps);
 
-      sg.cs = ccs;
+            ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
-      SliderPanel.showConservationSlider();
-    }
-    else // remove ConservationColouring
-    {
-      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
-      sg.cs = ccs.cs;
-    }
+            sg.cs = ccs;
 
-    refresh();
-  }
+            SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+            SliderPanel.showConservationSlider();
+        }
+        else // remove ConservationColouring
+        {
+            ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
+            sg.cs = ccs.cs;
+        }
 
-  protected void groupName_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-    String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
-        "Enter new group name", "Edit group name",
-        JOptionPane.QUESTION_MESSAGE);
+        refresh();
+    }
 
-    if (reply == null)
-    {
-      return;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void groupName_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
+        String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+                "Enter new group name", "Edit group name",
+                JOptionPane.QUESTION_MESSAGE);
+
+        if (reply == null)
+        {
+            return;
+        }
+
+        sg.setName(reply);
+        groupName.setText(reply);
     }
 
-    sg.setName(reply);
-    groupName.setText(reply);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void analyze_actionPerformed(ActionEvent e)
+    {
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
+        JInternalFrame frame = new JInternalFrame();
+        frame.setContentPane(cap);
+        Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
+
+        SequenceGroup sg = getGroup();
+        StringBuffer sb = new StringBuffer();
+
+        for (int i = 0; i < sg.sequences.size(); i++)
+        {
+            Sequence tmp = (Sequence) sg.sequences.get(i);
+            sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
+            sb.append("\n");
+        }
+
+        sb.append("Something amazing will happen soon");
+        cap.setText(sb.toString());
+    }
 
-  protected void analyze_actionPerformed(ActionEvent e)
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(cap);
-    Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    SequenceGroup getGroup()
+    {
+        SequenceGroup sg = ap.av.getSelectionGroup();
 
-    SequenceGroup sg = getGroup();
-    StringBuffer sb = new StringBuffer();
+        // this method won't add a new group if it already exists
+        ap.av.alignment.addGroup(sg);
 
-    for (int i = 0; i < sg.sequences.size(); i++)
-    {
-      Sequence tmp = (Sequence) sg.sequences.get(i);
-      sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
-      sb.append("\n");
+        return sg;
     }
 
-    sb.append("Something amazing will happen soon");
-    cap.setText(sb.toString());
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    void sequenceName_actionPerformed(ActionEvent e)
+    {
+        String id = sequence.getName();
+        String s = (String) JOptionPane.showInternalInputDialog(ap,
+                "Edit sequence name",
+                "Edit sequence name (" + sequence.getName() + ")",
+                JOptionPane.PLAIN_MESSAGE, null, null, id);
+
+        if (s != null)
+        {
+            if (s.indexOf(" ") > -1)
+            {
+                JOptionPane.showMessageDialog(ap,
+                    "Spaces have been converted to \"_\"",
+                    "No spaces allowed in Sequence Name",
+                    JOptionPane.WARNING_MESSAGE);
+            }
+
+            s = s.replace(' ', '_');
+            sequence.setName(s);
+            ap.repaint();
+        }
+    }
 
-  SequenceGroup getGroup()
-  {
-    SequenceGroup sg = ap.av.getSelectionGroup();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    void unGroupMenuItem_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = ap.av.getSelectionGroup();
+        ap.av.alignment.deleteGroup(sg);
+        ap.av.setSelectionGroup(null);
+        refresh();
+    }
 
-    // this method won't add a new group if it already exists
-    ap.av.alignment.addGroup(sg);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    void pdbMenuItem_actionPerformed(ActionEvent e)
+    {
+        if (sequence.getPDBId() == null)
+        {
+            return;
+        }
+
+        try
+        {
+            EBIFetchClient ebi = new EBIFetchClient();
+            String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
+                    null);
+
+            PDBfile pdb = new PDBfile(result);
+
+            rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
+            JInternalFrame frame = new JInternalFrame();
+            frame.setContentPane(rc);
+            Desktop.addInternalFrame(frame,
+                sequence.getName() + " " + sequence.getPDBId(), 400, 400);
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
 
-    return sg;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void outline_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = getGroup();
+        Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+                Color.BLUE);
 
-  void sequenceName_actionPerformed(ActionEvent e)
-  {
-    String id = sequence.getName();
-    String s = (String) JOptionPane.showInternalInputDialog(ap,
-        "Edit sequence name",
-        "Edit sequence name (" + sequence.getName() + ")",
-        JOptionPane.PLAIN_MESSAGE, null, null, id);
+        if (col != null)
+        {
+            sg.setOutlineColour(col);
+        }
 
-    if (s != null)
-    {
-      if(s.indexOf(" ")>-1)
-        JOptionPane.showMessageDialog(ap, "Spaces have been converted to \"_\"",
-            "No spaces allowed in Sequence Name", JOptionPane.WARNING_MESSAGE);
-        s = s.replace(' ', '_');
-        sequence.setName(s);
-        ap.repaint();
-    }
-  }
-
-  void unGroupMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    ap.av.alignment.deleteGroup(sg);
-    ap.av.setSelectionGroup(null);
-    refresh();
-  }
-
-  void pdbMenuItem_actionPerformed(ActionEvent e)
-  {
-    if (sequence.getPDBId() == null)
-    {
-      return;
+        refresh();
     }
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void showBoxes_actionPerformed(ActionEvent e)
     {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
-                                      null);
-
-      PDBfile pdb = new PDBfile(result);
-
-      rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(rc);
-      Desktop.addInternalFrame(frame,
-                               sequence.getName() + " " + sequence.getPDBId(),
-                               400, 400);
+        getGroup().setDisplayBoxes(showBoxes.isSelected());
+        refresh();
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void showText_actionPerformed(ActionEvent e)
     {
-      ex.printStackTrace();
+        getGroup().setDisplayText(showText.isSelected());
+        refresh();
     }
-  }
 
-  protected void outline_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-    Color col = JColorChooser.showDialog(this, "Select Outline Colour",
-                                         Color.BLUE);
-
-    if (col != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void showColourText_actionPerformed(ActionEvent e)
     {
-      sg.setOutlineColour(col);
+        getGroup().setColourText(showColourText.isSelected());
+        refresh();
     }
-
-    refresh();
-  }
-
-  public void showBoxes_actionPerformed(ActionEvent e)
-  {
-    getGroup().setDisplayBoxes(showBoxes.isSelected());
-    refresh();
-  }
-
-  public void showText_actionPerformed(ActionEvent e)
-  {
-    getGroup().setDisplayText(showText.isSelected());
-    refresh();
-  }
-
-  public void showColourText_actionPerformed(ActionEvent e)
-  {
-    getGroup().setColourText(showColourText.isSelected());
-    refresh();
-  }
 }
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b16ae32..8a3c372 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -18,300 +18,358 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
 import jalview.bin.*;
+
 import jalview.io.*;
+
 import jalview.jbgui.*;
+
 import jalview.schemes.*;
 
-public class Preferences
-    extends GPreferences
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences extends GPreferences
 {
-  static boolean preferencesLoaded = false;
-  public static boolean showFullscreen = false;
-  public static boolean showFullId = true;
-  public static boolean showAnnotation = true;
-  public static boolean showConservation = true;
-  public static boolean showQuality = true;
-  public static boolean showIdentity = true;
-  public static String fontName = "SansSerif";
-  public static String fontSize = "10";
-  public static String fontStyle = Font.PLAIN + "";
-  public static char gapSymbol = '-';
-  public static String defaultColour = null;
-  public static boolean showStartupFile = true;
-  public static String startupFile =
-      "http://www.jalview.org/examples/exampleFile.jar";
-  JInternalFrame frame;
-
-  public Preferences()
-  {
-    initPreferences();
-
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Preferences", 480, 390);
-
-    fullID.setSelected(showFullId);
-
-    String string = Cache.getProperty("SHOW_FULLSCREEN");
-    boolean value = false;
-
-    if (string != null)
-    {
-      value = Boolean.valueOf(string).booleanValue();
-    }
+    static boolean preferencesLoaded = false;
 
-    fullScreen.setSelected(value);
-    annotations.setSelected(showAnnotation);
+    /** DOCUMENT ME!! */
+    public static boolean showFullscreen = false;
 
-    conservation.setEnabled(showAnnotation);
-    quality.setEnabled(showAnnotation);
-    identity.setEnabled(showAnnotation);
+    /** DOCUMENT ME!! */
+    public static boolean showFullId = true;
 
-    conservation.setSelected(showConservation);
-    quality.setSelected(showQuality);
-    identity.setSelected(showIdentity);
+    /** DOCUMENT ME!! */
+    public static boolean showAnnotation = true;
 
-    for (int i = 0; i < 12; i++)
-    {
-      colour.addItem(ColourSchemeProperty.getColourName(i));
-    }
+    /** DOCUMENT ME!! */
+    public static boolean showConservation = true;
 
-    string = Cache.getProperty("DEFAULT_COLOUR");
+    /** DOCUMENT ME!! */
+    public static boolean showQuality = true;
 
-    if (string != null)
-    {
-      colour.setSelectedItem(string);
-    }
-    else
-    {
-      colour.setSelectedIndex(11);
-    }
+    /** DOCUMENT ME!! */
+    public static boolean showIdentity = true;
 
-    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
-        .getAvailableFontFamilyNames();
+    /** DOCUMENT ME!! */
+    public static String fontName = "SansSerif";
 
-    for (int i = 0; i < fonts.length; i++)
-    {
-      fontNameCB.addItem(fonts[i]);
-    }
+    /** DOCUMENT ME!! */
+    public static String fontSize = "10";
+
+    /** DOCUMENT ME!! */
+    public static String fontStyle = Font.PLAIN + "";
 
-    for (int i = 1; i < 31; i++)
+    /** DOCUMENT ME!! */
+    public static char gapSymbol = '-';
+
+    /** DOCUMENT ME!! */
+    public static String defaultColour = null;
+
+    /** DOCUMENT ME!! */
+    public static boolean showStartupFile = true;
+
+    /** DOCUMENT ME!! */
+    public static String startupFile = "http://www.jalview.org/examples/exampleFile.jar";
+    JInternalFrame frame;
+
+    /**
+     * Creates a new Preferences object.
+     */
+    public Preferences()
     {
-      fontSizeCB.addItem(i + "");
-    }
+        initPreferences();
 
-    fontStyleCB.addItem("plain");
-    fontStyleCB.addItem("bold");
-    fontStyleCB.addItem("italic");
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "Preferences", 480, 390);
 
-    fontNameCB.setSelectedItem(fontName);
-    fontSizeCB.setSelectedItem(fontSize);
-    fontStyleCB.setSelectedItem(fontStyle);
+        fullID.setSelected(showFullId);
 
-    gapSymbolCB.addItem("-");
-    gapSymbolCB.addItem(".");
+        String string = Cache.getProperty("SHOW_FULLSCREEN");
+        boolean value = false;
 
-    gapSymbolCB.setSelectedItem(gapSymbol + "");
+        if (string != null)
+        {
+            value = Boolean.valueOf(string).booleanValue();
+        }
 
-    startupCheckbox.setSelected(showStartupFile);
-    startupFileTextfield.setText(startupFile);
-  }
+        fullScreen.setSelected(value);
+        annotations.setSelected(showAnnotation);
 
-  public static void initPreferences()
-  {
-    String string = Cache.getProperty("SHOW_FULL_ID");
+        conservation.setEnabled(showAnnotation);
+        quality.setEnabled(showAnnotation);
+        identity.setEnabled(showAnnotation);
 
-    if (string != null)
-    {
-      showFullId = Boolean.valueOf(string).booleanValue();
-    }
+        conservation.setSelected(showConservation);
+        quality.setSelected(showQuality);
+        identity.setSelected(showIdentity);
 
-    string = Cache.getProperty("SHOW_FULLSCREEN");
+        for (int i = 0; i < 12; i++)
+        {
+            colour.addItem(ColourSchemeProperty.getColourName(i));
+        }
 
-    if (string != null)
-    {
-      showFullscreen = Boolean.valueOf(string).booleanValue();
-    }
+        string = Cache.getProperty("DEFAULT_COLOUR");
 
-    string = Cache.getProperty("SHOW_ANNOTATIONS");
+        if (string != null)
+        {
+            colour.setSelectedItem(string);
+        }
+        else
+        {
+            colour.setSelectedIndex(11);
+        }
 
-    if (string != null)
-    {
-      showAnnotation = Boolean.valueOf(string).booleanValue();
-    }
+        String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+                                                     .getAvailableFontFamilyNames();
 
-    string = Cache.getProperty("SHOW_CONSERVATION");
+        for (int i = 0; i < fonts.length; i++)
+        {
+            fontNameCB.addItem(fonts[i]);
+        }
 
-    if (string != null)
-    {
-      showConservation = Boolean.valueOf(string).booleanValue();
-    }
+        for (int i = 1; i < 31; i++)
+        {
+            fontSizeCB.addItem(i + "");
+        }
 
-    string = Cache.getProperty("SHOW_QUALITY");
+        fontStyleCB.addItem("plain");
+        fontStyleCB.addItem("bold");
+        fontStyleCB.addItem("italic");
 
-    if (string != null)
-    {
-      showQuality = Boolean.valueOf(string).booleanValue();
-    }
+        fontNameCB.setSelectedItem(fontName);
+        fontSizeCB.setSelectedItem(fontSize);
+        fontStyleCB.setSelectedItem(fontStyle);
 
-    string = Cache.getProperty("SHOW_IDENTITY");
+        gapSymbolCB.addItem("-");
+        gapSymbolCB.addItem(".");
 
-    if (string != null)
-    {
-      showIdentity = Boolean.valueOf(string).booleanValue();
-    }
+        gapSymbolCB.setSelectedItem(gapSymbol + "");
 
-    string = Cache.getProperty("GAP_SYMBOL");
+        startupCheckbox.setSelected(showStartupFile);
+        startupFileTextfield.setText(startupFile);
+    }
 
-    if (string != null)
+    /**
+     * DOCUMENT ME!
+     */
+    public static void initPreferences()
     {
-      gapSymbol = string.charAt(0);
-    }
+        String string = Cache.getProperty("SHOW_FULL_ID");
 
-    string = Cache.getProperty("SHOW_FULL_ID");
+        if (string != null)
+        {
+            showFullId = Boolean.valueOf(string).booleanValue();
+        }
 
-    if (string != null)
-    {
-      showFullId = Boolean.valueOf(string).booleanValue();
-    }
+        string = Cache.getProperty("SHOW_FULLSCREEN");
 
-    string = Cache.getProperty("FONT_NAME");
+        if (string != null)
+        {
+            showFullscreen = Boolean.valueOf(string).booleanValue();
+        }
 
-    if (string != null)
-    {
-      fontName = string;
-    }
+        string = Cache.getProperty("SHOW_ANNOTATIONS");
 
-    string = Cache.getProperty("FONT_STYLE");
+        if (string != null)
+        {
+            showAnnotation = Boolean.valueOf(string).booleanValue();
+        }
 
-    if (string != null)
-    {
-      fontStyle = string;
-    }
+        string = Cache.getProperty("SHOW_CONSERVATION");
 
-    string = Cache.getProperty("FONT_SIZE");
+        if (string != null)
+        {
+            showConservation = Boolean.valueOf(string).booleanValue();
+        }
 
-    if (string != null)
-    {
-      fontSize = string;
-    }
+        string = Cache.getProperty("SHOW_QUALITY");
 
-    string = Cache.getProperty("DEFAULT_COLOUR");
+        if (string != null)
+        {
+            showQuality = Boolean.valueOf(string).booleanValue();
+        }
 
-    if (string != null)
-    {
-      defaultColour = string;
-    }
+        string = Cache.getProperty("SHOW_IDENTITY");
+
+        if (string != null)
+        {
+            showIdentity = Boolean.valueOf(string).booleanValue();
+        }
 
-    string = Cache.getProperty("STARTUP_FILE");
+        string = Cache.getProperty("GAP_SYMBOL");
 
-    if (string != null)
-    {
-      startupFile = string;
-    }
+        if (string != null)
+        {
+            gapSymbol = string.charAt(0);
+        }
 
-    string = Cache.getProperty("SHOW_STARTUP_FILE");
+        string = Cache.getProperty("SHOW_FULL_ID");
 
-    if (string != null)
-    {
-      showStartupFile = Boolean.valueOf(string).booleanValue();
-    }
+        if (string != null)
+        {
+            showFullId = Boolean.valueOf(string).booleanValue();
+        }
 
-    preferencesLoaded = true;
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    showFullId = fullID.isSelected();
-    showFullscreen = fullScreen.isSelected();
-    showAnnotation = annotations.isSelected();
-    showConservation = conservation.isSelected();
-    showQuality = quality.isSelected();
-    showIdentity = identity.isSelected();
-    defaultColour = colour.getSelectedItem().toString();
-    gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);
-    fontName = fontNameCB.getSelectedItem().toString();
-    fontSize = fontSizeCB.getSelectedItem().toString();
-    fontStyle = fontStyleCB.getSelectedItem().toString();
-    startupFile = startupFileTextfield.getText();
-    showStartupFile = startupCheckbox.isSelected();
-
-    Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));
-    Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString(showFullscreen));
-
-    Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString(showAnnotation));
-    Cache.setProperty("SHOW_CONSERVATION",
-                      Boolean.toString(showConservation));
-    Cache.setProperty("SHOW_QUALITY", Boolean.toString(showQuality));
-    Cache.setProperty("SHOW_IDENTITY", Boolean.toString(showIdentity));
-
-    Cache.setProperty("DEFAULT_COLOUR", defaultColour);
-    Cache.setProperty("GAP_SYMBOL", gapSymbol + "");
-
-    Cache.setProperty("FONT_NAME", fontName);
-    Cache.setProperty("FONT_STYLE", fontStyle);
-    Cache.setProperty("FONT_SIZE", fontSize);
-
-    Cache.setProperty("STARTUP_FILE", startupFile);
-    Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));
-
-    try
-    {
-      frame.setClosed(true);
+        string = Cache.getProperty("FONT_NAME");
+
+        if (string != null)
+        {
+            fontName = string;
+        }
+
+        string = Cache.getProperty("FONT_STYLE");
+
+        if (string != null)
+        {
+            fontStyle = string;
+        }
+
+        string = Cache.getProperty("FONT_SIZE");
+
+        if (string != null)
+        {
+            fontSize = string;
+        }
+
+        string = Cache.getProperty("DEFAULT_COLOUR");
+
+        if (string != null)
+        {
+            defaultColour = string;
+        }
+
+        string = Cache.getProperty("STARTUP_FILE");
+
+        if (string != null)
+        {
+            startupFile = string;
+        }
+
+        string = Cache.getProperty("SHOW_STARTUP_FILE");
+
+        if (string != null)
+        {
+            showStartupFile = Boolean.valueOf(string).booleanValue();
+        }
+
+        preferencesLoaded = true;
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ok_actionPerformed(ActionEvent e)
     {
-    }
-  }
-
-  public void startupFileTextfield_mouseClicked()
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"),
-        new String[]
+        showFullId = fullID.isSelected();
+        showFullscreen = fullScreen.isSelected();
+        showAnnotation = annotations.isSelected();
+        showConservation = conservation.isSelected();
+        showQuality = quality.isSelected();
+        showIdentity = identity.isSelected();
+        defaultColour = colour.getSelectedItem().toString();
+        gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);
+        fontName = fontNameCB.getSelectedItem().toString();
+        fontSize = fontSizeCB.getSelectedItem().toString();
+        fontStyle = fontStyleCB.getSelectedItem().toString();
+        startupFile = startupFileTextfield.getText();
+        showStartupFile = startupCheckbox.isSelected();
+
+        Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));
+        Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString(showFullscreen));
+
+        Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString(showAnnotation));
+        Cache.setProperty("SHOW_CONSERVATION",
+            Boolean.toString(showConservation));
+        Cache.setProperty("SHOW_QUALITY", Boolean.toString(showQuality));
+        Cache.setProperty("SHOW_IDENTITY", Boolean.toString(showIdentity));
+
+        Cache.setProperty("DEFAULT_COLOUR", defaultColour);
+        Cache.setProperty("GAP_SYMBOL", gapSymbol + "");
+
+        Cache.setProperty("FONT_NAME", fontName);
+        Cache.setProperty("FONT_STYLE", fontStyle);
+        Cache.setProperty("FONT_SIZE", fontSize);
+
+        Cache.setProperty("STARTUP_FILE", startupFile);
+        Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));
+
+        try
         {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "jar"
-    },
-        new String[]
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
         {
-        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-    }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Select startup file");
-
-    int value = chooser.showOpenDialog(this);
+        }
+    }
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    /**
+     * DOCUMENT ME!
+     */
+    public void startupFileTextfield_mouseClicked()
     {
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
-                                    chooser.getSelectedFormat());
-      startupFileTextfield.setText(chooser.getSelectedFile()
-                                   .getAbsolutePath());
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"),
+                new String[]
+                {
+                    "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+                    "jar"
+                },
+                new String[]
+                {
+                    "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+                }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Select startup file");
+
+        int value = chooser.showOpenDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                chooser.getSelectedFormat());
+            startupFileTextfield.setText(chooser.getSelectedFile()
+                                                .getAbsolutePath());
+        }
     }
-  }
 
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void cancel_actionPerformed(ActionEvent e)
     {
-      frame.setClosed(true);
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void annotations_actionPerformed(ActionEvent e)
     {
+        conservation.setEnabled(annotations.isSelected());
+        quality.setEnabled(annotations.isSelected());
+        identity.setEnabled(annotations.isSelected());
     }
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    conservation.setEnabled(annotations.isSelected());
-    quality.setEnabled(annotations.isSelected());
-    identity.setEnabled(annotations.isSelected());
-  }
 }
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index daee862..17b5dfa 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -18,144 +18,173 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
 
 import java.awt.event.*;
-import javax.swing.event.*;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import java.util.*;
 
-public class RedundancyPanel
-    extends GSliderPanel
-{
-  AlignFrame af;
-  AlignmentPanel ap;
-  Stack historyList = new Stack(); // simpler than synching with alignFrame.
+import javax.swing.event.*;
 
-  public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
-  {
-    this.ap = ap;
-    this.af = af;
-    label.setText("Enter the redundancy threshold");
 
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        valueField.setText(slider.getValue() + "");
-      }
-    });
-
-    slider.setMinimum(0);
-    slider.setMaximum(100);
-    slider.setValue(100);
-  }
-
-  public void applyButton_actionPerformed(ActionEvent e)
-  {
-    float threshold = slider.getValue();
-    Vector del;
-    HistoryItem it;
-    historyList.push(it = new HistoryItem("Remove redundancy",
-                                          ap.av.alignment, HistoryItem.HIDE));
-
-    if ( (historyList.size() == 1) ||
-        !af.historyList.contains(historyList.firstElement()))
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RedundancyPanel extends GSliderPanel
+{
+    AlignFrame af;
+    AlignmentPanel ap;
+    Stack historyList = new Stack(); // simpler than synching with alignFrame.
+
+    /**
+     * Creates a new RedundancyPanel object.
+     *
+     * @param ap DOCUMENT ME!
+     * @param af DOCUMENT ME!
+     */
+    public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
     {
-      af.addHistoryItem( (HistoryItem) historyList.firstElement());
-      af.updateEditMenuBar();
+        this.ap = ap;
+        this.af = af;
+        label.setText("Enter the redundancy threshold");
+
+        slider.addChangeListener(new ChangeListener()
+            {
+                public void stateChanged(ChangeEvent evt)
+                {
+                    valueField.setText(slider.getValue() + "");
+                }
+            });
+
+        slider.setMinimum(0);
+        slider.setMaximum(100);
+        slider.setValue(100);
     }
 
-    undoButton.setEnabled(true);
-
-    SequenceGroup sg = ap.av.getSelectionGroup();
-
-    if ( (sg != null) && (sg.getSize() >= 1))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void applyButton_actionPerformed(ActionEvent e)
     {
-      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
-
-      for (int i = 0; i < del.size(); i++)
-      {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
+        float threshold = slider.getValue();
+        Vector del;
+        HistoryItem it;
+        historyList.push(it = new HistoryItem("Remove redundancy",
+                    ap.av.alignment, HistoryItem.HIDE));
+
+        if ((historyList.size() == 1) ||
+                !af.historyList.contains(historyList.firstElement()))
         {
-          sg.deleteSequence( (SequenceI) del.elementAt(i), true);
+            af.addHistoryItem((HistoryItem) historyList.firstElement());
+            af.updateEditMenuBar();
         }
-      }
-    }
-    else
-    {
-      Vector s = new Vector();
-      int i = 0;
 
-      while (i < ap.av.alignment.getHeight())
-      {
-        s.addElement(ap.av.alignment.getSequenceAt(i));
-        i++;
-      }
+        undoButton.setEnabled(true);
 
-      del = ap.av.alignment.removeRedundancy(threshold, s);
-    }
+        SequenceGroup sg = ap.av.getSelectionGroup();
 
-    // This has to be done before the restoreHistoryItem method of alignFrame will
-    // actually restore these sequences.
-    if (del.size() > 0)
-    {
-      for (int i = 0, j = del.size(); i < j; i++)
-      {
-        SequenceI sq = (SequenceI) del.elementAt(i);
-        sq.deleteChars(0, sq.getLength());
-      }
-    }
+        if ((sg != null) && (sg.getSize() >= 1))
+        {
+            del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
+
+            for (int i = 0; i < del.size(); i++)
+            {
+                if (sg.sequences.contains((SequenceI) del.elementAt(i)))
+                {
+                    sg.deleteSequence((SequenceI) del.elementAt(i), true);
+                }
+            }
+        }
+        else
+        {
+            Vector s = new Vector();
+            int i = 0;
 
-    ap.av.firePropertyChange("alignment", null,
-                             ap.av.getAlignment().getSequences());
-    ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
+            while (i < ap.av.alignment.getHeight())
+            {
+                s.addElement(ap.av.alignment.getSequenceAt(i));
+                i++;
+            }
 
-    if (ap.av.getAlignment().getHeight() < 1)
-    {
-      try
-      {
-        af.setClosed(true);
-      }
-      catch (Exception ex)
-      {
-      }
-    }
+            del = ap.av.alignment.removeRedundancy(threshold, s);
+        }
 
-    ap.av.updateConservation();
-    ap.av.updateConsensus();
-    af.updateEditMenuBar();
-    ap.repaint();
-  }
+        // This has to be done before the restoreHistoryItem method of alignFrame will
+        // actually restore these sequences.
+        if (del.size() > 0)
+        {
+            for (int i = 0, j = del.size(); i < j; i++)
+            {
+                SequenceI sq = (SequenceI) del.elementAt(i);
+                sq.deleteChars(0, sq.getLength());
+            }
+        }
 
-  public void undoButton_actionPerformed(ActionEvent e)
-  {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    af.restoreHistoryItem(hi);
+        ap.av.firePropertyChange("alignment", null,
+            ap.av.getAlignment().getSequences());
+        ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
 
-    if (historyList.size() == 0)
-    {
-      undoButton.setEnabled(false);
+        if (ap.av.getAlignment().getHeight() < 1)
+        {
+            try
+            {
+                af.setClosed(true);
+            }
+            catch (Exception ex)
+            {
+            }
+        }
 
-      if (af.historyList.contains(hi))
-      {
-        af.historyList.remove(hi);
+        ap.av.updateConservation();
+        ap.av.updateConsensus();
         af.updateEditMenuBar();
-      }
+        ap.repaint();
     }
-  }
 
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void undoButton_actionPerformed(ActionEvent e)
     {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
+        HistoryItem hi = (HistoryItem) historyList.pop();
+        af.restoreHistoryItem(hi);
+
+        if (historyList.size() == 0)
+        {
+            undoButton.setEnabled(false);
+
+            if (af.historyList.contains(hi))
+            {
+                af.historyList.remove(hi);
+                af.updateEditMenuBar();
+            }
+        }
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void valueField_actionPerformed(ActionEvent e)
     {
-      valueField.setText(slider.getValue() + "");
+        try
+        {
+            int i = Integer.parseInt(valueField.getText());
+            slider.setValue(i);
+        }
+        catch (Exception ex)
+        {
+            valueField.setText(slider.getValue() + "");
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index c3384f9..fbbf269 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -18,620 +18,745 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.math.*;
+
+import jalview.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
+import java.util.*;
+
 import javax.swing.*;
 
-import jalview.datamodel.*;
-import jalview.math.*;
-import jalview.util.*;
 
-public class RotatableCanvas
-    extends JPanel implements MouseListener,
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RotatableCanvas extends JPanel implements MouseListener,
     MouseMotionListener, KeyListener
 //RubberbandListener,
 //SequenceSelectionListener
 {
-  RotatableMatrix idmat = new RotatableMatrix(3, 3);
-  RotatableMatrix objmat = new RotatableMatrix(3, 3);
-  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
-
-  //RubberbandRectangle rubberband;
-  boolean drawAxes = true;
-  int omx = 0;
-  int mx = 0;
-  int omy = 0;
-  int my = 0;
-  Image img;
-  Graphics ig;
-  Dimension prefsize;
-  float[] centre = new float[3];
-  float[] width = new float[3];
-  float[] max = new float[3];
-  float[] min = new float[3];
-  float maxwidth;
-  float scale;
-  int npoint;
-  Vector points;
-  float[][] orig;
-  float[][] axes;
-  int startx;
-  int starty;
-  int lastx;
-  int lasty;
-  int rectx1;
-  int recty1;
-  int rectx2;
-  int recty2;
-  float scalefactor = 1;
-  AlignViewport av;
-
-  //  Controller    controller;
-  public RotatableCanvas(AlignViewport av, Vector points, int npoint)
-  {
-    this.points = points;
-    this.npoint = npoint;
-    this.av = av;
-    ToolTipManager.sharedInstance().registerComponent(this);
-    ToolTipManager.sharedInstance().setInitialDelay(0);
-    ToolTipManager.sharedInstance().setDismissDelay(10000);
-    PaintRefresher.Register(this, av.alignment);
-
-    prefsize = getPreferredSize();
-    orig = new float[npoint][3];
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-
-      for (int j = 0; j < 3; j++)
-      {
-        orig[i][j] = sp.coord[j];
-      }
-    }
-
-    //Initialize the matrices to identity
-    for (int i = 0; i < 3; i++)
+    RotatableMatrix idmat = new RotatableMatrix(3, 3);
+    RotatableMatrix objmat = new RotatableMatrix(3, 3);
+    RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+
+    //RubberbandRectangle rubberband;
+    boolean drawAxes = true;
+    int omx = 0;
+    int mx = 0;
+    int omy = 0;
+    int my = 0;
+    Image img;
+    Graphics ig;
+    Dimension prefsize;
+    float[] centre = new float[3];
+    float[] width = new float[3];
+    float[] max = new float[3];
+    float[] min = new float[3];
+    float maxwidth;
+    float scale;
+    int npoint;
+    Vector points;
+    float[][] orig;
+    float[][] axes;
+    int startx;
+    int starty;
+    int lastx;
+    int lasty;
+    int rectx1;
+    int recty1;
+    int rectx2;
+    int recty2;
+    float scalefactor = 1;
+    AlignViewport av;
+
+    //  Controller    controller;
+    public RotatableCanvas(AlignViewport av, Vector points, int npoint)
     {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
+        this.points = points;
+        this.npoint = npoint;
+        this.av = av;
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
+        PaintRefresher.Register(this, av.alignment);
+
+        prefsize = getPreferredSize();
+        orig = new float[npoint][3];
+
+        for (int i = 0; i < npoint; i++)
         {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
+            SequencePoint sp = (SequencePoint) points.elementAt(i);
+
+            for (int j = 0; j < 3; j++)
+            {
+                orig[i][j] = sp.coord[j];
+            }
         }
-        else
+
+        //Initialize the matrices to identity
+        for (int i = 0; i < 3; i++)
         {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
+            for (int j = 0; j < 3; j++)
+            {
+                if (i != j)
+                {
+                    idmat.addElement(i, j, 0);
+                    objmat.addElement(i, j, 0);
+                    rotmat.addElement(i, j, 0);
+                }
+                else
+                {
+                    idmat.addElement(i, j, 0);
+                    objmat.addElement(i, j, 0);
+                    rotmat.addElement(i, j, 0);
+                }
+            }
         }
-      }
-    }
 
-    axes = new float[3][3];
-    initAxes();
+        axes = new float[3][3];
+        initAxes();
 
-    findCentre();
-    findWidth();
+        findCentre();
+        findWidth();
 
-    scale = findScale();
+        scale = findScale();
 
-    //    System.out.println("Scale factor = " + scale);
-    addMouseListener(this);
-    addKeyListener(this);
+        //    System.out.println("Scale factor = " + scale);
+        addMouseListener(this);
+        addKeyListener(this);
 
-    // if (getParent() != null) {
-    //   getParent().addKeyListener(this);
-    //}
-    addMouseMotionListener(this);
-
-    // Add rubberband
-    //   rubberband  = new RubberbandRectangle(this);
-    //  rubberband.setActive(true);
-    //   rubberband.addListener(this);
-  }
-
-  /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
-     redrawneeded = true;
-     repaint();
-     return true;
-   }
-
-   public void removeNotify() {
-     controller.removeListener(this);
-     super.removeNotify();
-   }*/
-  public void initAxes()
-  {
-    for (int i = 0; i < 3; i++)
+        // if (getParent() != null) {
+        //   getParent().addKeyListener(this);
+        //}
+        addMouseMotionListener(this);
+
+        // Add rubberband
+        //   rubberband  = new RubberbandRectangle(this);
+        //  rubberband.setActive(true);
+        //   rubberband.addListener(this);
+    }
+
+    /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
+       redrawneeded = true;
+       repaint();
+       return true;
+     }
+
+     public void removeNotify() {
+       controller.removeListener(this);
+       super.removeNotify();
+     }*/
+    public void initAxes()
     {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
-        {
-          axes[i][j] = 0;
-        }
-        else
+        for (int i = 0; i < 3; i++)
         {
-          axes[i][j] = 1;
+            for (int j = 0; j < 3; j++)
+            {
+                if (i != j)
+                {
+                    axes[i][j] = 0;
+                }
+                else
+                {
+                    axes[i][j] = 1;
+                }
+            }
         }
-      }
     }
-  }
 
-  public void findWidth()
-  {
-    max = new float[3];
-    min = new float[3];
+    /**
+     * DOCUMENT ME!
+     */
+    public void findWidth()
+    {
+        max = new float[3];
+        min = new float[3];
 
-    max[0] = (float) - 1e30;
-    max[1] = (float) - 1e30;
-    max[2] = (float) - 1e30;
+        max[0] = (float) -1e30;
+        max[1] = (float) -1e30;
+        max[2] = (float) -1e30;
 
-    min[0] = (float) 1e30;
-    min[1] = (float) 1e30;
-    min[2] = (float) 1e30;
+        min[0] = (float) 1e30;
+        min[1] = (float) 1e30;
+        min[2] = (float) 1e30;
 
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < npoint; j++)
-      {
-        SequencePoint sp = (SequencePoint) points.elementAt(j);
+        for (int i = 0; i < 3; i++)
+        {
+            for (int j = 0; j < npoint; j++)
+            {
+                SequencePoint sp = (SequencePoint) points.elementAt(j);
+
+                if (sp.coord[i] >= max[i])
+                {
+                    max[i] = sp.coord[i];
+                }
+
+                if (sp.coord[i] <= min[i])
+                {
+                    min[i] = sp.coord[i];
+                }
+            }
+        }
+
+        //    System.out.println("xmax " + max[0] + " min " + min[0]);
+        //System.out.println("ymax " + max[1] + " min " + min[1]);
+        //System.out.println("zmax " + max[2] + " min " + min[2]);
+        width[0] = Math.abs(max[0] - min[0]);
+        width[1] = Math.abs(max[1] - min[1]);
+        width[2] = Math.abs(max[2] - min[2]);
 
-        if (sp.coord[i] >= max[i])
+        maxwidth = width[0];
+
+        if (width[1] > width[0])
         {
-          max[i] = sp.coord[i];
+            maxwidth = width[1];
         }
 
-        if (sp.coord[i] <= min[i])
+        if (width[2] > width[1])
         {
-          min[i] = sp.coord[i];
+            maxwidth = width[2];
         }
-      }
+
+        //System.out.println("Maxwidth = " + maxwidth);
     }
 
-    //    System.out.println("xmax " + max[0] + " min " + min[0]);
-    //System.out.println("ymax " + max[1] + " min " + min[1]);
-    //System.out.println("zmax " + max[2] + " min " + min[2]);
-    width[0] = Math.abs(max[0] - min[0]);
-    width[1] = Math.abs(max[1] - min[1]);
-    width[2] = Math.abs(max[2] - min[2]);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float findScale()
+    {
+        int dim;
+        int width;
+        int height;
 
-    maxwidth = width[0];
+        if (getWidth() != 0)
+        {
+            width = getWidth();
+            height = getHeight();
+        }
+        else
+        {
+            width = prefsize.width;
+            height = prefsize.height;
+        }
 
-    if (width[1] > width[0])
-    {
-      maxwidth = width[1];
-    }
+        if (width < height)
+        {
+            dim = width;
+        }
+        else
+        {
+            dim = height;
+        }
 
-    if (width[2] > width[1])
-    {
-      maxwidth = width[2];
+        return (float) ((dim * scalefactor) / (2 * maxwidth));
     }
 
-    //System.out.println("Maxwidth = " + maxwidth);
-  }
+    /**
+     * DOCUMENT ME!
+     */
+    public void findCentre()
+    {
+        //Find centre coordinate
+        findWidth();
 
-  public float findScale()
-  {
-    int dim;
-    int width;
-    int height;
+        centre[0] = (max[0] + min[0]) / 2;
+        centre[1] = (max[1] + min[1]) / 2;
+        centre[2] = (max[2] + min[2]) / 2;
 
-    if (getWidth() != 0)
-    {
-      width = getWidth();
-      height = getHeight();
+        //    System.out.println("Centre x " + centre[0]);
+        //System.out.println("Centre y " + centre[1]);
+        //System.out.println("Centre z " + centre[2]);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension getPreferredSize()
     {
-      width = prefsize.width;
-      height = prefsize.height;
+        if (prefsize != null)
+        {
+            return prefsize;
+        }
+        else
+        {
+            return new Dimension(400, 400);
+        }
     }
 
-    if (width < height)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension getMinimumSize()
     {
-      dim = width;
+        return getPreferredSize();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      dim = height;
-    }
+        //Only create the image at the beginning -
+        if ((img == null) || (prefsize.width != getWidth()) ||
+                (prefsize.height != getHeight()))
+        {
+            prefsize.width = getWidth();
+            prefsize.height = getHeight();
 
-    return (float) ( (dim * scalefactor) / (2 * maxwidth));
-  }
+            scale = findScale();
 
-  public void findCentre()
-  {
-    //Find centre coordinate
-    findWidth();
+            //      System.out.println("New scale = " + scale);
+            img = createImage(getWidth(), getHeight());
+            ig = img.getGraphics();
+        }
 
-    centre[0] = (max[0] + min[0]) / 2;
-    centre[1] = (max[1] + min[1]) / 2;
-    centre[2] = (max[2] + min[2]) / 2;
+        drawBackground(ig, Color.black);
+        drawScene(ig);
 
-    //    System.out.println("Centre x " + centre[0]);
-    //System.out.println("Centre y " + centre[1]);
-    //System.out.println("Centre z " + centre[2]);
-  }
+        if (drawAxes == true)
+        {
+            drawAxes(ig);
+        }
+
+        g.drawImage(img, 0, 0, this);
+    }
 
-  public Dimension getPreferredSize()
-  {
-    if (prefsize != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void drawAxes(Graphics g)
     {
-      return prefsize;
+        g.setColor(Color.yellow);
+
+        for (int i = 0; i < 3; i++)
+        {
+            g.drawLine(getWidth() / 2, getHeight() / 2,
+                (int) ((axes[i][0] * scale * max[0]) + (getWidth() / 2)),
+                (int) ((axes[i][1] * scale * max[1]) + (getHeight() / 2)));
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param col DOCUMENT ME!
+     */
+    public void drawBackground(Graphics g, Color col)
     {
-      return new Dimension(400, 400);
+        g.setColor(col);
+        g.fillRect(0, 0, prefsize.width, prefsize.height);
     }
-  }
-
-  public Dimension getMinimumSize()
-  {
-    return getPreferredSize();
-  }
-
-  public void paintComponent(Graphics g)
-  {
-    //Only create the image at the beginning -
-    if ( (img == null) || (prefsize.width != getWidth()) ||
-        (prefsize.height != getHeight()))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void drawScene(Graphics g)
     {
-      prefsize.width = getWidth();
-      prefsize.height = getHeight();
+        boolean darker = false;
 
-      scale = findScale();
+        int halfwidth = getWidth() / 2;
+        int halfheight = getHeight() / 2;
 
-      //      System.out.println("New scale = " + scale);
-      img = createImage(getWidth(), getHeight());
-      ig = img.getGraphics();
-    }
+        for (int i = 0; i < npoint; i++)
+        {
+            SequencePoint sp = (SequencePoint) points.elementAt(i);
+            int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) +
+                halfwidth;
+            int y = (int) ((float) (sp.coord[1] - centre[1]) * scale) +
+                halfheight;
+            float z = sp.coord[1] - centre[2];
+
+            if (sp.sequence.getColor() == Color.black)
+            {
+                g.setColor(Color.white);
+            }
+            else
+            {
+                g.setColor(sp.sequence.getColor());
+            }
+
+            if (av.getSelectionGroup() != null)
+            {
+                if (av.getSelectionGroup().sequences.contains(
+                            ((SequencePoint) points.elementAt(i)).sequence))
+                {
+                    g.setColor(Color.gray);
+                }
+            }
+
+            if (z < 0)
+            {
+                g.setColor(g.getColor().darker());
+            }
+
+            g.fillRect(x - 3, y - 3, 6, 6);
+            g.setColor(Color.red);
+        }
 
-    drawBackground(ig, Color.black);
-    drawScene(ig);
+        //    //Now the rectangle
+        //    if (rectx2 != -1 && recty2 != -1) {
+        //      g.setColor(Color.white);
+        //
+        //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+        //    }
+    }
 
-    if (drawAxes == true)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension minimumsize()
     {
-      drawAxes(ig);
+        return prefsize;
     }
 
-    g.drawImage(img, 0, 0, this);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension preferredsize()
+    {
+        return prefsize;
+    }
 
-  public void drawAxes(Graphics g)
-  {
-    g.setColor(Color.yellow);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void keyTyped(KeyEvent evt)
+    {
+    }
 
-    for (int i = 0; i < 3; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void keyReleased(KeyEvent evt)
     {
-      g.drawLine(getWidth() / 2, getHeight() / 2,
-                 (int) ( (axes[i][0] * scale * max[0]) + (getWidth() / 2)),
-                 (int) ( (axes[i][1] * scale * max[1]) + (getHeight() / 2)));
     }
-  }
 
-  public void drawBackground(Graphics g, Color col)
-  {
-    g.setColor(col);
-    g.fillRect(0, 0, prefsize.width, prefsize.height);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void keyPressed(KeyEvent evt)
+    {
+        requestFocus();
+
+        if (evt.getKeyCode() == KeyEvent.VK_UP)
+        {
+            scalefactor = (float) (scalefactor * 1.1);
+            scale = findScale();
+        }
+        else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+        {
+            scalefactor = (float) (scalefactor * 0.9);
+            scale = findScale();
+        }
+        else if (evt.getKeyChar() == 's')
+        {
+            System.err.println("DEBUG: Rectangle selection"); // log.debug
 
-  public void drawScene(Graphics g)
-  {
-    boolean darker = false;
+            if ((rectx2 != -1) && (recty2 != -1))
+            {
+                rectSelect(rectx1, recty1, rectx2, recty2);
+            }
+        }
 
-    int halfwidth = getWidth() / 2;
-    int halfheight = getHeight() / 2;
+        repaint();
+    }
 
-    for (int i = 0; i < npoint; i++)
+    /**
+     * DOCUMENT ME!
+     */
+    public void printPoints()
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int x = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +
-          halfwidth;
-      int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +
-          halfheight;
-      float z = sp.coord[1] - centre[2];
-
-      if (sp.sequence.getColor() == Color.black)
-      {
-        g.setColor(Color.white);
-      }
-      else
-      {
-        g.setColor(sp.sequence.getColor());
-      }
-
-      if (av.getSelectionGroup() != null)
-      {
-        if (av.getSelectionGroup().sequences.contains(
-            ( (SequencePoint) points.elementAt(i)).sequence))
+        for (int i = 0; i < npoint; i++)
         {
-          g.setColor(Color.gray);
-        }
-      }
+            SequencePoint sp = (SequencePoint) points.elementAt(i);
+            Format.print(System.out, "%5d ", i);
 
-      if (z < 0)
-      {
-        g.setColor(g.getColor().darker());
-      }
+            for (int j = 0; j < 3; j++)
+            {
+                Format.print(System.out, "%13.3f  ", sp.coord[j]);
+            }
 
-      g.fillRect(x - 3, y - 3, 6, 6);
-      g.setColor(Color.red);
+            System.out.println();
+        }
     }
 
-    //    //Now the rectangle
-    //    if (rectx2 != -1 && recty2 != -1) {
-    //      g.setColor(Color.white);
-    //
-    //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
-    //    }
-  }
-
-  public Dimension minimumsize()
-  {
-    return prefsize;
-  }
-
-  public Dimension preferredsize()
-  {
-    return prefsize;
-  }
-
-  public void keyTyped(KeyEvent evt)
-  {
-  }
-
-  public void keyReleased(KeyEvent evt)
-  {
-  }
-
-  public void keyPressed(KeyEvent evt)
-  {
-    requestFocus();
-
-    if (evt.getKeyCode() == KeyEvent.VK_UP)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
     {
-      scalefactor = (float) (scalefactor * 1.1);
-      scale = findScale();
     }
-    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
     {
-      scalefactor = (float) (scalefactor * 0.9);
-      scale = findScale();
     }
-    else if (evt.getKeyChar() == 's')
-    {
-      System.err.println("DEBUG: Rectangle selection"); // log.debug
 
-      if ( (rectx2 != -1) && (recty2 != -1))
-      {
-        rectSelect(rectx1, recty1, rectx2, recty2);
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
+    {
     }
 
-    repaint();
-  }
-
-  public void printPoints()
-  {
-    for (int i = 0; i < npoint; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      Format.print(System.out, "%5d ", i);
-
-      for (int j = 0; j < 3; j++)
-      {
-        Format.print(System.out, "%13.3f  ", sp.coord[j]);
-      }
-
-      System.out.println();
     }
-  }
-
-  public void mouseClicked(MouseEvent evt)
-  {
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {
-  }
 
-  public void mouseExited(MouseEvent evt)
-  {
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
+    {
+        int x = evt.getX();
+        int y = evt.getY();
 
-  public void mousePressed(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int y = evt.getY();
+        mx = x;
+        my = y;
 
-    mx = x;
-    my = y;
+        omx = mx;
+        omy = my;
 
-    omx = mx;
-    omy = my;
+        startx = x;
+        starty = y;
 
-    startx = x;
-    starty = y;
+        rectx1 = x;
+        recty1 = y;
 
-    rectx1 = x;
-    recty1 = y;
+        rectx2 = -1;
+        recty2 = -1;
 
-    rectx2 = -1;
-    recty2 = -1;
+        SequenceI found = findPoint(x, y);
 
-    SequenceI found = findPoint(x, y);
+        if (found != null)
+        {
+            if (av.getSelectionGroup() != null)
+            {
+                av.getSelectionGroup().addOrRemove(found, true);
+                PaintRefresher.Refresh(this, av.alignment);
+            }
+            else
+            {
+                av.setSelectionGroup(new SequenceGroup());
+                av.getSelectionGroup().addOrRemove(found, true);
+                av.getSelectionGroup().setEndRes(av.alignment.getWidth());
+            }
+        }
 
-    if (found != null)
-    {
-      if (av.getSelectionGroup() != null)
-      {
-        av.getSelectionGroup().addOrRemove(found, true);
-        PaintRefresher.Refresh(this, av.alignment);
-      }
-      else
-      {
-        av.setSelectionGroup(new SequenceGroup());
-        av.getSelectionGroup().addOrRemove(found, true);
-        av.getSelectionGroup().setEndRes(av.alignment.getWidth());
-      }
+        repaint();
     }
 
-    repaint();
-  }
-
-  // private void fireSequenceSelectionEvent(Selection sel) {
-  //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
-  //}
-  public void mouseMoved(MouseEvent evt)
-  {
-    SequenceI found = findPoint(evt.getX(), evt.getY());
-
-    if (found != null)
-    {
-      this.setToolTipText(found.getName());
-    }
-    else
+    // private void fireSequenceSelectionEvent(Selection sel) {
+    //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
+    //}
+    public void mouseMoved(MouseEvent evt)
     {
-      this.setToolTipText(null);
-    }
-  }
+        SequenceI found = findPoint(evt.getX(), evt.getY());
 
-  public void mouseDragged(MouseEvent evt)
-  {
-    mx = evt.getX();
-    my = evt.getY();
-
-    //Check if this is a rectangle drawing drag
-    if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
-    {
-      //      rectx2 = evt.getX();
-      //      recty2 = evt.getY();
+        if (found != null)
+        {
+            this.setToolTipText(found.getName());
+        }
+        else
+        {
+            this.setToolTipText(null);
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
     {
-      rotmat.setIdentity();
+        mx = evt.getX();
+        my = evt.getY();
 
-      rotmat.rotate( (float) (my - omy), 'x');
-      rotmat.rotate( (float) (mx - omx), 'y');
+        //Check if this is a rectangle drawing drag
+        if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
+        {
+            //      rectx2 = evt.getX();
+            //      recty2 = evt.getY();
+        }
+        else
+        {
+            rotmat.setIdentity();
 
-      for (int i = 0; i < npoint; i++)
-      {
-        SequencePoint sp = (SequencePoint) points.elementAt(i);
-        sp.coord[0] -= centre[0];
-        sp.coord[1] -= centre[1];
-        sp.coord[2] -= centre[2];
+            rotmat.rotate((float) (my - omy), 'x');
+            rotmat.rotate((float) (mx - omx), 'y');
 
-        //Now apply the rotation matrix
-        sp.coord = rotmat.vectorMultiply(sp.coord);
+            for (int i = 0; i < npoint; i++)
+            {
+                SequencePoint sp = (SequencePoint) points.elementAt(i);
+                sp.coord[0] -= centre[0];
+                sp.coord[1] -= centre[1];
+                sp.coord[2] -= centre[2];
 
-        //Now translate back again
-        sp.coord[0] += centre[0];
-        sp.coord[1] += centre[1];
-        sp.coord[2] += centre[2];
-      }
+                //Now apply the rotation matrix
+                sp.coord = rotmat.vectorMultiply(sp.coord);
 
-      for (int i = 0; i < 3; i++)
-      {
-        axes[i] = rotmat.vectorMultiply(axes[i]);
-      }
+                //Now translate back again
+                sp.coord[0] += centre[0];
+                sp.coord[1] += centre[1];
+                sp.coord[2] += centre[2];
+            }
 
-      omx = mx;
-      omy = my;
+            for (int i = 0; i < 3; i++)
+            {
+                axes[i] = rotmat.vectorMultiply(axes[i]);
+            }
 
-      paint(this.getGraphics());
-    }
-  }
+            omx = mx;
+            omy = my;
 
-  public void rectSelect(int x1, int y1, int x2, int y2)
-  {
-    boolean changedSel = false;
+            paint(this.getGraphics());
+        }
+    }
 
-    for (int i = 0; i < npoint; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param x2 DOCUMENT ME!
+     * @param y2 DOCUMENT ME!
+     */
+    public void rectSelect(int x1, int y1, int x2, int y2)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int tmp1 = (int) ( ( (sp.coord[0] - centre[0]) * scale) +
-                        ( (float) getWidth() / 2.0));
-      int tmp2 = (int) ( ( (sp.coord[1] - centre[1]) * scale) +
-                        ( (float) getHeight() / 2.0));
-
-      if ( (tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
-      {
-        if (av != null)
+        boolean changedSel = false;
+
+        for (int i = 0; i < npoint; i++)
         {
-          if (!av.getSelectionGroup().sequences.contains(sp.sequence))
-          {
-            changedSel = true;
-            av.getSelectionGroup().addSequence(sp.sequence, true);
-          }
+            SequencePoint sp = (SequencePoint) points.elementAt(i);
+            int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale) +
+                ((float) getWidth() / 2.0));
+            int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) +
+                ((float) getHeight() / 2.0));
+
+            if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
+            {
+                if (av != null)
+                {
+                    if (!av.getSelectionGroup().sequences.contains(sp.sequence))
+                    {
+                        changedSel = true;
+                        av.getSelectionGroup().addSequence(sp.sequence, true);
+                    }
+                }
+            }
         }
-      }
-    }
 
-    // if (changedSel) {
-    //    fireSequenceSelectionEvent(av.getSelection());
-    // }
-  }
+        // if (changedSel) {
+        //    fireSequenceSelectionEvent(av.getSelection());
+        // }
+    }
 
-  public SequenceI findPoint(int x, int y)
-  {
-    int halfwidth = getWidth() / 2;
-    int halfheight = getHeight() / 2;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param x DOCUMENT ME!
+     * @param y DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI findPoint(int x, int y)
+    {
+        int halfwidth = getWidth() / 2;
+        int halfheight = getHeight() / 2;
 
-    int found = -1;
+        int found = -1;
 
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +
-          halfwidth;
-      int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +
-          halfheight;
-
-      if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
-      {
-        found = i;
-      }
-    }
+        for (int i = 0; i < npoint; i++)
+        {
+            SequencePoint sp = (SequencePoint) points.elementAt(i);
+            int px = (int) ((float) (sp.coord[0] - centre[0]) * scale) +
+                halfwidth;
+            int py = (int) ((float) (sp.coord[1] - centre[1]) * scale) +
+                halfheight;
+
+            if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+            {
+                found = i;
+            }
+        }
 
-    if (found != -1)
-    {
-      return ( (SequencePoint) points.elementAt(found)).sequence;
-    }
-    else
-    {
-      return null;
+        if (found != -1)
+        {
+            return ((SequencePoint) points.elementAt(found)).sequence;
+        }
+        else
+        {
+            return null;
+        }
     }
-  }
 
-  /*  public boolean handleRubberbandEvent(RubberbandEvent evt) {
-      System.out.println("Rubberband handler called in RotatableCanvas with " +
-                         evt.getBounds());
+    /*  public boolean handleRubberbandEvent(RubberbandEvent evt) {
+        System.out.println("Rubberband handler called in RotatableCanvas with " +
+                           evt.getBounds());
 
-      Rubberband rb = (Rubberband)evt.getSource();
+        Rubberband rb = (Rubberband)evt.getSource();
 
-      // Clear the current selection (instance variable)
-      //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {
-      //   clearSelection();
-      //}
+        // Clear the current selection (instance variable)
+        //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {
+        //   clearSelection();
+        //}
 
-      if (rb.getComponent() == this) {
-        Rectangle bounds = evt.getBounds();
-   rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);
-      }
+        if (rb.getComponent() == this) {
+          Rectangle bounds = evt.getBounds();
+     rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);
+        }
 
-      redrawneeded = true;
-      paint(this.getGraphics());
+        redrawneeded = true;
+        paint(this.getGraphics());
 
-      return true;
-    }*/
+        return true;
+      }*/
 }
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 73a9e6e..486b87a 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -18,227 +18,264 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.*;
+
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-import jalview.datamodel.*;
 
-public class ScalePanel
-    extends JPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScalePanel extends JPanel
 {
-  protected int offy = 4;
-  public int width;
-  protected AlignViewport av;
-  AlignmentPanel ap;
-  boolean stretchingGroup = false;
-
-  int min, max; //used by mouseDragged to see if user
-  // wants to delete columns
-
-  public ScalePanel(AlignViewport av, AlignmentPanel ap)
-  {
-    this.av = av;
-    this.ap = ap;
-
-    addMouseListener(new MouseAdapter()
+    protected int offy = 4;
+
+    /** DOCUMENT ME!! */
+    public int width;
+    protected AlignViewport av;
+    AlignmentPanel ap;
+    boolean stretchingGroup = false;
+    int min; //used by mouseDragged to see if user
+    int max; //used by mouseDragged to see if user
+
+    // wants to delete columns
+    public ScalePanel(AlignViewport av, AlignmentPanel ap)
     {
-      public void mousePressed(MouseEvent evt)
-      {
-        doMousePressed(evt);
-      }
-
-      public void mouseReleased(MouseEvent evt)
-      {
-        doMouseReleased(evt);
-      }
-    });
-    addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseDragged(MouseEvent evt)
-      {
-        doMouseDragged(evt);
-      }
-    });
-  }
-
-  public void doMousePressed(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int res = (x / av.getCharWidth()) + av.getStartRes();
-    SequenceGroup sg = null;
-
-    min=res;
-    max=res;
-
-    if (av.getColumnSelection().contains(res))
-    {
-      av.getColumnSelection().removeElement(res);
-      ap.annotationPanel.removeEditableColumn(res);
+        this.av = av;
+        this.ap = ap;
+
+        addMouseListener(new MouseAdapter()
+            {
+                public void mousePressed(MouseEvent evt)
+                {
+                    doMousePressed(evt);
+                }
+
+                public void mouseReleased(MouseEvent evt)
+                {
+                    doMouseReleased(evt);
+                }
+            });
+        addMouseMotionListener(new MouseMotionAdapter()
+            {
+                public void mouseDragged(MouseEvent evt)
+                {
+                    doMouseDragged(evt);
+                }
+            });
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMousePressed(MouseEvent evt)
     {
-      av.getColumnSelection().addElement(res);
-      sg = new SequenceGroup();
+        int x = evt.getX();
+        int res = (x / av.getCharWidth()) + av.getStartRes();
+        SequenceGroup sg = null;
+
+        min = res;
+        max = res;
+
+        if (av.getColumnSelection().contains(res))
+        {
+            av.getColumnSelection().removeElement(res);
+            ap.annotationPanel.removeEditableColumn(res);
+        }
+        else
+        {
+            av.getColumnSelection().addElement(res);
+            sg = new SequenceGroup();
 
-      for (int i = 0; i < av.alignment.getSequences().size(); i++)
-      {
-        sg.addSequence(av.alignment.getSequenceAt(i), false);
-      }
+            for (int i = 0; i < av.alignment.getSequences().size(); i++)
+            {
+                sg.addSequence(av.alignment.getSequenceAt(i), false);
+            }
 
-      sg.setStartRes(res);
-      sg.setEndRes(res);
+            sg.setStartRes(res);
+            sg.setEndRes(res);
+        }
 
+        av.setSelectionGroup(sg);
+        ap.repaint();
     }
 
-    av.setSelectionGroup(sg);
-    ap.repaint();
-  }
-
-  public void doMouseReleased(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int res = (x / av.getCharWidth()) + av.getStartRes();
-
-    if(av.getColumnSelection()!=null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseReleased(MouseEvent evt)
     {
-      for(int i=0; i<av.getColumnSelection().size(); i++)
-      {
-        ap.annotationPanel.addEditableColumn(
-            av.getColumnSelection().columnAt(i));
-      }
+        int x = evt.getX();
+        int res = (x / av.getCharWidth()) + av.getStartRes();
+
+        if (av.getColumnSelection() != null)
+        {
+            for (int i = 0; i < av.getColumnSelection().size(); i++)
+            {
+                ap.annotationPanel.addEditableColumn(av.getColumnSelection()
+                                                       .columnAt(i));
+            }
+        }
+
+        if (!stretchingGroup)
+        {
+            ap.repaint();
+
+            return;
+        }
+
+        SequenceGroup sg = av.getSelectionGroup();
+
+        if (res > sg.getStartRes())
+        {
+            sg.setEndRes(res);
+        }
+        else if (res < sg.getStartRes())
+        {
+            sg.setStartRes(res);
+        }
+
+        stretchingGroup = false;
+        ap.repaint();
     }
 
-    if (!stretchingGroup)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseDragged(MouseEvent evt)
     {
-      ap.repaint();
-      return;
+        int x = evt.getX();
+        int res = (x / av.getCharWidth()) + av.getStartRes();
+
+        if (res < min)
+        {
+            min = res;
+        }
+
+        if (res > max)
+        {
+            max = res;
+        }
+
+        SequenceGroup sg = av.getSelectionGroup();
+
+        if (sg != null)
+        {
+            stretchingGroup = true;
+
+            if (!av.getColumnSelection().contains(res))
+            {
+                av.getColumnSelection().addElement(res);
+            }
+
+            if (res > sg.getStartRes())
+            {
+                sg.setEndRes(res);
+            }
+            else if (res < sg.getStartRes())
+            {
+                sg.setStartRes(res);
+            }
+
+            for (int i = min; i <= max; i++)
+            {
+                if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
+                {
+                    av.getColumnSelection().removeElement(i);
+                    ap.annotationPanel.removeEditableColumn(res);
+                }
+                else
+                {
+                    av.getColumnSelection().addElement(i);
+                }
+            }
+
+            ap.repaint();
+        }
     }
 
-    SequenceGroup sg = av.getSelectionGroup();
-
-    if (res > sg.getStartRes())
-    {
-      sg.setEndRes(res);
-    }
-    else if (res < sg.getStartRes())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      sg.setStartRes(res);
+        drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
     }
 
-    stretchingGroup = false;
-    ap.repaint();
-  }
-
-  public void doMouseDragged(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int res = (x / av.getCharWidth()) + av.getStartRes();
-
-    if(res < min)
-      min = res;
-    if(res>max)
-      max = res;
-
-    SequenceGroup sg = av.getSelectionGroup();
-
-    if (sg != null)
+    // scalewidth will normally be screenwidth,
+    public void drawScale(Graphics g, int startx, int endx, int width,
+        int height)
     {
-      stretchingGroup = true;
-      if (!av.getColumnSelection().contains(res))
-      {
-        av.getColumnSelection().addElement(res);
-      }
-
-
-      if (res > sg.getStartRes())
-      {
-        sg.setEndRes(res);
-      }
-      else if (res < sg.getStartRes())
-      {
-        sg.setStartRes(res);
-      }
-
-      for(int i=min; i<=max; i++)
-      {
-        if (i < sg.getStartRes() || i > sg.getEndRes())
-         {
-           av.getColumnSelection().removeElement(i);
-           ap.annotationPanel.removeEditableColumn(res);
-         }
-        else
-          av.getColumnSelection().addElement(i);
-      }
-      ap.repaint();
-    }
-  }
-
-  public void paintComponent(Graphics g)
-  {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
-  }
-
-  // scalewidth will normally be screenwidth,
-  public void drawScale(Graphics g, int startx, int endx, int width,
-                        int height)
-  {
-    Graphics2D gg = (Graphics2D) g;
-    gg.setFont(av.getFont());
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
-
-    //Fill in the background
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, width, height);
-    gg.setColor(Color.black);
-
-    //Fill the selected columns
-    ColumnSelection cs = av.getColumnSelection();
-    gg.setColor(new Color(220, 0, 0));
-
-    for (int i = 0; i < cs.size(); i++)
-    {
-      int sel = cs.columnAt(i);
-
-      if ( (sel >= startx) && (sel <= endx))
-      {
-        gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,
+        Graphics2D gg = (Graphics2D) g;
+        gg.setFont(av.getFont());
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
+
+        //Fill in the background
+        gg.setColor(Color.white);
+        gg.fillRect(0, 0, width, height);
+        gg.setColor(Color.black);
+
+        //Fill the selected columns
+        ColumnSelection cs = av.getColumnSelection();
+        gg.setColor(new Color(220, 0, 0));
+
+        for (int i = 0; i < cs.size(); i++)
+        {
+            int sel = cs.columnAt(i);
+
+            if ((sel >= startx) && (sel <= endx))
+            {
+                gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
                     getHeight());
-      }
-    }
-
-    // Draw the scale numbers
-    gg.setColor(Color.black);
-
-    int scalestartx = (startx / 10) * 10;
-
-    FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = av.charHeight - fm.getDescent();
-
-    if ( (scalestartx % 10) == 0)
-    {
-      scalestartx += 5;
-    }
-
-    for (int i = scalestartx; i < endx; i += 5)
-    {
-      if ( (i % 10) == 0)
-      {
-        gg.drawString(String.valueOf(i),
-                      (i - startx - 1) * av.charWidth, y);
-        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
-                            (av.charWidth / 2)), y + 2,
-                    (int) ( ( (i - startx - 1) * av.charWidth) +
-                           (av.charWidth / 2)), y + (fm.getDescent() * 2));
-      }
-      else
-      {
-        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
-                            (av.charWidth / 2)), y + fm.getDescent(),
-                    (int) ( ( (i - startx - 1) * av.charWidth) +
-                           (av.charWidth / 2)), y + (fm.getDescent() * 2));
-      }
+            }
+        }
+
+        // Draw the scale numbers
+        gg.setColor(Color.black);
+
+        int scalestartx = (startx / 10) * 10;
+
+        FontMetrics fm = gg.getFontMetrics(av.getFont());
+        int y = av.charHeight - fm.getDescent();
+
+        if ((scalestartx % 10) == 0)
+        {
+            scalestartx += 5;
+        }
+
+        for (int i = scalestartx; i < endx; i += 5)
+        {
+            if ((i % 10) == 0)
+            {
+                gg.drawString(String.valueOf(i),
+                    (i - startx - 1) * av.charWidth, y);
+                gg.drawLine((int) (((i - startx - 1) * av.charWidth) +
+                    (av.charWidth / 2)), y + 2,
+                    (int) (((i - startx - 1) * av.charWidth) +
+                    (av.charWidth / 2)), y + (fm.getDescent() * 2));
+            }
+            else
+            {
+                gg.drawLine((int) (((i - startx - 1) * av.charWidth) +
+                    (av.charWidth / 2)), y + fm.getDescent(),
+                    (int) (((i - startx - 1) * av.charWidth) +
+                    (av.charWidth / 2)), y + (fm.getDescent() * 2));
+            }
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c442465..841f929 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -18,574 +18,641 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.*;
+
 import java.awt.*;
 import java.awt.image.*;
+
 import javax.swing.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
 
-public class SeqCanvas
-    extends JComponent
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqCanvas extends JComponent
 {
-  FeatureRenderer fr;
-  SequenceRenderer sr;
-  BufferedImage img;
-  Graphics2D gg;
-  int imgWidth;
-  int imgHeight;
-  AlignViewport av;
-  boolean showScores = false;
-  boolean displaySearch = false;
-  int[] searchResults = null;
-  int chunkHeight;
-  int chunkWidth;
-  boolean fastPaint = false;
-  int LABEL_WEST;
-  int LABEL_EAST;
-
-
-  public SeqCanvas(AlignViewport av)
-  {
-    this.av = av;
-    fr = new FeatureRenderer(av);
-    sr = new SequenceRenderer(av);
-    setLayout(new BorderLayout());
-    PaintRefresher.Register(this, av.alignment);
-    setBackground(Color.white);
-  }
-
-  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
-  {
-    int scalestartx = startx - (startx % 10) + 10;
-
-    g.setColor(Color.black);
-
-    // NORTH SCALE
-    for (int i = scalestartx; i < endx; i += 10)
+    FeatureRenderer fr;
+    SequenceRenderer sr;
+    BufferedImage img;
+    Graphics2D gg;
+    int imgWidth;
+    int imgHeight;
+    AlignViewport av;
+    boolean showScores = false;
+    boolean displaySearch = false;
+    int[] searchResults = null;
+    int chunkHeight;
+    int chunkWidth;
+    boolean fastPaint = false;
+    int LABEL_WEST;
+    int LABEL_EAST;
+
+    /**
+     * Creates a new SeqCanvas object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public SeqCanvas(AlignViewport av)
     {
-      String string = String.valueOf(i);
-      g.drawString(string, (i - startx - 1) * av.charWidth,
-                   ypos - (av.charHeight / 2));
-
-      g.drawLine( ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2),
-                 (ypos + 2) - (av.charHeight / 2),
-                 ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
-                 2);
+        this.av = av;
+        fr = new FeatureRenderer(av);
+        sr = new SequenceRenderer(av);
+        setLayout(new BorderLayout());
+        PaintRefresher.Register(this, av.alignment);
+        setBackground(Color.white);
     }
-  }
 
-  void drawWestScale(Graphics g, int startx, int endx, int ypos)
-  {
-    FontMetrics fm = getFontMetrics(av.getFont());
-    ypos += av.charHeight;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param startx DOCUMENT ME!
+     * @param endx DOCUMENT ME!
+     * @param ypos DOCUMENT ME!
+     */
+    void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+    {
+        int scalestartx = startx - (startx % 10) + 10;
+
+        g.setColor(Color.black);
 
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+        // NORTH SCALE
+        for (int i = scalestartx; i < endx; i += 10)
+        {
+            String string = String.valueOf(i);
+            g.drawString(string, (i - startx - 1) * av.charWidth,
+                ypos - (av.charHeight / 2));
+
+            g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+                (ypos + 2) - (av.charHeight / 2),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
+                2);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param startx DOCUMENT ME!
+     * @param endx DOCUMENT ME!
+     * @param ypos DOCUMENT ME!
+     */
+    void drawWestScale(Graphics g, int startx, int endx, int ypos)
     {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = startx;
-      int value = -1;
+        FontMetrics fm = getFontMetrics(av.getFont());
+        ypos += av.charHeight;
 
-      while (index < endx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        // EAST SCALE
+        for (int i = 0; i < av.alignment.getHeight(); i++)
         {
-          index++;
+            SequenceI seq = av.alignment.getSequenceAt(i);
+            int index = startx;
+            int value = -1;
 
-          continue;
-        }
+            while (index < endx)
+            {
+                if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+                {
+                    index++;
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+                    continue;
+                }
 
-        break;
-      }
+                value = av.alignment.getSequenceAt(i).findPosition(index);
 
-      if (value != -1)
-      {
-        int x = LABEL_WEST - fm.stringWidth(value + "");
-        g.drawString(value + "", x,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-      }
-    }
-  }
+                break;
+            }
 
-  void drawEastScale(Graphics g, int startx, int endx, int ypos)
-  {
-    ypos += av.charHeight;
+            if (value != -1)
+            {
+                int x = LABEL_WEST - fm.stringWidth(value + "");
+                g.drawString(value + "", x,
+                    (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+            }
+        }
+    }
 
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param startx DOCUMENT ME!
+     * @param endx DOCUMENT ME!
+     * @param ypos DOCUMENT ME!
+     */
+    void drawEastScale(Graphics g, int startx, int endx, int ypos)
     {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = endx;
-      int value = -1;
+        ypos += av.charHeight;
 
-      while (index > startx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        // EAST SCALE
+        for (int i = 0; i < av.alignment.getHeight(); i++)
         {
-          index--;
+            SequenceI seq = av.alignment.getSequenceAt(i);
+            int index = endx;
+            int value = -1;
 
-          continue;
-        }
+            while (index > startx)
+            {
+                if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+                {
+                    index--;
+
+                    continue;
+                }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+                value = av.alignment.getSequenceAt(i).findPosition(index);
 
-        break;
-      }
+                break;
+            }
 
-      if (value != -1)
-      {
-        g.drawString(value + "", 0,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-      }
+            if (value != -1)
+            {
+                g.drawString(value + "", 0,
+                    (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+            }
+        }
     }
-  }
 
-  public void fastPaint(int horizontal, int vertical)
-  {
-    if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param horizontal DOCUMENT ME!
+     * @param vertical DOCUMENT ME!
+     */
+    public void fastPaint(int horizontal, int vertical)
     {
-      return;
-    }
+        if (((horizontal == 0) && (vertical == 0)) || (gg == null))
+        {
+            return;
+        }
 
-    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
-                -vertical * av.charHeight);
+        gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
+            -vertical * av.charHeight);
 
-    int sr = av.startRes;
-    int er = av.endRes;
-    int ss = av.startSeq;
-    int es = av.endSeq;
-    int transX = 0;
-    int transY = 0;
+        int sr = av.startRes;
+        int er = av.endRes;
+        int ss = av.startSeq;
+        int es = av.endSeq;
+        int transX = 0;
+        int transY = 0;
 
-    if (horizontal > 0) // scrollbar pulled right, image to the left
-    {
-      transX = (er - sr - horizontal) * av.charWidth;
-      sr = er - horizontal;
-    }
-    else if (horizontal < 0)
-    {
-      er = sr - horizontal;
-    }
-    else if (vertical > 0) // scroll down
-    {
-      ss = es - vertical;
-
-      if (ss < av.startSeq)
-      { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
-      }
-      else
-      {
-        transY = imgHeight - (vertical * av.charHeight);
-      }
-    }
-    else if (vertical < 0)
-    {
-      es = ss - vertical;
+        if (horizontal > 0) // scrollbar pulled right, image to the left
+        {
+            transX = (er - sr - horizontal) * av.charWidth;
+            sr = er - horizontal;
+        }
+        else if (horizontal < 0)
+        {
+            er = sr - horizontal;
+        }
+        else if (vertical > 0) // scroll down
+        {
+            ss = es - vertical;
 
-      if (es > av.endSeq)
-      {
-        es = av.endSeq;
-      }
-    }
+            if (ss < av.startSeq)
+            { // ie scrolling too fast, more than a page at a time
+                ss = av.startSeq;
+            }
+            else
+            {
+                transY = imgHeight - (vertical * av.charHeight);
+            }
+        }
+        else if (vertical < 0)
+        {
+            es = ss - vertical;
 
-    gg.translate(transX, transY);
-
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, (er - sr + 1) * av.charWidth,
-                (es - ss) * av.charHeight);
-    drawPanel(gg, sr, er, ss, es, sr, ss, 0);
-    gg.translate( -transX, -transY);
-
-    fastPaint = true;
-    repaint();
-  }
-
-  /**
-   * Definitions of startx and endx (hopefully):
-   * SMJS This is what I'm working towards!
-   *   startx is the first residue (starting at 0) to display.
-   *   endx   is the last residue to display (starting at 0).
-   *   starty is the first sequence to display (starting at 0).
-   *   endy   is the last sequence to display (starting at 0).
-   * NOTE 1: The av limits are set in setFont in this class and
-   * in the adjustment listener in SeqPanel when the scrollbars move.
-   */
-
-
-  // Set this to false to force a full panel paint
-  public void paintComponent(Graphics g)
-  {
-    if (img!=null
-        && (fastPaint  ||  getWidth() !=  g.getClipBounds().width
-            ||  getHeight() != g.getClipBounds().height))
-    {
-      g.drawImage(img, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
+            if (es > av.endSeq)
+            {
+                es = av.endSeq;
+            }
+        }
 
-    // this draws the whole of the alignment
-    imgWidth = getWidth();
-    imgHeight = getHeight();
+        gg.translate(transX, transY);
 
-    imgWidth -= (imgWidth % av.charWidth);
-    imgHeight -= (imgHeight % av.charHeight);
+        gg.setColor(Color.white);
+        gg.fillRect(0, 0, (er - sr + 1) * av.charWidth,
+            (es - ss) * av.charHeight);
+        drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+        gg.translate(-transX, -transY);
 
-    if ( (imgWidth < 1) || (imgHeight < 1))
-    {
-      return;
+        fastPaint = true;
+        repaint();
     }
 
-    img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
-    gg = (Graphics2D) img.getGraphics();
-    gg.setFont(av.getFont());
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
+    /**
+     * Definitions of startx and endx (hopefully):
+     * SMJS This is what I'm working towards!
+     *   startx is the first residue (starting at 0) to display.
+     *   endx   is the last residue to display (starting at 0).
+     *   starty is the first sequence to display (starting at 0).
+     *   endy   is the last sequence to display (starting at 0).
+     * NOTE 1: The av limits are set in setFont in this class and
+     * in the adjustment listener in SeqPanel when the scrollbars move.
+     */
+
+    // Set this to false to force a full panel paint
+    public void paintComponent(Graphics g)
+    {
+        if ((img != null) &&
+                (fastPaint || (getWidth() != g.getClipBounds().width) ||
+                (getHeight() != g.getClipBounds().height)))
+        {
+            g.drawImage(img, 0, 0, this);
+            fastPaint = false;
 
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, imgWidth, imgHeight);
+            return;
+        }
 
-    chunkWidth = getWrappedCanvasWidth(getWidth());
-    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+        // this draws the whole of the alignment
+        imgWidth = getWidth();
+        imgHeight = getHeight();
 
-    av.setChunkHeight(chunkHeight);
-    av.setChunkWidth(chunkWidth);
+        imgWidth -= (imgWidth % av.charWidth);
+        imgHeight -= (imgHeight % av.charHeight);
 
-    if (av.getWrapAlignment())
-    {
-      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
-    }
-    else
-    {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
-                av.startRes, av.startSeq, 0);
-    }
+        if ((imgWidth < 1) || (imgHeight < 1))
+        {
+            return;
+        }
 
-    g.drawImage(img, 0, 0, this);
-  }
+        img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
+        gg = (Graphics2D) img.getGraphics();
+        gg.setFont(av.getFont());
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
 
-  public int getWrappedCanvasWidth(int cwidth)
-  {
-    FontMetrics fm = getFontMetrics(av.getFont());
+        gg.setColor(Color.white);
+        gg.fillRect(0, 0, imgWidth, imgHeight);
 
-    LABEL_EAST = 0;
-    LABEL_WEST = 0;
+        chunkWidth = getWrappedCanvasWidth(getWidth());
+        chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+        av.setChunkHeight(chunkHeight);
+        av.setChunkWidth(chunkWidth);
+
+        if (av.getWrapAlignment())
+        {
+            drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+        }
+        else
+        {
+            drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
+                av.startRes, av.startSeq, 0);
+        }
+
+        g.drawImage(img, 0, 0, this);
     }
 
-    if (av.scaleLeftWrapped)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cwidth DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWrappedCanvasWidth(int cwidth)
     {
-      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
-    }
+        FontMetrics fm = getFontMetrics(av.getFont());
 
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-  }
+        LABEL_EAST = 0;
+        LABEL_WEST = 0;
 
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
-                               int startRes)
-  {
-    AlignmentI al = av.getAlignment();
+        if (av.scaleRightWrapped)
+        {
+            LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+        }
 
-    FontMetrics fm = getFontMetrics(av.getFont());
+        if (av.scaleLeftWrapped)
+        {
+            LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+        }
 
-    int LABEL_EAST = 0;
+        return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    }
 
-    if (av.scaleRightWrapped)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param canvasWidth DOCUMENT ME!
+     * @param canvasHeight DOCUMENT ME!
+     * @param startRes DOCUMENT ME!
+     */
+    public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
+        int startRes)
     {
-      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
-    }
+        AlignmentI al = av.getAlignment();
 
-    int LABEL_WEST = 0;
+        FontMetrics fm = getFontMetrics(av.getFont());
 
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
-    }
+        int LABEL_EAST = 0;
 
-    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+        if (av.scaleRightWrapped)
+        {
+            LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+        }
 
-    av.endRes = av.startRes + cWidth;
+        int LABEL_WEST = 0;
 
-    int endx = (startRes + cWidth) - 1;
-    int ypos = 2 * av.charHeight;
+        if (av.scaleLeftWrapped)
+        {
+            LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+        }
 
-    while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
-    {
-      g.setColor(Color.black);
-
-      if (av.scaleLeftWrapped)
-      {
-        drawWestScale(g, startRes, endx, ypos);
-      }
-
-      if (av.scaleRightWrapped)
-      {
-        g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);
-        drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);
-      }
-
-      g.translate(LABEL_WEST, 0);
-
-      if (av.scaleAboveWrapped)
-      {
-        drawNorthScale(g, startRes, endx, ypos);
-      }
-
-      // When printing we have an extra clipped region,
-      // the Printable page which we need to account for here
-      Shape clip = g.getClip();
-
-      if (clip == null)
-      {
-        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
-      }
-      else
-      {
-        g.setClip(0, (int) clip.getBounds().getY(),
-                  cWidth * av.charWidth, (int) clip.getBounds().getHeight());
-      }
-
-      drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
-      g.setClip(clip);
-      g.translate( -LABEL_WEST, 0);
-
-      ypos += cHeight;
-      startRes += cWidth;
-      endx = (startRes + cWidth) - 1;
-
-      if (endx > al.getWidth())
-      {
-        endx = al.getWidth();
-      }
-    }
-  }
+        int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+        int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-  synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
-                                     int y2, int startx, int starty, int offset)
-  {
-    Graphics2D g = (Graphics2D) g1;
-    g.setFont(av.getFont());
-    sr.renderGaps(av.renderGaps);
+        av.endRes = av.startRes + cWidth;
 
-    SequenceI nextSeq;
+        int endx = (startRes + cWidth) - 1;
+        int ypos = 2 * av.charHeight;
 
-    /// First draw the sequences
-    /////////////////////////////
-    for (int i = y1; i < y2; i++)
-    {
-      nextSeq = av.alignment.getSequenceAt(i);
-
-      sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
-                      x1, x2, (x1 - startx) * av.charWidth,
-                      offset +
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                      av.charWidth, av.charHeight);
-
-      if (av.showSequenceFeatures)
-      {
-        fr.drawSequence(g, nextSeq,
-                        av.alignment.findAllGroups(nextSeq), x1, x2,
-                        (x1 - startx) * av.charWidth,
-                        offset +
-                        AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                        av.charWidth, av.charHeight);
-      }
-    }
+        while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+        {
+            g.setColor(Color.black);
 
-    //
-    /////////////////////////////////////
-    // Now outline any areas if necessary
-    /////////////////////////////////////
-    SequenceGroup group = av.getSelectionGroup();
-    java.util.Vector groups = av.alignment.getGroups();
+            if (av.scaleLeftWrapped)
+            {
+                drawWestScale(g, startRes, endx, ypos);
+            }
 
-    int sx = -1;
-    int sy = -1;
-    int ex = -1;
-    int groupIndex = -1;
+            if (av.scaleRightWrapped)
+            {
+                g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);
+                drawEastScale(g, startRes, endx, ypos);
+                g.translate(-(canvasWidth - LABEL_EAST + av.charWidth), 0);
+            }
 
-    if ( (group == null) && (groups.size() > 0))
-    {
-      group = (SequenceGroup) groups.elementAt(0);
-      groupIndex = 0;
-    }
+            g.translate(LABEL_WEST, 0);
 
-    if (group != null)
-    {
-      do
-      {
-        int oldY = -1;
-        int i = 0;
-        boolean inGroup = false;
-        int top = -1;
-        int bottom = -1;
-
-        for (i = y1; i < y2; i++)
-        {
-          sx = (group.getStartRes() - startx) * av.charWidth;
-          sy = offset +
-              AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
-                av.charWidth) -
-              1;
-
-          if ( (sx < getWidth()) && (ex > 0) &&
-              group.sequences.contains(av.alignment.getSequenceAt(
-                  i)))
-          {
-            if ( (bottom == -1) &&
-                !group.sequences.contains(
-                    av.alignment.getSequenceAt(i + 1)))
+            if (av.scaleAboveWrapped)
             {
-              bottom = sy + av.charHeight;
+                drawNorthScale(g, startRes, endx, ypos);
             }
 
-            if (!inGroup)
+            // When printing we have an extra clipped region,
+            // the Printable page which we need to account for here
+            Shape clip = g.getClip();
+
+            if (clip == null)
             {
-              if ( ( (top == -1) && (i == 0)) ||
-                  !group.sequences.contains(
-                      av.alignment.getSequenceAt(i - 1)))
-              {
-                top = sy;
-              }
-
-              oldY = sy;
-              inGroup = true;
-
-              if (group == av.getSelectionGroup())
-              {
-                g.setStroke(new BasicStroke(1,
-                                            BasicStroke.CAP_BUTT,
-                                            BasicStroke.JOIN_ROUND, 3f,
-                                            new float[]
-                                            {5f, 3f}, 0f));
-                g.setColor(Color.RED);
-              }
-              else
-              {
-                g.setStroke(new BasicStroke());
-                g.setColor(group.getOutlineColour());
-              }
+                g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
             }
-          }
-          else
-          {
-            if (inGroup)
+            else
             {
-              g.drawLine(sx, oldY, sx, sy);
-              g.drawLine(sx + ex, oldY, sx + ex, sy);
-
-              if (top != -1)
-              {
-                g.drawLine(sx, top, sx + ex, top);
-                top = -1;
-              }
-
-              if (bottom != -1)
-              {
-                g.drawLine(sx, bottom, sx + ex, bottom);
-                bottom = -1;
-              }
-
-              inGroup = false;
+                g.setClip(0, (int) clip.getBounds().getY(),
+                    cWidth * av.charWidth, (int) clip.getBounds().getHeight());
+            }
+
+            drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+            g.setClip(clip);
+            g.translate(-LABEL_WEST, 0);
+
+            ypos += cHeight;
+            startRes += cWidth;
+            endx = (startRes + cWidth) - 1;
+
+            if (endx > al.getWidth())
+            {
+                endx = al.getWidth();
             }
-          }
         }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g1 DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param x2 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param y2 DOCUMENT ME!
+     * @param startx DOCUMENT ME!
+     * @param starty DOCUMENT ME!
+     * @param offset DOCUMENT ME!
+     */
+    synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
+        int y2, int startx, int starty, int offset)
+    {
+        Graphics2D g = (Graphics2D) g1;
+        g.setFont(av.getFont());
+        sr.renderGaps(av.renderGaps);
 
-        if (inGroup)
+        SequenceI nextSeq;
+
+        /// First draw the sequences
+        /////////////////////////////
+        for (int i = y1; i < y2; i++)
         {
-          if (top != -1)
-          {
-            g.drawLine(sx, top, sx + ex, top);
-            top = -1;
-          }
-
-          if (bottom != -1)
-          {
-            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
-            bottom = -1;
-          }
-
-          sy = offset +
-              AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          g.drawLine(sx, oldY, sx, sy);
-          g.drawLine(sx + ex, oldY, sx + ex, sy);
-          inGroup = false;
+            nextSeq = av.alignment.getSequenceAt(i);
+
+            sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
+                x1, x2, (x1 - startx) * av.charWidth,
+                offset + ((i - starty) * av.charHeight), av.charWidth,
+                av.charHeight);
+
+            if (av.showSequenceFeatures)
+            {
+                fr.drawSequence(g, nextSeq,
+                    av.alignment.findAllGroups(nextSeq), x1, x2,
+                    (x1 - startx) * av.charWidth,
+                    offset + ((i - starty) * av.charHeight), av.charWidth,
+                    av.charHeight);
+            }
         }
 
-        groupIndex++;
+        //
+        /////////////////////////////////////
+        // Now outline any areas if necessary
+        /////////////////////////////////////
+        SequenceGroup group = av.getSelectionGroup();
+        java.util.Vector groups = av.alignment.getGroups();
+
+        int sx = -1;
+        int sy = -1;
+        int ex = -1;
+        int groupIndex = -1;
 
-        if (groupIndex >= groups.size())
+        if ((group == null) && (groups.size() > 0))
         {
-          break;
+            group = (SequenceGroup) groups.elementAt(0);
+            groupIndex = 0;
         }
 
-        group = (SequenceGroup) groups.elementAt(groupIndex);
-      }
-      while (groupIndex < groups.size());
-    }
 
-    /// Highlight search Results once all sequences have been drawn
-    //////////////////////////////////////////////////////////
-    if (displaySearch)
-    {
-      for (int r = 0; r < searchResults.length; r += 3)
-      {
-        int searchSeq = searchResults[r];
+        if (group != null)
+        {
+            do
+            {
+                int oldY = -1;
+                int i = 0;
+                boolean inGroup = false;
+                int top = -1;
+                int bottom = -1;
+
+                for (i = y1; i < y2; i++)
+                {
+                    sx = (group.getStartRes() - startx) * av.charWidth;
+                    sy = offset + ((i - starty) * av.charHeight);
+                    ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
+                        1;
+
+
+                    if ((sx < (x2-x1)*av.charWidth) &&
+                            group.sequences.contains(av.alignment.getSequenceAt(
+                                    i)))
+                    {
+                        if ((bottom == -1) &&
+                                !group.sequences.contains(
+                                    av.alignment.getSequenceAt(i + 1)))
+                        {
+                            bottom = sy + av.charHeight;
+                        }
+
+                        if (!inGroup)
+                        {
+                            if (((top == -1) && (i == 0)) ||
+                                    !group.sequences.contains(
+                                        av.alignment.getSequenceAt(i - 1)))
+                            {
+                                top = sy;
+                            }
+
+                            oldY = sy;
+                            inGroup = true;
+
+                            if (group == av.getSelectionGroup())
+                            {
+                                g.setStroke(new BasicStroke(1,
+                                        BasicStroke.CAP_BUTT,
+                                        BasicStroke.JOIN_ROUND, 3f,
+                                        new float[] { 5f, 3f }, 0f));
+                                g.setColor(Color.RED);
+                            }
+                            else
+                            {
+                                g.setStroke(new BasicStroke());
+                                g.setColor(group.getOutlineColour());
+                            }
+                        }
+                    }
+                    else
+                    {
+                        if (inGroup)
+                        {
+                            g.drawLine(sx, oldY, sx, sy);
+                            g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+                            if (top != -1)
+                            {
+                                g.drawLine(sx, top, sx + ex, top);
+                                top = -1;
+                            }
+
+                            if (bottom != -1)
+                            {
+                                g.drawLine(sx, bottom, sx + ex, bottom);
+                                bottom = -1;
+                            }
+
+                            inGroup = false;
+                        }
+                    }
+                }
+
+
+                if (inGroup)
+                {
+                    if (top != -1)
+                    {
+                        g.drawLine(sx, top, sx + ex, top);
+                        top = -1;
+                    }
+
+                    if (bottom != -1)
+                    {
+                        g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+                        bottom = -1;
+                    }
+
+                    sy = offset + ((i - starty) * av.charHeight);
+                    g.drawLine(sx, oldY, sx, sy);
+                    g.drawLine(sx + ex, oldY, sx + ex, sy);
+                    inGroup = false;
+                }
+
+                groupIndex++;
+
+                if (groupIndex >= groups.size())
+                {
+                    break;
+                }
+
+                group = (SequenceGroup) groups.elementAt(groupIndex);
+            }
+            while (groupIndex < groups.size());
+        }
 
-        if ( (searchSeq >= y1) && (searchSeq < y2))
+        /// Highlight search Results once all sequences have been drawn
+        //////////////////////////////////////////////////////////
+        if (displaySearch)
         {
-          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
+            for (int r = 0; r < searchResults.length; r += 3)
+            {
+                int searchSeq = searchResults[r];
+
+                if ((searchSeq >= y1) && (searchSeq < y2))
+                {
+                    SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
 
-          int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
-          int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
+                    int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
+                    int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
 
-          SequenceRenderer ssr = (SequenceRenderer) sr;
+                    SequenceRenderer ssr = (SequenceRenderer) sr;
 
-          if (searchStart < x1)
-          {
-            searchStart = x1;
-          }
+                    if (searchStart < x1)
+                    {
+                        searchStart = x1;
+                    }
 
-          if (searchEnd > x2)
-          {
-            searchEnd = x2;
-          }
+                    if (searchEnd > x2)
+                    {
+                        searchEnd = x2;
+                    }
 
-          ssr.drawHighlightedText(seq, searchStart, searchEnd,
-                                  (searchStart - startx) * av.charWidth,
-                                  offset +
-                                  AlignmentUtil.getPixelHeight(starty,
-              searchSeq,
-              av.charHeight), av.charWidth, av.charHeight);
+                    ssr.drawHighlightedText(seq, searchStart, searchEnd,
+                        (searchStart - startx) * av.charWidth,
+                        offset + ((searchSeq - starty) * av.charHeight),
+                        av.charWidth, av.charHeight);
+                }
+            }
         }
-      }
     }
-  }
 
-  public void highlightSearchResults(int[] results)
-  {
-    // results are in the order sequence, startRes, endRes
-    if (results == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param results DOCUMENT ME!
+     */
+    public void highlightSearchResults(int[] results)
     {
-      displaySearch = false;
-    }
-    else
-    {
-      displaySearch = true;
-    }
+        // results are in the order sequence, startRes, endRes
+        if (results == null)
+        {
+            displaySearch = false;
+        }
+        else
+        {
+            displaySearch = true;
+        }
 
-    searchResults = results;
+        searchResults = results;
 
-    repaint();
-  }
+        repaint();
+    }
 }
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 2718ddb..db120e1 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -18,827 +18,912 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
+import java.util.*;
+
 import javax.swing.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
 
-public class SeqPanel
-    extends JPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqPanel extends JPanel
 {
-  public SeqCanvas seqCanvas;
-  public AlignmentPanel ap;
-  protected int lastres;
-  protected int startseq;
-  int startEdit = -1;
-  int endEdit = -1;
-  protected AlignViewport av;
-
-  // if character is inserted or deleted, we will need to recalculate the conservation
-  int seqEditOccurred = -1;
-  ScrollThread scrollThread = null;
-  boolean mouseDragging = false;
-  boolean editingSeqs = false;
-  boolean groupEditing = false;
-
-  //////////////////////////////////////////
-  /////Everything below this is for defining the boundary of the rubberband
-  //////////////////////////////////////////
-  int oldSeq = -1;
-  boolean changeEndSeq = false;
-  boolean changeStartSeq = false;
-  boolean changeEndRes = false;
-  boolean changeStartRes = false;
-  SequenceGroup stretchGroup = null;
-  boolean remove = false;
-
-  public SeqPanel(AlignViewport avp, AlignmentPanel p)
-  {
-    ToolTipManager.sharedInstance().registerComponent(this);
-    ToolTipManager.sharedInstance().setInitialDelay(0);
-    ToolTipManager.sharedInstance().setDismissDelay(10000);
-    this.av = avp;
-    setBackground(Color.white);
-
-    seqCanvas = new SeqCanvas(avp);
-    setLayout(new BorderLayout());
-    add(seqCanvas, BorderLayout.CENTER);
-
-    ap = p;
-
-    addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseMoved(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
+    /** DOCUMENT ME!! */
+    public SeqCanvas seqCanvas;
+
+    /** DOCUMENT ME!! */
+    public AlignmentPanel ap;
+    protected int lastres;
+    protected int startseq;
+    int startEdit = -1;
+    int endEdit = -1;
+    protected AlignViewport av;
+
+    // if character is inserted or deleted, we will need to recalculate the conservation
+    int seqEditOccurred = -1;
+    ScrollThread scrollThread = null;
+    boolean mouseDragging = false;
+    boolean editingSeqs = false;
+    boolean groupEditing = false;
+
+    //////////////////////////////////////////
+    /////Everything below this is for defining the boundary of the rubberband
+    //////////////////////////////////////////
+    int oldSeq = -1;
+    boolean changeEndSeq = false;
+    boolean changeStartSeq = false;
+    boolean changeEndRes = false;
+    boolean changeStartRes = false;
+    SequenceGroup stretchGroup = null;
+    boolean remove = false;
+
+    /**
+     * Creates a new SeqPanel object.
+     *
+     * @param avp DOCUMENT ME!
+     * @param p DOCUMENT ME!
+     */
+    public SeqPanel(AlignViewport avp, AlignmentPanel p)
+    {
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
+        this.av = avp;
+        setBackground(Color.white);
+
+        seqCanvas = new SeqCanvas(avp);
+        setLayout(new BorderLayout());
+        add(seqCanvas, BorderLayout.CENTER);
+
+        ap = p;
+
+        addMouseMotionListener(new MouseMotionAdapter()
+            {
+                public void mouseMoved(MouseEvent evt)
+                {
+                    if (av.getWrapAlignment())
+                    {
+                        return;
+                    }
+
+                    doMouseMoved(evt);
+                }
+
+                public void mouseDragged(MouseEvent evt)
+                {
+                    if (av.getWrapAlignment())
+                    {
+                        return;
+                    }
+
+                    if (editingSeqs)
+                    {
+                        doMouseDragged(evt);
+                    }
+                    else
+                    {
+                        doMouseDraggedDefineMode(evt);
+                    }
+                }
+            });
+
+        addMouseListener(new MouseAdapter()
+            {
+                public void mouseReleased(MouseEvent evt)
+                {
+                    if (av.getWrapAlignment())
+                    {
+                        return;
+                    }
+
+                    if (editingSeqs)
+                    {
+                        doMouseReleased(evt);
+                    }
+                    else
+                    {
+                        doMouseReleasedDefineMode(evt);
+                    }
+                }
+
+                public void mousePressed(MouseEvent evt)
+                {
+                    if (av.getWrapAlignment())
+                    {
+                        return;
+                    }
+
+                    if (evt.isShiftDown() || evt.isAltDown() ||
+                            evt.isControlDown())
+                    {
+                        if (evt.isAltDown() || evt.isControlDown())
+                        {
+                            groupEditing = true;
+                        }
+
+                        editingSeqs = true;
+                        doMousePressed(evt);
+                    }
+                    else
+                    {
+                        doMousePressedDefineMode(evt);
+                    }
+                }
+
+                public void mouseExited(MouseEvent evt)
+                {
+                    if (av.getWrapAlignment() || editingSeqs)
+                    {
+                        return;
+                    }
+
+                    doMouseExitedDefineMode(evt);
+                }
+
+                public void mouseEntered(MouseEvent evt)
+                {
+                    if (av.getWrapAlignment() || editingSeqs)
+                    {
+                        return;
+                    }
+
+                    doMouseEnteredDefineMode(evt);
+                }
+            });
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseReleased(MouseEvent evt)
+    {
+        if (seqEditOccurred > -1)
         {
-          return;
+            editOccurred(seqEditOccurred);
         }
 
-        doMouseMoved(evt);
-      }
+        startseq = -1;
+        lastres = -1;
+        seqEditOccurred = -1;
+        editingSeqs = false;
+        groupEditing = false;
 
-      public void mouseDragged(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+        ap.repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMousePressed(MouseEvent evt)
+    {
+        ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                av.alignment, HistoryItem.EDIT));
+
+        int seq;
+        int res;
+
+        int x = evt.getX();
+        int y = evt.getY();
 
-        if (editingSeqs)
+        res = (x / av.getCharWidth()) + av.getStartRes();
+        seq = (y / av.getCharHeight()) + av.getStartSeq();
+
+        if ((seq < av.getAlignment().getHeight()) &&
+                (res < av.getAlignment().getSequenceAt(seq).getLength()))
         {
-          doMouseDragged(evt);
+            startseq = seq;
+            lastres = res;
         }
         else
         {
-          doMouseDraggedDefineMode(evt);
+            startseq = -1;
+            lastres = -1;
         }
-      }
-    });
 
-    addMouseListener(new MouseAdapter()
+        startEdit = lastres;
+        endEdit = lastres;
+
+        return;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseMoved(MouseEvent evt)
     {
-      public void mouseReleased(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+        int res = 0;
+        int seq = 0;
+        int x = evt.getX();
+        int y = evt.getY();
 
-        if (editingSeqs)
+        if (av.wrapAlignment)
         {
-          doMouseReleased(evt);
-        }
-        else
-        {
-          doMouseReleasedDefineMode(evt);
-        }
-      }
+            y -= (2 * av.charHeight);
 
-      public void mousePressed(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+            int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-        if (evt.isShiftDown() || evt.isAltDown() ||
-            evt.isControlDown())
-        {
-          if (evt.isAltDown() || evt.isControlDown())
-          {
-            groupEditing = true;
-          }
+            res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) +
+                (x / av.getCharWidth()) + av.getStartRes();
 
-          editingSeqs = true;
-          doMousePressed(evt);
+            y %= chunkHeight;
+            seq = (y / av.getCharHeight()) + av.getStartSeq();
         }
         else
         {
-          doMousePressedDefineMode(evt);
+            res = (x / av.getCharWidth()) + av.getStartRes();
+            seq = (y / av.getCharHeight()) + av.getStartSeq();
         }
-      }
 
-      public void mouseExited(MouseEvent evt)
-      {
-        if (av.getWrapAlignment() || editingSeqs)
+        if (seq >= av.getAlignment().getHeight())
         {
-          return;
+            return;
         }
 
-        doMouseExitedDefineMode(evt);
-      }
+        SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-      public void mouseEntered(MouseEvent evt)
-      {
-        if (av.getWrapAlignment() || editingSeqs)
+        if (res > sequence.getLength())
         {
-          return;
+            return;
         }
 
-        doMouseEnteredDefineMode(evt);
-      }
-    });
-  }
-
-
-  public void doMouseReleased(MouseEvent evt)
-  {
-    if (seqEditOccurred > -1)
-    {
-      editOccurred(seqEditOccurred);
-    }
+        Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
+                "");
+        String aa = "";
 
-    startseq = -1;
-    lastres = -1;
-    seqEditOccurred = -1;
-    editingSeqs = false;
-    groupEditing = false;
+        if (obj != null)
+        {
+            aa = obj.toString();
+        }
 
-    ap.repaint();
-  }
+        StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                sequence.getName());
 
-  public void doMousePressed(MouseEvent evt)
-  {
-    ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                 av.alignment, HistoryItem.EDIT));
+        if (aa != "")
+        {
+            text.append("  Residue: " + aa + " (" +
+                av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+        }
 
-    int seq;
-    int res;
+        ap.alignFrame.statusBar.setText(text.toString());
 
-    int x = evt.getX();
-    int y = evt.getY();
+        // use aa to see if the mouse pointer is on a
+        if (av.showSequenceFeatures)
+        {
+            Vector features = sequence.getSequenceFeatures();
+            Enumeration e = features.elements();
+            StringBuffer sbuffer = new StringBuffer();
 
-    res = (x / av.getCharWidth()) + av.getStartRes();
-    seq = (y / av.getCharHeight()) + av.getStartSeq();
+            while (e.hasMoreElements())
+            {
+                SequenceFeature sf = (SequenceFeature) e.nextElement();
+
+                if ((sf.getStart() <= sequence.findPosition(res)) &&
+                        (sf.getEnd() >= sequence.findPosition(res)))
+                {
+                    if (sbuffer.length() > 0)
+                    {
+                        sbuffer.append("; ");
+                    }
+
+                    sbuffer.append(sf.getType() + " " + sf.getDescription());
+
+                    if (sf.getStatus().length() > 0)
+                    {
+                        sbuffer.append(" (" + sf.getStatus() + ")");
+                    }
+                }
+            }
 
-    if ( (seq < av.getAlignment().getHeight()) &&
-        (res < av.getAlignment().getSequenceAt(seq).getLength()))
-    {
-      startseq = seq;
-      lastres = res;
-    }
-    else
-    {
-      startseq = -1;
-      lastres = -1;
+            this.setToolTipText(sbuffer.toString());
+        }
     }
 
-    startEdit = lastres;
-    endEdit = lastres;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseDragged(MouseEvent evt)
+    {
+        // If we're dragging we're editing
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    return;
-  }
+        if (res < 0)
+        {
+            res = 0;
+        }
 
-  public void doMouseMoved(MouseEvent evt)
-  {
-    int res = 0;
-    int seq = 0;
-    int x = evt.getX();
-    int y = evt.getY();
+        if ((lastres == -1) || (lastres == res))
+        {
+            return;
+        }
 
-    if (av.wrapAlignment)
-    {
-      y -= (2 * av.charHeight);
+        boolean dragRight = true;
 
-      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+        if ((res < av.getAlignment().getWidth()) && (res < lastres))
+        {
+            dragRight = false;
+        }
 
-      res = (int) ( (y / chunkHeight) * (getWidth() / av.charWidth)) +
-          (x / av.getCharWidth()) + av.getStartRes();
+        if (res != lastres)
+        {
+            // Group editing
+            if (groupEditing)
+            {
+                SequenceGroup sg = av.getSelectionGroup();
+
+                if (sg == null)
+                {
+                    lastres = -1;
+
+                    return;
+                }
+
+                // drag to right
+                if (dragRight)
+                {
+                    sg.setEndRes(sg.getEndRes() + (res - lastres));
+                }
+
+                // drag to left
+                else
+                {
+                    /// Are we able to delete?
+                    // ie are all columns blank?
+                    boolean deleteAllowed = false;
+
+                    for (int s = 0; s < sg.getSize(); s++)
+                    {
+                        SequenceI seq = sg.getSequenceAt(s);
+
+                        for (int j = res; j < lastres; j++)
+                        {
+                            if (seq.getSequence().length() <= j)
+                            {
+                                continue;
+                            }
+
+                            if (!jalview.util.Comparison.isGap(
+                                        seq.getSequence().charAt(j)))
+                            {
+                                // Not a gap, block edit not valid
+                                res = j + 1;
+                                deleteAllowed = false;
+
+                                continue;
+                            }
+
+                            deleteAllowed = true;
+                        }
+                    }
+
+                    if (!deleteAllowed)
+                    {
+                        lastres = -1;
+
+                        return;
+                    }
+
+                    sg.setEndRes(sg.getEndRes() - (lastres - res));
+                }
+
+                for (int i = 0; i < sg.getSize(); i++)
+                {
+                    SequenceI s = sg.getSequenceAt(i);
+                    int k = av.alignment.findIndex(s);
+
+                    // drag to right
+                    if (dragRight)
+                    {
+                        for (int j = lastres; j < res; j++)
+                        {
+                            insertChar(j, k);
+                        }
+                    }
+
+                    // drag to left
+                    else
+                    {
+                        for (int j = res; j < lastres; j++)
+                        {
+                            if (s.getLength() > j)
+                            {
+                                deleteChar(res, k);
+                            }
+                        }
+                    }
+                }
+            }
+            else /////Editing a single sequence///////////
+            {
+                if ((res < av.getAlignment().getWidth()) && (res > lastres))
+                {
+                    // dragging to the right
+                    for (int j = lastres; j < res; j++)
+                    {
+                        insertChar(j, startseq);
+                    }
+                }
+                else if ((res < av.getAlignment().getWidth()) &&
+                        (res < lastres))
+                {
+                    // dragging to the left
+                    for (int j = lastres; j > res; j--)
+                    {
+                        if (jalview.util.Comparison.isGap(
+                                    av.alignment.getSequenceAt(startseq)
+                                                    .getSequence().charAt(res)))
+                        {
+                            deleteChar(res, startseq);
+                        }
+                        else
+                        {
+                            break;
+                        }
+                    }
+                }
+            }
+        }
 
-      y %= chunkHeight;
-      seq = (y / av.getCharHeight()) + av.getStartSeq();
-    }
-    else
-    {
-      res = (x / av.getCharWidth()) + av.getStartRes();
-      seq = (y / av.getCharHeight()) + av.getStartSeq();
+        endEdit = res;
+        lastres = res;
+        seqCanvas.repaint();
     }
 
-    if (seq >= av.getAlignment().getHeight())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seqstart DOCUMENT ME!
+     * @param seqend DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     */
+    public void drawChars(int seqstart, int seqend, int start)
     {
-      return;
+        seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
+            seqend, av.getStartRes(), av.getStartSeq(), 0);
+        seqCanvas.repaint();
     }
 
-    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
-    if (res > sequence.getLength())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param j DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    public void insertChar(int j, int seq)
     {
-      return;
+        av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
+        seqEditOccurred = seq;
     }
 
-    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
-                                                  "");
-    String aa = "";
-
-    if (obj != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param j DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    public void deleteChar(int j, int seq)
     {
-      aa = obj.toString();
-    }
+        av.alignment.getSequenceAt(seq).deleteCharAt(j);
+        seqEditOccurred = seq;
 
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
-
-    if (aa != "")
-    {
-      text.append("  Residue: " + aa + " (" +
-                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+        av.alignment.getWidth();
+        seqCanvas.repaint();
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
-
-    // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    void editOccurred(int i)
     {
-      Vector features = sequence.getSequenceFeatures();
-      Enumeration e = features.elements();
-      StringBuffer sbuffer = new StringBuffer();
-
-      while (e.hasMoreElements())
-      {
-        SequenceFeature sf = (SequenceFeature) e.nextElement();
-
-        if ( (sf.getStart() <= sequence.findPosition(res)) &&
-            (sf.getEnd() >= sequence.findPosition(res)))
+        if (endEdit == startEdit)
         {
-          if (sbuffer.length() > 0)
-          {
-            sbuffer.append("; ");
-          }
-
-          sbuffer.append(sf.getType() + " " + sf.getDescription());
-
-          if (sf.getStatus().length() > 0)
-          {
-            sbuffer.append(" (" + sf.getStatus() + ")");
-          }
+            ap.alignFrame.historyList.pop();
+            ap.alignFrame.updateEditMenuBar();
         }
-      }
-
-      this.setToolTipText(sbuffer.toString());
-    }
-  }
 
-  public void doMouseDragged(MouseEvent evt)
-  {
-    // If we're dragging we're editing
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
-    if (res < 0)
-    {
-      res = 0;
-    }
-
-    if ( (lastres == -1) || (lastres == res))
-    {
-      return;
-    }
+        av.updateConservation();
+        av.updateConsensus();
 
-    boolean dragRight = true;
+        // Y O Y CLUSTALX
+        ColourSchemeI cs = av.getGlobalColourScheme();
 
-    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
-    {
-      dragRight = false;
-    }
-
-    if (res != lastres)
-    {
-      // Group editing
-      if (groupEditing)
-      {
-        SequenceGroup sg = av.getSelectionGroup();
-
-        if (sg == null)
+        if (av.getSelectionGroup() != null)
         {
-          lastres = -1;
-
-          return;
+            av.getSelectionGroup().recalcConservation();
         }
 
-        // drag to right
-        if (dragRight)
+        if (cs instanceof ConservationColourScheme)
         {
-          sg.setEndRes(sg.getEndRes() + (res - lastres));
+            ConservationColourScheme ccs = (ConservationColourScheme) cs;
+            Conservation c = new Conservation("All",
+                    ResidueProperties.propHash, 3, av.alignment.getSequences(),
+                    0, av.alignment.getWidth() - 1);
+            c.calculate();
+            c.verdict(false, av.ConsPercGaps);
+
+            if (ccs.cs instanceof ClustalxColourScheme)
+            {
+                ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
+                cxs.resetClustalX(av.alignment.getSequences(),
+                    av.alignment.getWidth());
+                ccs = new ConservationColourScheme(c, cxs);
+                av.setGlobalColourScheme(ccs);
+            }
+            else
+            {
+                ccs = new ConservationColourScheme(c, ccs.cs);
+                av.setGlobalColourScheme(ccs);
+            }
         }
-        // drag to left
-        else
-        {
-          /// Are we able to delete?
-          // ie are all columns blank?
-          boolean deleteAllowed = false;
 
-          for (int s = 0; s < sg.getSize(); s++)
-          {
-            SequenceI seq = sg.getSequenceAt(s);
+        if (cs instanceof ClustalxColourScheme)
+        {
+            ((ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
+                av.alignment.getWidth());
+            av.setGlobalColourScheme(cs);
+        }
+    }
 
-            for (int j = res; j < lastres; j++)
-            {
-              if (seq.getSequence().length() <= j)
-              {
-                continue;
-              }
-
-              if (!jalview.util.Comparison.isGap(
-                  seq.getSequence().charAt(j)))
-              {
-                // Not a gap, block edit not valid
-                res = j + 1;
-                deleteAllowed = false;
-
-                continue;
-              }
-
-              deleteAllowed = true;
-            }
-          }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMousePressedDefineMode(MouseEvent evt)
+    {
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+        int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
+        oldSeq = seq;
 
-          if (!deleteAllowed)
-          {
-            lastres = -1;
+        SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
+        if ((sequence == null) || (res > sequence.getLength()))
+        {
             return;
-          }
-
-          sg.setEndRes(sg.getEndRes() - (lastres - res));
         }
 
-        for (int i = 0; i < sg.getSize(); i++)
+        stretchGroup = av.getSelectionGroup();
+
+        if (stretchGroup == null)
         {
-          SequenceI s = sg.getSequenceAt(i);
-          int k = av.alignment.findIndex(s);
+            stretchGroup = av.alignment.findGroup(sequence);
 
-          // drag to right
-          if (dragRight)
-          {
-            for (int j = lastres; j < res; j++)
-            {
-              insertChar(j, k);
-            }
-          }
-          // drag to left
-          else
-          {
-            for (int j = res; j < lastres; j++)
+            if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
+                    (res < stretchGroup.getEndRes()))
             {
-              if (s.getLength() > j)
-              {
-                deleteChar(res, k);
-              }
-            }
-          }
-        }
-      }
-      else /////Editing a single sequence///////////
-      {
-        if ( (res < av.getAlignment().getWidth()) && (res > lastres))
-        {
-          // dragging to the right
-          for (int j = lastres; j < res; j++)
-          {
-            insertChar(j, startseq);
-          }
-        }
-        else if ( (res < av.getAlignment().getWidth()) &&
-                 (res < lastres))
-        {
-          // dragging to the left
-          for (int j = lastres; j > res; j--)
-          {
-            if (jalview.util.Comparison.isGap(
-                av.alignment.getSequenceAt(startseq)
-                .getSequence().charAt(res)))
-            {
-              deleteChar(res, startseq);
+                av.setSelectionGroup(stretchGroup);
             }
             else
             {
-              break;
+                stretchGroup = null;
             }
-          }
         }
-      }
-    }
-
-    endEdit = res;
-    lastres = res;
-    seqCanvas.repaint();
-  }
-
-  public void drawChars(int seqstart, int seqend, int start)
-  {
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
-                        seqend, av.getStartRes(), av.getStartSeq(), 0);
-    seqCanvas.repaint();
-  }
-
-  public void insertChar(int j, int seq)
-  {
-    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-    seqEditOccurred = seq;
-  }
-
-  public void deleteChar(int j, int seq)
-  {
-    av.alignment.getSequenceAt(seq).deleteCharAt(j);
-    seqEditOccurred = seq;
-
-    av.alignment.getWidth();
-    seqCanvas.repaint();
-  }
-
-  void editOccurred(int i)
-  {
-    if (endEdit == startEdit)
-    {
-      ap.alignFrame.historyList.pop();
-      ap.alignFrame.updateEditMenuBar();
-    }
-
-    av.updateConservation();
-    av.updateConsensus();
-
-    // Y O Y CLUSTALX
-    ColourSchemeI cs = av.getGlobalColourScheme();
-
-    if(av.getSelectionGroup()!=null)
-      av.getSelectionGroup().recalcConservation();
-
-
-    if (cs instanceof ConservationColourScheme)
-    {
-      ConservationColourScheme ccs = (ConservationColourScheme) cs;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        av.alignment.getSequences(), 0,
-                                        av.alignment.getWidth() - 1);
-      c.calculate();
-      c.verdict(false, av.ConsPercGaps);
-
-      if (ccs.cs instanceof ClustalxColourScheme)
-      {
-
-        ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
-        cxs.resetClustalX(av.alignment.getSequences(),
-                          av.alignment.getWidth());
-        ccs = new ConservationColourScheme(c, cxs);
-        av.setGlobalColourScheme(ccs);
-      }
-      else
-      {
-        ccs = new ConservationColourScheme(c, ccs.cs);
-        av.setGlobalColourScheme(ccs);
-      }
-    }
-
-    if (cs instanceof ClustalxColourScheme)
-    {
-      ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                 av.alignment.getWidth());
-      av.setGlobalColourScheme(cs);
-    }
-  }
-
-  public void doMousePressedDefineMode(MouseEvent evt)
-  {
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
-    oldSeq = seq;
+        else if (!stretchGroup.sequences.contains(sequence) ||
+                (stretchGroup.getStartRes() > res) ||
+                (stretchGroup.getEndRes() < res))
+        {
+            stretchGroup = null;
 
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+            SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
 
-    if ( (sequence == null) || (res > sequence.getLength()))
-    {
-      return;
-    }
+            if (allGroups != null)
+            {
+                for (int i = 0; i < allGroups.length; i++)
+                {
+                    if ((allGroups[i].getStartRes() <= res) &&
+                            (allGroups[i].getEndRes() >= res))
+                    {
+                        stretchGroup = allGroups[i];
+                        av.setSelectionGroup(stretchGroup);
+
+                        break;
+                    }
+                }
+            }
+        }
 
-    stretchGroup = av.getSelectionGroup();
+        if (stretchGroup == null)
+        {
+            // define a new group here
+            SequenceGroup sg = new SequenceGroup();
+            sg.setStartRes(res);
+            sg.setEndRes(res);
+            sg.addSequence(sequence, false);
+            av.setSelectionGroup(sg);
+            stretchGroup = sg;
+
+            if (av.getConservationSelected())
+            {
+                SliderPanel.setConservationSlider(ap,
+                    av.getGlobalColourScheme(), "Background");
+            }
 
-    if (stretchGroup == null)
-    {
-      stretchGroup = av.alignment.findGroup(sequence);
-
-      if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
-          (res < stretchGroup.getEndRes()))
-      {
-        av.setSelectionGroup(stretchGroup);
-      }
-      else
-      {
-        stretchGroup = null;
-      }
-    }
-    else if (!stretchGroup.sequences.contains(sequence) ||
-             (stretchGroup.getStartRes() > res) ||
-             (stretchGroup.getEndRes() < res))
-    {
-      stretchGroup = null;
+            if (av.getAbovePIDThreshold())
+            {
+                SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                    "Background");
+            }
+        }
+        else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+        {
+            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
+            pop.show(this, evt.getX(), evt.getY());
 
-      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+            // edit the properties of existing group
+        }
 
-      if (allGroups != null)
-      {
-        for (int i = 0; i < allGroups.length; i++)
+        if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
         {
-          if ( (allGroups[i].getStartRes() <= res) &&
-              (allGroups[i].getEndRes() >= res))
-          {
-            stretchGroup = allGroups[i];
-            av.setSelectionGroup(stretchGroup);
-
-            break;
-          }
+            // Edit end res position of selected group
+            changeEndRes = true;
+        }
+        else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
+        {
+            // Edit end res position of selected group
+            changeStartRes = true;
         }
-      }
-    }
 
-    if (stretchGroup == null)
-    {
-      // define a new group here
-      SequenceGroup sg = new SequenceGroup();
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      sg.addSequence(sequence, false);
-      av.setSelectionGroup(sg);
-      stretchGroup = sg;
-
-      if (av.getConservationSelected())
-      {
-        SliderPanel.setConservationSlider(ap,
-                                          av.getGlobalColourScheme(),
-                                          "Background");
-      }
-
-      if (av.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                       "Background");
-      }
-    }
-    else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
-    {
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
-      pop.show(this, evt.getX(), evt.getY());
+        stretchGroup.getWidth();
 
-      // edit the properties of existing group
+        seqCanvas.repaint();
     }
 
-    if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseReleasedDefineMode(MouseEvent evt)
     {
-      // Edit end res position of selected group
-      changeEndRes = true;
-    }
-    else if ( (stretchGroup != null) && (stretchGroup.getStartRes() == res))
-    {
-      // Edit end res position of selected group
-      changeStartRes = true;
-    }
-
-    stretchGroup.getWidth();
+        if (mouseDragging)
+        {
+            stretchGroup.recalcConservation();
+            mouseDragging = false;
+        }
 
-    seqCanvas.repaint();
-  }
+        if (stretchGroup == null)
+        {
+            return;
+        }
 
-  public void doMouseReleasedDefineMode(MouseEvent evt)
-  {
-    if(mouseDragging)
-    {
-      stretchGroup.recalcConservation();
-      mouseDragging = false;
-    }
+        if (stretchGroup.cs instanceof ClustalxColourScheme)
+        {
+            ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.sequences,
+                stretchGroup.getWidth());
+        }
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
+        if (stretchGroup.cs instanceof ConservationColourScheme)
+        {
+            ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
+            stretchGroup.cs = ccs;
+            SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                stretchGroup.getName());
+        }
+        else
+        {
+            SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                stretchGroup.getName());
+        }
 
-    if (stretchGroup.cs instanceof ClustalxColourScheme)
-    {
-      ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.sequences,
-                                                     stretchGroup.getWidth());
+        changeEndRes = false;
+        changeStartRes = false;
+        stretchGroup = null;
+        PaintRefresher.Refresh(av.alignment);
     }
 
-    if (stretchGroup.cs instanceof ConservationColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseDraggedDefineMode(MouseEvent evt)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
-      stretchGroup.cs = ccs;
-      SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                                        stretchGroup.getName());
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+        int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
 
-    }
-    else
-    {
-      SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
-                                     stretchGroup.getName());
-    }
+        if (stretchGroup == null)
+        {
+            return;
+        }
 
-    changeEndRes = false;
-    changeStartRes = false;
-    stretchGroup = null;
-    PaintRefresher.Refresh(av.alignment);
-  }
+        if (res > av.alignment.getWidth())
+        {
+            res = av.alignment.getWidth() - 1;
+        }
 
-  public void doMouseDraggedDefineMode(MouseEvent evt)
-  {
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
+        if (stretchGroup.getEndRes() == res)
+        {
+            // Edit end res position of selected group
+            changeEndRes = true;
+        }
+        else if (stretchGroup.getStartRes() == res)
+        {
+            // Edit start res position of selected group
+            changeStartRes = true;
+        }
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
+        if (res < av.getStartRes())
+        {
+            res = av.getStartRes();
+        }
+        else if (res > av.getEndRes())
+        {
+            res = av.getEndRes();
+        }
 
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
+        if (changeEndRes)
+        {
+            if (res > (stretchGroup.getStartRes() - 1))
+            {
+                stretchGroup.setEndRes(res);
+            }
+        }
+        else if (changeStartRes)
+        {
+            if (res < (stretchGroup.getEndRes() + 1))
+            {
+                stretchGroup.setStartRes(res);
+            }
+        }
 
-    if (stretchGroup.getEndRes() == res)
-    {
-      // Edit end res position of selected group
-      changeEndRes = true;
-    }
-    else if (stretchGroup.getStartRes() == res)
-    {
-      // Edit start res position of selected group
-      changeStartRes = true;
-    }
+        int dragDirection = 0;
 
-    if (res < av.getStartRes())
-    {
-      res = av.getStartRes();
-    }
-    else if (res > av.getEndRes())
-    {
-      res = av.getEndRes();
-    }
+        if (y > oldSeq)
+        {
+            dragDirection = 1;
+        }
+        else if (y < oldSeq)
+        {
+            dragDirection = -1;
+        }
 
-    if (changeEndRes)
-    {
-      if (res > (stretchGroup.getStartRes() - 1))
-      {
-        stretchGroup.setEndRes(res);
-      }
-    }
-    else if (changeStartRes)
-    {
-      if (res < (stretchGroup.getEndRes() + 1))
-      {
-        stretchGroup.setStartRes(res);
-      }
-    }
+        while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
+        {
+            // This routine ensures we don't skip any sequences, as the
+            // selection is quite slow.
+            Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-    int dragDirection = 0;
+            oldSeq += dragDirection;
 
-    if (y > oldSeq)
-    {
-      dragDirection = 1;
-    }
-    else if (y < oldSeq)
-    {
-      dragDirection = -1;
-    }
+            Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-    while ( (y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
-    {
-      // This routine ensures we don't skip any sequences, as the
-      // selection is quite slow.
-      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+            if (stretchGroup.sequences.contains(nextSeq))
+            {
+                stretchGroup.deleteSequence(seq, false);
+            }
+            else
+            {
+                if (seq != null)
+                {
+                    stretchGroup.addSequence(seq, false);
+                }
 
-      oldSeq += dragDirection;
+                stretchGroup.addSequence(nextSeq, false);
+            }
+        }
 
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+        oldSeq = y;
+        mouseDragging = true;
 
-      if (stretchGroup.sequences.contains(nextSeq))
-      {
-          stretchGroup.deleteSequence(seq, false);
-      }
-      else
-      {
-        if (seq != null)
+        if (scrollThread != null)
         {
-          stretchGroup.addSequence(seq, false);
+            scrollThread.setEvent(evt);
         }
-        stretchGroup.addSequence(nextSeq, false);
-      }
-    }
 
-    oldSeq = y;
-    mouseDragging = true;
-
-    if (scrollThread != null)
-    {
-      scrollThread.setEvent(evt);
-    }
-
-    seqCanvas.repaint();
-  }
-
-  public void doMouseEnteredDefineMode(MouseEvent e)
-  {
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
+        seqCanvas.repaint();
     }
-  }
 
-  public void doMouseExitedDefineMode(MouseEvent e)
-  {
-    if (av.getWrapAlignment())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void doMouseEnteredDefineMode(MouseEvent e)
     {
-      return;
-    }
-
-    if (mouseDragging)
-    {
-      scrollThread = new ScrollThread();
-    }
-  }
-
-  // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
-  {
-    MouseEvent evt;
-    boolean running = false;
-
-    public ScrollThread()
-    {
-      start();
+        if (scrollThread != null)
+        {
+            scrollThread.running = false;
+        }
     }
 
-    public void setEvent(MouseEvent e)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void doMouseExitedDefineMode(MouseEvent e)
     {
-      evt = e;
-    }
+        if (av.getWrapAlignment())
+        {
+            return;
+        }
 
-    public void stopScrolling()
-    {
-      running = false;
+        if (mouseDragging)
+        {
+            scrollThread = new ScrollThread();
+        }
     }
 
-    public void run()
+    // this class allows scrolling off the bottom of the visible alignment
+    class ScrollThread extends Thread
     {
-      running = true;
+        MouseEvent evt;
+        boolean running = false;
 
-      while (running)
-      {
-        if (evt != null)
+        public ScrollThread()
         {
-          if (mouseDragging && (evt.getY() < 0) &&
-              (av.getStartSeq() > 0))
-          {
-            running = ap.scrollUp(true);
-          }
-
-          if (mouseDragging && (evt.getY() >= getHeight()) &&
-              (av.alignment.getHeight() > av.getEndSeq()))
-          {
-            running = ap.scrollUp(false);
-          }
+            start();
+        }
 
-          if (mouseDragging && (evt.getX() < 0))
-          {
-            running = ap.scrollRight(true);
-          }
-          else if (mouseDragging && (evt.getX() >= getWidth()))
-          {
-            running = ap.scrollRight(false);
-          }
+        public void setEvent(MouseEvent e)
+        {
+            evt = e;
         }
 
-        try
+        public void stopScrolling()
         {
-          Thread.sleep(75);
+            running = false;
         }
-        catch (Exception ex)
+
+        public void run()
         {
+            running = true;
+
+            while (running)
+            {
+                if (evt != null)
+                {
+                    if (mouseDragging && (evt.getY() < 0) &&
+                            (av.getStartSeq() > 0))
+                    {
+                        running = ap.scrollUp(true);
+                    }
+
+                    if (mouseDragging && (evt.getY() >= getHeight()) &&
+                            (av.alignment.getHeight() > av.getEndSeq()))
+                    {
+                        running = ap.scrollUp(false);
+                    }
+
+                    if (mouseDragging && (evt.getX() < 0))
+                    {
+                        running = ap.scrollRight(true);
+                    }
+                    else if (mouseDragging && (evt.getX() >= getWidth()))
+                    {
+                        running = ap.scrollRight(false);
+                    }
+                }
+
+                try
+                {
+                    Thread.sleep(75);
+                }
+                catch (Exception ex)
+                {
+                }
+            }
         }
-      }
     }
-  }
 }
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 896fda5..e36160a 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -18,237 +18,321 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-
 import jalview.datamodel.*;
+
 import jalview.schemes.*;
 
+import java.awt.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class SequenceRenderer
 {
-  AlignViewport av;
-  FontMetrics fm;
-  boolean renderGaps = true;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void renderGaps(boolean b)
-  {
-    renderGaps = b;
-  }
-
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    getBoxColour(cs, seq, i);
-
-    return resBoxColour;
-  }
-
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    if (cs != null)
+    AlignViewport av;
+    FontMetrics fm;
+    boolean renderGaps = true;
+    SequenceGroup currentSequenceGroup = null;
+    SequenceGroup[] allGroups = null;
+    Color resBoxColour;
+    Graphics graphics;
+
+    /**
+     * Creates a new SequenceRenderer object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public SequenceRenderer(AlignViewport av)
     {
-      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+        this.av = av;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void renderGaps(boolean b)
     {
-      resBoxColour = Color.white;
+        renderGaps = b;
     }
-  }
-
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
-  {
-    allGroups = sg;
-
-    graphics = g;
 
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);
-
-    fm = g.getFontMetrics();
-    drawText(seq, start, end, x1, y1, (int) width, height);
-  }
-
-  public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
-                        int width, int height)
-  {
-    int i = start;
-    int length = seq.getLength();
-
-    int curStart = -1;
-    int curWidth = width;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+    {
+        getBoxColour(cs, seq, i);
 
-    Color tempColour = null;
+        return resBoxColour;
+    }
 
-    while ( (i <= end) && (i < length))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param i DOCUMENT ME!
+     */
+    void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
     {
-      if (inCurrentSequenceGroup(i))
-      {
-        if (currentSequenceGroup.getDisplayBoxes())
+        if (cs != null)
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
+            resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
         }
         else
         {
-          resBoxColour = Color.white;
-        }
-      }
-      else if (av.getShowBoxes())
-      {
-        getBoxColour(av.getGlobalColourScheme(), seq, i);
-      }
-      else
-      {
-        resBoxColour = Color.white;
-      }
-
-      if (resBoxColour != tempColour)
-      {
-        if (tempColour != null)
-        {
-          graphics.fillRect(x1 + (width * (curStart - start)), y1,
-                            curWidth, height);
+            resBoxColour = Color.white;
         }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param sg DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
+        int start, int end, int x1, int y1, int width, int height)
+    {
+        allGroups = sg;
 
-        graphics.setColor(resBoxColour);
+        graphics = g;
 
-        curStart = i;
-        curWidth = width;
-        tempColour = resBoxColour;
-      }
-      else
-      {
-        curWidth += width;
-      }
+        drawBoxes(seq, start, end, x1, y1, (int) width, height);
 
-      i++;
+        fm = g.getFontMetrics();
+        drawText(seq, start, end, x1, y1, (int) width, height);
     }
 
-    graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
-                      height);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
+        int width, int height)
+    {
+        int i = start;
+        int length = seq.getLength();
 
-  public void drawText(SequenceI seq, int start, int end, int x1, int y1,
-                       int width, int height)
-  {
-    int pady = height / 5;
-    int charOffset = 0;
-    char s;
+        int curStart = -1;
+        int curWidth = width;
 
-    // Need to find the sequence position here.
-    String sequence = seq.getSequence();
+        Color tempColour = null;
 
-    for (int i = start; i <= end; i++)
-    {
-      graphics.setColor(Color.black);
-
-      if (i < sequence.length())
-      {
-        s = sequence.charAt(i);
-      }
-      else
-      {
-        s = ' ';
-      }
-
-      if (!renderGaps && jalview.util.Comparison.isGap(s))
-      {
-        continue;
-      }
-
-      if (inCurrentSequenceGroup(i))
-      {
-        if (!currentSequenceGroup.getDisplayText())
+        while ((i <= end) && (i < length))
         {
-          continue;
+            if (inCurrentSequenceGroup(i))
+            {
+                if (currentSequenceGroup.getDisplayBoxes())
+                {
+                    getBoxColour(currentSequenceGroup.cs, seq, i);
+                }
+                else
+                {
+                    resBoxColour = Color.white;
+                }
+            }
+            else if (av.getShowBoxes())
+            {
+                getBoxColour(av.getGlobalColourScheme(), seq, i);
+            }
+            else
+            {
+                resBoxColour = Color.white;
+            }
+
+            if (resBoxColour != tempColour)
+            {
+                if (tempColour != null)
+                {
+                    graphics.fillRect(x1 + (width * (curStart - start)), y1,
+                        curWidth, height);
+                }
+
+                graphics.setColor(resBoxColour);
+
+                curStart = i;
+                curWidth = width;
+                tempColour = resBoxColour;
+            }
+            else
+            {
+                curWidth += width;
+            }
+
+            i++;
         }
 
-        if (currentSequenceGroup.getColourText())
+        graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
+            height);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public void drawText(SequenceI seq, int start, int end, int x1, int y1,
+        int width, int height)
+    {
+        int pady = height / 5;
+        int charOffset = 0;
+        char s;
+
+        // Need to find the sequence position here.
+        String sequence = seq.getSequence();
+
+        for (int i = start; i <= end; i++)
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
-          graphics.setColor(resBoxColour.darker());
+            graphics.setColor(Color.black);
+
+            if (i < sequence.length())
+            {
+                s = sequence.charAt(i);
+            }
+            else
+            {
+                s = ' ';
+            }
+
+            if (!renderGaps && jalview.util.Comparison.isGap(s))
+            {
+                continue;
+            }
+
+            if (inCurrentSequenceGroup(i))
+            {
+                if (!currentSequenceGroup.getDisplayText())
+                {
+                    continue;
+                }
+
+                if (currentSequenceGroup.getColourText())
+                {
+                    getBoxColour(currentSequenceGroup.cs, seq, i);
+                    graphics.setColor(resBoxColour.darker());
+                }
+            }
+            else
+            {
+                if (!av.getShowText())
+                {
+                    continue;
+                }
+
+                if (av.getColourText())
+                {
+                    getBoxColour(av.getGlobalColourScheme(), seq, i);
+
+                    if (av.getShowBoxes())
+                    {
+                        graphics.setColor(resBoxColour.darker());
+                    }
+                    else
+                    {
+                        graphics.setColor(resBoxColour);
+                    }
+                }
+            }
+
+            charOffset = (width - fm.charWidth(s)) / 2;
+            graphics.drawString(String.valueOf(s),
+                charOffset + x1 + (width * (i - start)), (y1 + height) - pady);
         }
-      }
-      else
-      {
-        if (!av.getShowText())
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    boolean inCurrentSequenceGroup(int res)
+    {
+        if (allGroups == null)
         {
-          continue;
+            return false;
         }
 
-        if (av.getColourText())
+        for (int i = 0; i < allGroups.length; i++)
         {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
-
-          if (av.getShowBoxes())
-          {
-            graphics.setColor(resBoxColour.darker());
-          }
-          else
-          {
-            graphics.setColor(resBoxColour);
-          }
-        }
-      }
+            if ((allGroups[i].getStartRes() <= res) &&
+                    (allGroups[i].getEndRes() >= res))
+            {
+                currentSequenceGroup = allGroups[i];
 
-      charOffset = (width - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1 + (width * (i - start)),
-                          (y1 + height) - pady);
-    }
-  }
+                return true;
+            }
+        }
 
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if (allGroups == null)
-    {
-      return false;
+        return false;
     }
 
-    for (int i = 0; i < allGroups.length; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+        int y1, int width, int height)
     {
-      if ( (allGroups[i].getStartRes() <= res) &&
-          (allGroups[i].getEndRes() >= res))
-      {
-        currentSequenceGroup = allGroups[i];
-
-        return true;
-      }
-    }
+        int pady = height / 5;
+        int charOffset = 0;
+        graphics.setColor(Color.BLACK);
+        graphics.fillRect(x1, y1, width * (end - start + 1), height);
+        graphics.setColor(Color.white);
 
-    return false;
-  }
+        char s = '~';
 
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
-                                  int y1, int width, int height)
-  {
-    int pady = height / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.BLACK);
-    graphics.fillRect(x1, y1, width * (end - start + 1), height);
-    graphics.setColor(Color.white);
-
-    char s = '~';
-
-    // Need to find the sequence position here.
-    for (int i = start; i <= end; i++)
-    {
-      if (i < seq.getLength())
-      {
-        s = seq.getSequence().charAt(i);
-      }
-
-      charOffset = (width - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1 + (width * (i - start)),
-                          (y1 + height) - pady);
+        // Need to find the sequence position here.
+        for (int i = start; i <= end; i++)
+        {
+            if (i < seq.getLength())
+            {
+                s = seq.getSequence().charAt(i);
+            }
+
+            charOffset = (width - fm.charWidth(s)) / 2;
+            graphics.drawString(String.valueOf(s),
+                charOffset + x1 + (width * (i - start)), (y1 + height) - pady);
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 1a62fff..c18cc05 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -18,270 +18,336 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
 
 import java.awt.event.*;
+
+import java.util.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
 
-public class SliderPanel
-    extends GSliderPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SliderPanel extends GSliderPanel
 {
-  static JInternalFrame conservationSlider;
-  static JInternalFrame PIDSlider;
-  AlignmentPanel ap;
-  boolean forConservation = true;
-  ColourSchemeI cs;
-
-  public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
-                     ColourSchemeI cs)
-  {
-    this.ap = ap;
-    this.cs = cs;
-    forConservation = forConserve;
-    undoButton.setVisible(false);
-    applyButton.setVisible(false);
-
-    if (forConservation)
-    {
-      label.setText("Enter value to increase conservation visibility");
-      slider.setMinimum(0);
-      slider.setMaximum(50);
-    }
-    else
-    {
-      label.setText("Enter % identity above which to colour residues");
-      slider.setMinimum(0);
-      slider.setMaximum(100);
-    }
-
-    slider.addChangeListener(new ChangeListener()
+    static JInternalFrame conservationSlider;
+    static JInternalFrame PIDSlider;
+    AlignmentPanel ap;
+    boolean forConservation = true;
+    ColourSchemeI cs;
+
+    /**
+     * Creates a new SliderPanel object.
+     *
+     * @param ap DOCUMENT ME!
+     * @param value DOCUMENT ME!
+     * @param forConserve DOCUMENT ME!
+     * @param cs DOCUMENT ME!
+     */
+    public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
+        ColourSchemeI cs)
     {
-      public void stateChanged(ChangeEvent evt)
-      {
-        valueField.setText(slider.getValue() + "");
-        valueChanged(slider.getValue());
-      }
-    });
-
-    slider.setValue(value);
-    valueField.setText(value + "");
-  }
-
-  public static int setConservationSlider(AlignmentPanel ap,
-                                          ColourSchemeI cs, String source)
-  {
-    SliderPanel sp = null;
-    ConservationColourScheme ccs = (ConservationColourScheme) cs;
-
-    if (conservationSlider == null)
-    {
-      sp = new SliderPanel(ap, ccs.inc, true, cs);
-      conservationSlider = new JInternalFrame();
-      conservationSlider.setContentPane(sp);
-      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-    else
-    {
-      sp = (SliderPanel) conservationSlider.getContentPane();
-      sp.cs = cs;
-    }
+        this.ap = ap;
+        this.cs = cs;
+        forConservation = forConserve;
+        undoButton.setVisible(false);
+        applyButton.setVisible(false);
 
-    conservationSlider.setTitle("Conservation Colour Increment  (" +
-                                source + ")");
+        if (forConservation)
+        {
+            label.setText("Enter value to increase conservation visibility");
+            slider.setMinimum(0);
+            slider.setMaximum(50);
+        }
+        else
+        {
+            label.setText("Enter % identity above which to colour residues");
+            slider.setMinimum(0);
+            slider.setMaximum(100);
+        }
 
-    if (ap.av.alignment.getGroups() != null)
-    {
-      sp.setAllGroupsCheckEnabled(true);
+        slider.addChangeListener(new ChangeListener()
+            {
+                public void stateChanged(ChangeEvent evt)
+                {
+                    valueField.setText(slider.getValue() + "");
+                    valueChanged(slider.getValue());
+                }
+            });
+
+        slider.setValue(value);
+        valueField.setText(value + "");
     }
-    else
-    {
-      sp.setAllGroupsCheckEnabled(false);
-    }
-
-    return sp.getValue();
-  }
 
-  public static void showConservationSlider()
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ap DOCUMENT ME!
+     * @param cs DOCUMENT ME!
+     * @param source DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static int setConservationSlider(AlignmentPanel ap,
+        ColourSchemeI cs, String source)
     {
-      PIDSlider.setClosed(true);
-      PIDSlider = null;
-    }
-    catch (Exception ex)
-    {
-    }
+        SliderPanel sp = null;
+        ConservationColourScheme ccs = (ConservationColourScheme) cs;
 
-    if (!conservationSlider.isVisible())
-    {
-      Desktop.addInternalFrame(conservationSlider,
-                               conservationSlider.getTitle(), 420, 90, false);
-      conservationSlider.addInternalFrameListener(new javax.swing.event.
-                                                  InternalFrameAdapter()
-      {
-        public void internalFrameClosed(
-            javax.swing.event.InternalFrameEvent e)
+        if (conservationSlider == null)
         {
-          conservationSlider = null;
+            sp = new SliderPanel(ap, ccs.inc, true, cs);
+            conservationSlider = new JInternalFrame();
+            conservationSlider.setContentPane(sp);
+            conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+        }
+        else
+        {
+            sp = (SliderPanel) conservationSlider.getContentPane();
+            sp.cs = cs;
         }
-      });
-      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-  }
 
-  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
-                                       String source)
-  {
-    SliderPanel pid = null;
+        conservationSlider.setTitle("Conservation Colour Increment  (" +
+            source + ")");
 
-    int threshold = 50;
+        if (ap.av.alignment.getGroups() != null)
+        {
+            sp.setAllGroupsCheckEnabled(true);
+        }
+        else
+        {
+            sp.setAllGroupsCheckEnabled(false);
+        }
 
-    if (cs instanceof ResidueColourScheme)
-    {
-      threshold = ( ( (ResidueColourScheme) cs).getThreshold());
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      threshold = ( ( (ScoreColourScheme) cs).getThreshold());
+        return sp.getValue();
     }
 
-    if (PIDSlider == null)
+    /**
+     * DOCUMENT ME!
+     */
+    public static void showConservationSlider()
     {
-      pid = new SliderPanel(ap, threshold, false, cs);
-      PIDSlider = new JInternalFrame();
-      PIDSlider.setContentPane(pid);
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+        try
+        {
+            PIDSlider.setClosed(true);
+            PIDSlider = null;
+        }
+        catch (Exception ex)
+        {
+        }
+
+        if (!conservationSlider.isVisible())
+        {
+            Desktop.addInternalFrame(conservationSlider,
+                conservationSlider.getTitle(), 420, 90, false);
+            conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+                {
+                    public void internalFrameClosed(
+                        javax.swing.event.InternalFrameEvent e)
+                    {
+                        conservationSlider = null;
+                    }
+                });
+            conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ap DOCUMENT ME!
+     * @param cs DOCUMENT ME!
+     * @param source DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
+        String source)
     {
-      pid = (SliderPanel) PIDSlider.getContentPane();
-      pid.cs = cs;
-    }
+        SliderPanel pid = null;
 
-    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+        int threshold = 50;
 
-    if (ap.av.alignment.getGroups() != null)
-    {
-      pid.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      pid.setAllGroupsCheckEnabled(false);
-    }
+        if (cs instanceof ResidueColourScheme)
+        {
+            threshold = (((ResidueColourScheme) cs).getThreshold());
+        }
+        else if (cs instanceof ScoreColourScheme)
+        {
+            threshold = (((ScoreColourScheme) cs).getThreshold());
+        }
 
-    return pid.getValue();
-  }
+        if (PIDSlider == null)
+        {
+            pid = new SliderPanel(ap, threshold, false, cs);
+            PIDSlider = new JInternalFrame();
+            PIDSlider.setContentPane(pid);
+            PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+        }
+        else
+        {
+            pid = (SliderPanel) PIDSlider.getContentPane();
+            pid.cs = cs;
+        }
 
-  public static void showPIDSlider()
-  {
-    try
-    {
-      conservationSlider.setClosed(true);
-      conservationSlider = null;
-    }
-    catch (Exception ex)
-    {
+        PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+
+        if (ap.av.alignment.getGroups() != null)
+        {
+            pid.setAllGroupsCheckEnabled(true);
+        }
+        else
+        {
+            pid.setAllGroupsCheckEnabled(false);
+        }
+
+        return pid.getValue();
     }
 
-    if (!PIDSlider.isVisible())
+    /**
+     * DOCUMENT ME!
+     */
+    public static void showPIDSlider()
     {
-      Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
-                               false);
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-      PIDSlider.addInternalFrameListener(new javax.swing.event.
-                                         InternalFrameAdapter()
-      {
-        public void internalFrameClosed(
-            javax.swing.event.InternalFrameEvent e)
+        try
         {
-          PIDSlider = null;
+            conservationSlider.setClosed(true);
+            conservationSlider = null;
+        }
+        catch (Exception ex)
+        {
+        }
+
+        if (!PIDSlider.isVisible())
+        {
+            Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
+                false);
+            PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+            PIDSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+                {
+                    public void internalFrameClosed(
+                        javax.swing.event.InternalFrameEvent e)
+                    {
+                        PIDSlider = null;
+                    }
+                });
+            PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
         }
-      });
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
-  }
 
-  public void valueChanged(int i)
-  {
-    if (cs == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void valueChanged(int i)
     {
-      return;
-    }
+        if (cs == null)
+        {
+            return;
+        }
 
-    ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
+        ColourSchemeI toChange = null;
+        Vector allGroups = null;
+        int groupIndex = 0;
 
-    if (allGroupsCheck.isSelected())
-    {
-      allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size() - 1;
+        if (allGroupsCheck.isSelected())
+        {
+            allGroups = ap.av.alignment.getGroups();
+            groupIndex = allGroups.size() - 1;
+        }
+        else
+        {
+            toChange = cs;
+        }
+
+        while (groupIndex > -1)
+        {
+            if (allGroups != null)
+            {
+                toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
+
+                if (toChange == null)
+                {
+                    groupIndex--;
+
+                    continue;
+                }
+            }
+
+            if (forConservation)
+            {
+                if (toChange instanceof ConservationColourScheme)
+                {
+                    ((ConservationColourScheme) toChange).inc = i;
+                }
+            }
+            else
+            {
+                ((ResidueColourScheme) toChange).setThreshold(i);
+            }
+
+            groupIndex--;
+        }
+
+        ap.seqPanel.seqCanvas.repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAllGroupsCheckEnabled(boolean b)
     {
-      toChange = cs;
+        allGroupsCheck.setEnabled(b);
     }
 
-    while (groupIndex > -1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void valueField_actionPerformed(ActionEvent e)
     {
-      if (allGroups != null)
-      {
-        toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;
-        if(toChange==null)
+        try
         {
-          groupIndex--;
-          continue;
+            int i = Integer.parseInt(valueField.getText());
+            slider.setValue(i);
         }
-      }
-
-      if (forConservation)
-      {
-        if (toChange instanceof ConservationColourScheme)
+        catch (Exception ex)
         {
-          ( (ConservationColourScheme) toChange).inc = i;
+            valueField.setText(slider.getValue() + "");
         }
-      }
-      else
-      {
-        ( (ResidueColourScheme) toChange).setThreshold(i);
-      }
-
-      groupIndex--;
     }
 
-    ap.seqPanel.seqCanvas.repaint();
-  }
-
-  public void setAllGroupsCheckEnabled(boolean b)
-  {
-    allGroupsCheck.setEnabled(b);
-  }
-
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param value DOCUMENT ME!
+     */
+    public void setValue(int value)
     {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
+        slider.setValue(value);
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getValue()
     {
-      valueField.setText(slider.getValue() + "");
+        return Integer.parseInt(valueField.getText());
     }
-  }
-
-  public void setValue(int value)
-  {
-    slider.setValue(value);
-  }
-
-  public int getValue()
-  {
-    return Integer.parseInt(valueField.getText());
-  }
 }
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 6edab5d..aff93d7 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -20,99 +20,121 @@ package jalview.gui;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-public class SplashScreen
-    extends JPanel implements Runnable
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SplashScreen extends JPanel implements Runnable
 {
-  boolean visible = true;
-  JInternalFrame iframe;
-  Image image;
-  int fontSize = 11;
-  int yoffset = 30;
+    boolean visible = true;
+    JInternalFrame iframe;
+    Image image;
+    int fontSize = 11;
+    int yoffset = 30;
 
-  public SplashScreen(JInternalFrame iframe, Image i)
-  {
-    this.iframe = iframe;
-    image = i;
+    /**
+     * Creates a new SplashScreen object.
+     *
+     * @param iframe DOCUMENT ME!
+     * @param i DOCUMENT ME!
+     */
+    public SplashScreen(JInternalFrame iframe, Image i)
+    {
+        this.iframe = iframe;
+        image = i;
+
+        Thread t = new Thread(this);
+        t.start();
+        addMouseListener(new MouseAdapter()
+            {
+                public void mousePressed(MouseEvent evt)
+                {
+                    try
+                    {
+                        closeSplash();
+                    }
+                    catch (Exception ex)
+                    {
+                    }
+                }
+            });
+    }
 
-    Thread t = new Thread(this);
-    t.start();
-    addMouseListener(new MouseAdapter()
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
+    {
+        long startTime = System.currentTimeMillis() / 1000;
+
+        while (visible)
+        {
+            if (((System.currentTimeMillis() / 1000) - startTime) > 5)
+            {
+                visible = false;
+            }
+
+            try
+            {
+                Thread.sleep(1000);
+            }
+            catch (Exception ex)
+            {
+            }
+        }
+
+        closeSplash();
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void closeSplash()
     {
-      public void mousePressed(MouseEvent evt)
-      {
         try
         {
-          closeSplash();
+            iframe.setClosed(true);
         }
         catch (Exception ex)
         {
         }
-      }
-    });
-  }
-
-  public void run()
-  {
-    long startTime = System.currentTimeMillis() / 1000;
-
-    while (visible)
-    {
-      if ( ( (System.currentTimeMillis() / 1000) - startTime) > 5)
-      {
-        visible = false;
-      }
-
-      try
-      {
-        Thread.sleep(1000);
-      }
-      catch (Exception ex)
-      {
-      }
     }
 
-    closeSplash();
-  }
-
-  public void closeSplash()
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      iframe.setClosed(true);
-    }
-    catch (Exception ex)
-    {
-    }
-  }
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
+        g.setColor(Color.black);
+        g.setFont(new Font("Verdana", Font.BOLD, fontSize + 6));
 
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-    g.setColor(Color.black);
-    g.setFont(new Font("Verdana", Font.BOLD, fontSize + 6));
+        if (image != null)
+        {
+            g.drawImage(image, 5, yoffset + 12, this);
+        }
 
-    if (image != null)
-    {
-      g.drawImage(image, 5, yoffset + 12, this);
+        g.drawString("JalView 2005 ", 50, yoffset);
+        g.setFont(new Font("Verdana", Font.BOLD, fontSize + 2));
+        g.drawString("Version " + jalview.bin.Cache.VERSION +
+            "; Last updated: " + jalview.bin.Cache.BUILD_DATE, 180, yoffset);
+        g.setFont(new Font("Verdana", Font.BOLD, fontSize));
+        g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
+            50, yoffset + 20);
+        g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
+            50, yoffset + 24 + fontSize);
+        g.drawString("If  you use JalView, please cite: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),",
+            50, yoffset + 28 + (fontSize * 2));
+        g.drawString("\"The Jalview Java Alignment Editor\" Bioinformatics,  2004 12;426-7.",
+            50, yoffset + 32 + (fontSize * 3));
     }
-
-    g.drawString("JalView 2005 ", 50, yoffset);
-    g.setFont(new Font("Verdana", Font.BOLD, fontSize + 2));
-    g.drawString("Version " + jalview.bin.Cache.VERSION +
-                 "; Last updated: " + jalview.bin.Cache.BUILD_DATE, 180,
-                 yoffset);
-    g.setFont(new Font("Verdana", Font.BOLD, fontSize));
-    g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
-                 50, yoffset + 20);
-    g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
-                 50, yoffset + 24 + fontSize);
-    g.drawString("If  you use JalView, please cite: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),",
-                 50, yoffset + 28 + (fontSize * 2));
-    g.drawString(
-        "\"The Jalview Java Alignment Editor\" Bioinformatics,  2004 12;426-7.",
-        50, yoffset + 32 + (fontSize * 3));
-  }
 }
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 1fddc5b..d8ed3ee 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -18,611 +18,759 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
+
+import jalview.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
+
+import java.util.*;
+
 import javax.swing.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
 
-public class TreeCanvas
-    extends JPanel implements MouseListener, Runnable,
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     Printable
 {
-  public static final String PLACEHOLDER = " * ";
-  NJTree tree;
-  JScrollPane scrollPane;
-  AlignViewport av;
-  Font font;
-  int fontSize = 12;
-  boolean fitToWindow = true;
-  boolean showDistances = false;
-  boolean showBootstrap = false;
-  boolean markPlaceholders = false;
-  int offx = 20;
-  int offy = 20;
-  float threshold;
-  String longestName;
-  int labelLength = -1;
-
-  //RubberbandRectangle rubberband;
-  Vector listeners;
-  Hashtable nameHash = new Hashtable();
-  Hashtable nodeHash = new Hashtable();
-
-  public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,
-                    String label)
-  {
-    this.av = av;
-    this.tree = tree;
-    scrollPane = scroller;
-    addMouseListener(this);
-    tree.findHeight(tree.getTopNode());
-    longestName = label;
-
-    PaintRefresher.Register(this, av.alignment);
-  }
-
-  public void TreeSelectionChanged(Sequence sequence)
-  {
-    SequenceGroup selected = av.getSelectionGroup();
-
-    if (selected == null)
+    /** DOCUMENT ME!! */
+    public static final String PLACEHOLDER = " * ";
+    NJTree tree;
+    JScrollPane scrollPane;
+    AlignViewport av;
+    Font font;
+    int fontSize = 12;
+    boolean fitToWindow = true;
+    boolean showDistances = false;
+    boolean showBootstrap = false;
+    boolean markPlaceholders = false;
+    int offx = 20;
+    int offy = 20;
+    float threshold;
+    String longestName;
+    int labelLength = -1;
+
+    //RubberbandRectangle rubberband;
+    Vector listeners;
+    Hashtable nameHash = new Hashtable();
+    Hashtable nodeHash = new Hashtable();
+
+    /**
+     * Creates a new TreeCanvas object.
+     *
+     * @param av DOCUMENT ME!
+     * @param tree DOCUMENT ME!
+     * @param scroller DOCUMENT ME!
+     * @param label DOCUMENT ME!
+     */
+    public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,
+        String label)
     {
-      selected = new SequenceGroup();
-      av.setSelectionGroup(selected);
+        this.av = av;
+        this.tree = tree;
+        scrollPane = scroller;
+        addMouseListener(this);
+        tree.findHeight(tree.getTopNode());
+        longestName = label;
+
+        PaintRefresher.Register(this, av.alignment);
     }
 
-    selected.setEndRes(av.alignment.getWidth());
-    selected.addOrRemove(sequence, true);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sequence DOCUMENT ME!
+     */
+    public void TreeSelectionChanged(Sequence sequence)
+    {
+        SequenceGroup selected = av.getSelectionGroup();
+
+        if (selected == null)
+        {
+            selected = new SequenceGroup();
+            av.setSelectionGroup(selected);
+        }
 
-    PaintRefresher.Refresh(this, av.alignment);
-    repaint();
-  }
+        selected.setEndRes(av.alignment.getWidth());
+        selected.addOrRemove(sequence, true);
 
-  public void setTree(NJTree tree)
-  {
-    this.tree = tree;
-    tree.findHeight(tree.getTopNode());
-  }
+        PaintRefresher.Refresh(this, av.alignment);
+        repaint();
+    }
 
-  public void drawNode(Graphics g, SequenceNode node, float chunk,
-                       float scale, int width, int offx, int offy)
-  {
-    if (node == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tree DOCUMENT ME!
+     */
+    public void setTree(NJTree tree)
     {
-      return;
+        this.tree = tree;
+        tree.findHeight(tree.getTopNode());
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param node DOCUMENT ME!
+     * @param chunk DOCUMENT ME!
+     * @param scale DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param offx DOCUMENT ME!
+     * @param offy DOCUMENT ME!
+     */
+    public void drawNode(Graphics g, SequenceNode node, float chunk,
+        float scale, int width, int offx, int offy)
     {
-      // Drawing leaf node
-      float height = node.height;
-      float dist = node.dist;
-
-      int xstart = (int) ( (height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
-
-      int ypos = (int) (node.ycount * chunk) + offy;
-
-      if (node.element() instanceof SequenceI)
-      {
-        if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() ==
-            Color.white)
-        {
-          g.setColor(Color.black);
-        }
-        else
+        if (node == null)
         {
-          g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor()
-                     .darker());
+            return;
         }
-      }
-      else
-      {
-        g.setColor(Color.black);
-      }
-
-      // Draw horizontal line
-      g.drawLine(xstart, ypos, xend, ypos);
-
-      String nodeLabel = "";
 
-      if (showDistances && (node.dist > 0))
-      {
-        nodeLabel = new Format("%5.2f").form(node.dist);
-      }
-
-      if (showBootstrap)
-      {
-        if (showDistances)
+        if ((node.left() == null) && (node.right() == null))
         {
-          nodeLabel = nodeLabel + " : ";
+            // Drawing leaf node
+            float height = node.height;
+            float dist = node.dist;
+
+            int xstart = (int) ((height - dist) * scale) + offx;
+            int xend = (int) (height * scale) + offx;
+
+            int ypos = (int) (node.ycount * chunk) + offy;
+
+            if (node.element() instanceof SequenceI)
+            {
+                if (((SequenceI) ((SequenceNode) node).element()).getColor() == Color.white)
+                {
+                    g.setColor(Color.black);
+                }
+                else
+                {
+                    g.setColor(((SequenceI) ((SequenceNode) node).element()).getColor()
+                                .darker());
+                }
+            }
+            else
+            {
+                g.setColor(Color.black);
+            }
+
+            // Draw horizontal line
+            g.drawLine(xstart, ypos, xend, ypos);
+
+            String nodeLabel = "";
+
+            if (showDistances && (node.dist > 0))
+            {
+                nodeLabel = new Format("%5.2f").form(node.dist);
+            }
+
+            if (showBootstrap)
+            {
+                if (showDistances)
+                {
+                    nodeLabel = nodeLabel + " : ";
+                }
+
+                nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
+            }
+
+            if (!nodeLabel.equals(""))
+            {
+                g.drawString(nodeLabel, xstart, ypos - 10);
+            }
+
+            String name = (markPlaceholders && node.isPlaceholder())
+                ? (PLACEHOLDER + node.getName()) : node.getName();
+            FontMetrics fm = g.getFontMetrics(font);
+            int charWidth = fm.stringWidth(name) + 3;
+            int charHeight = fm.getHeight();
+
+            Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
+                    charWidth, charHeight);
+
+            nameHash.put((SequenceI) node.element(), rect);
+
+            // Colour selected leaves differently
+            SequenceGroup selected = av.getSelectionGroup();
+
+            if ((selected != null) &&
+                    selected.sequences.contains((SequenceI) node.element()))
+            {
+                g.setColor(Color.gray);
+
+                g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,
+                    charHeight);
+                g.setColor(Color.white);
+            }
+
+            g.drawString(name, xend + 10, ypos);
+            g.setColor(Color.black);
         }
+        else
+        {
+            drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
+                offy);
+            drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
+                offy);
 
-        nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
-      }
-
-      if (!nodeLabel.equals(""))
-      {
-        g.drawString(nodeLabel, xstart, ypos - 10);
-      }
+            float height = node.height;
+            float dist = node.dist;
 
-      String name = (markPlaceholders && node.isPlaceholder())
-          ? (PLACEHOLDER + node.getName()) : node.getName();
-      FontMetrics fm = g.getFontMetrics(font);
-      int charWidth = fm.stringWidth(name) + 3;
-      int charHeight = fm.getHeight();
+            int xstart = (int) ((height - dist) * scale) + offx;
+            int xend = (int) (height * scale) + offx;
+            int ypos = (int) (node.ycount * chunk) + offy;
 
-      Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
-                                     charWidth, charHeight);
+            g.setColor(((SequenceNode) node).color.darker());
 
-      nameHash.put( (SequenceI) node.element(), rect);
+            // Draw horizontal line
+            g.drawLine(xstart, ypos, xend, ypos);
+            g.fillRect(xend - 2, ypos - 2, 4, 4);
 
-      // Colour selected leaves differently
-      SequenceGroup selected = av.getSelectionGroup();
+            int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) +
+                offy;
+            int yend = (int) (((SequenceNode) node.right()).ycount * chunk) +
+                offy;
 
-      if ( (selected != null) &&
-          selected.sequences.contains( (SequenceI) node.element()))
-      {
-        g.setColor(Color.gray);
+            Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
+            nodeHash.put(node, pos);
 
-        g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,
-                   charHeight);
-        g.setColor(Color.white);
-      }
+            g.drawLine((int) (height * scale) + offx, ystart,
+                (int) (height * scale) + offx, yend);
 
-      g.drawString(name, xend + 10, ypos);
-      g.setColor(Color.black);
+            if (showDistances && (node.dist > 0))
+            {
+                g.drawString(new Format("%5.2f").form(node.dist), xstart,
+                    ypos - 5);
+            }
+        }
     }
-    else
-    {
-      drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
-               offy);
-      drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
-               offy);
 
-      float height = node.height;
-      float dist = node.dist;
-
-      int xstart = (int) ( (height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
-      int ypos = (int) (node.ycount * chunk) + offy;
-
-      g.setColor( ( (SequenceNode) node).color.darker());
-
-      // Draw horizontal line
-      g.drawLine(xstart, ypos, xend, ypos);
-      g.fillRect(xend - 2, ypos - 2, 4, 4);
-
-      int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) +
-          offy;
-      int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) +
-          offy;
-
-      Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
-      nodeHash.put(node, pos);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param x DOCUMENT ME!
+     * @param y DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object findElement(int x, int y)
+    {
+        Enumeration keys = nameHash.keys();
 
-      g.drawLine( (int) (height * scale) + offx, ystart,
-                 (int) (height * scale) + offx, yend);
+        while (keys.hasMoreElements())
+        {
+            Object ob = keys.nextElement();
+            Rectangle rect = (Rectangle) nameHash.get(ob);
+
+            if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
+                    (y <= (rect.y + rect.height)))
+            {
+                return ob;
+            }
+        }
 
-      if (showDistances && (node.dist > 0))
-      {
-        g.drawString(new Format("%5.2f").form(node.dist), xstart,
-                     ypos - 5);
-      }
-    }
-  }
+        keys = nodeHash.keys();
 
-  public Object findElement(int x, int y)
-  {
-    Enumeration keys = nameHash.keys();
+        while (keys.hasMoreElements())
+        {
+            Object ob = keys.nextElement();
+            Rectangle rect = (Rectangle) nodeHash.get(ob);
+
+            if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
+                    (y <= (rect.y + rect.height)))
+            {
+                return ob;
+            }
+        }
 
-    while (keys.hasMoreElements())
-    {
-      Object ob = keys.nextElement();
-      Rectangle rect = (Rectangle) nameHash.get(ob);
-
-      if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
-          (y <= (rect.y + rect.height)))
-      {
-        return ob;
-      }
+        return null;
     }
 
-    keys = nodeHash.keys();
-
-    while (keys.hasMoreElements())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pickBox DOCUMENT ME!
+     */
+    public void pickNodes(Rectangle pickBox)
     {
-      Object ob = keys.nextElement();
-      Rectangle rect = (Rectangle) nodeHash.get(ob);
-
-      if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
-          (y <= (rect.y + rect.height)))
-      {
-        return ob;
-      }
-    }
+        int width = getWidth();
+        int height = getHeight();
 
-    return null;
-  }
+        SequenceNode top = tree.getTopNode();
 
-  public void pickNodes(Rectangle pickBox)
-  {
-    int width = getWidth();
-    int height = getHeight();
+        float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();
 
-    SequenceNode top = tree.getTopNode();
+        if (top.count == 0)
+        {
+            top.count = ((SequenceNode) top.left()).count +
+                ((SequenceNode) top.right()).count;
+        }
 
-    float wscale = (float) ( (width * .8) - (offx * 2)) / tree.getMaxHeight();
+        float chunk = (float) (height - (offy * 2)) / top.count;
 
-    if (top.count == 0)
-    {
-      top.count = ( (SequenceNode) top.left()).count +
-          ( (SequenceNode) top.right()).count;
+        pickNode(pickBox, top, chunk, wscale, width, offx, offy);
     }
 
-    float chunk = (float) (height - (offy * 2)) / top.count;
-
-    pickNode(pickBox, top, chunk, wscale, width, offx, offy);
-  }
-
-  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
-                       float scale, int width, int offx, int offy)
-  {
-    if (node == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pickBox DOCUMENT ME!
+     * @param node DOCUMENT ME!
+     * @param chunk DOCUMENT ME!
+     * @param scale DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param offx DOCUMENT ME!
+     * @param offy DOCUMENT ME!
+     */
+    public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+        float scale, int width, int offx, int offy)
     {
-      return;
+        if (node == null)
+        {
+            return;
+        }
+
+        if ((node.left() == null) && (node.right() == null))
+        {
+            float height = node.height;
+            float dist = node.dist;
+
+            int xstart = (int) ((height - dist) * scale) + offx;
+            int xend = (int) (height * scale) + offx;
+
+            int ypos = (int) (node.ycount * chunk) + offy;
+
+            if (pickBox.contains(new Point(xend, ypos)))
+            {
+                if (node.element() instanceof SequenceI)
+                {
+                    SequenceI seq = (SequenceI) node.element();
+                    SequenceGroup sg = av.getSelectionGroup();
+
+                    if (sg != null)
+                    {
+                        sg.addOrRemove(seq, true);
+                    }
+                }
+            }
+        }
+        else
+        {
+            pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
+                offx, offy);
+            pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+                offx, offy);
+        }
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     */
+    public void setColor(SequenceNode node, Color c)
     {
-      float height = node.height;
-      float dist = node.dist;
-
-      int xstart = (int) ( (height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
-
-      int ypos = (int) (node.ycount * chunk) + offy;
+        if (node == null)
+        {
+            return;
+        }
 
-      if (pickBox.contains(new Point(xend, ypos)))
-      {
-        if (node.element() instanceof SequenceI)
+        if ((node.left() == null) && (node.right() == null))
         {
-          SequenceI seq = (SequenceI) node.element();
-          SequenceGroup sg = av.getSelectionGroup();
+            node.color = c;
 
-          if (sg != null)
-          {
-            sg.addOrRemove(seq, true);
-          }
+            if (node.element() instanceof SequenceI)
+            {
+                ((SequenceI) node.element()).setColor(c);
+            }
+        }
+        else
+        {
+            node.color = c;
+            setColor((SequenceNode) node.left(), c);
+            setColor((SequenceNode) node.right(), c);
         }
-      }
-    }
-    else
-    {
-      pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
-               offx, offy);
-      pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
-               offx, offy);
     }
-  }
 
-  public void setColor(SequenceNode node, Color c)
-  {
-    if (node == null)
+    /**
+     * DOCUMENT ME!
+     */
+    void startPrinting()
     {
-      return;
+        Thread thread = new Thread(this);
+        thread.start();
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    // put printing in a thread to avoid painting problems
+    public void run()
     {
-      node.color = c;
+        PrinterJob printJob = PrinterJob.getPrinterJob();
+        PageFormat pf = printJob.pageDialog(printJob.defaultPage());
 
-      if (node.element() instanceof SequenceI)
-      {
-        ( (SequenceI) node.element()).setColor(c);
-      }
-    }
-    else
-    {
-      node.color = c;
-      setColor( (SequenceNode) node.left(), c);
-      setColor( (SequenceNode) node.right(), c);
+        printJob.setPrintable(this, pf);
+
+        if (printJob.printDialog())
+        {
+            try
+            {
+                printJob.print();
+            }
+            catch (Exception PrintException)
+            {
+                PrintException.printStackTrace();
+            }
+        }
     }
-  }
 
-  void startPrinting()
-  {
-    Thread thread = new Thread(this);
-    thread.start();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pg DOCUMENT ME!
+     * @param pf DOCUMENT ME!
+     * @param pi DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     *
+     * @throws PrinterException DOCUMENT ME!
+     */
+    public int print(Graphics pg, PageFormat pf, int pi)
+        throws PrinterException
+    {
+        pg.setFont(font);
+        pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
 
-  // put printing in a thread to avoid painting problems
-  public void run()
-  {
-    PrinterJob printJob = PrinterJob.getPrinterJob();
-    PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+        int pwidth = (int) pf.getImageableWidth();
+        int pheight = (int) pf.getImageableHeight();
 
-    printJob.setPrintable(this, pf);
+        int noPages = getHeight() / pheight;
 
-    if (printJob.printDialog())
-    {
-      try
-      {
-        printJob.print();
-      }
-      catch (Exception PrintException)
-      {
-        PrintException.printStackTrace();
-      }
-    }
-  }
+        if (pi > noPages)
+        {
+            return Printable.NO_SUCH_PAGE;
+        }
 
-  public int print(Graphics pg, PageFormat pf, int pi)
-      throws PrinterException
-  {
-    pg.setFont(font);
-    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+        if (pwidth > getWidth())
+        {
+            pwidth = getWidth();
+        }
 
-    int pwidth = (int) pf.getImageableWidth();
-    int pheight = (int) pf.getImageableHeight();
+        if (fitToWindow)
+        {
+            if (pheight > getHeight())
+            {
+                pheight = getHeight();
+            }
 
-    int noPages = getHeight() / pheight;
+            noPages = 0;
+        }
+        else
+        {
+            FontMetrics fm = pg.getFontMetrics(font);
+            int height = fm.getHeight() * nameHash.size();
+            pg.translate(0, -pi * pheight);
+            pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);
+
+            // translate number of pages,
+            // height is screen size as this is the
+            // non overlapping text size
+            pheight = height;
+        }
 
-    if (pi > noPages)
-    {
-      return Printable.NO_SUCH_PAGE;
-    }
+        draw(pg, pwidth, pheight);
 
-    if (pwidth > getWidth())
-    {
-      pwidth = getWidth();
+        return Printable.PAGE_EXISTS;
     }
 
-    if (fitToWindow)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      if (pheight > getHeight())
-      {
-        pheight = getHeight();
-      }
+        super.paintComponent(g);
+        font = new Font("Verdana", Font.PLAIN, fontSize);
+        g.setFont(font);
 
-      noPages = 0;
-    }
-    else
-    {
-      FontMetrics fm = pg.getFontMetrics(font);
-      int height = fm.getHeight() * nameHash.size();
-      pg.translate(0, -pi * pheight);
-      pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);
-
-      // translate number of pages,
-      // height is screen size as this is the
-      // non overlapping text size
-      pheight = height;
-    }
+        FontMetrics fm = g.getFontMetrics(font);
 
-    draw(pg, pwidth, pheight);
-
-    return Printable.PAGE_EXISTS;
-  }
+        if (nameHash.size() == 0)
+        {
+            repaint();
+        }
 
-  public void paintComponent(Graphics g)
-  {
-    super.paintComponent(g);
-    font = new Font("Verdana", Font.PLAIN, fontSize);
-    g.setFont(font);
+        if (fitToWindow ||
+                (!fitToWindow &&
+                (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) +
+                offy))))
+        {
+            draw(g, scrollPane.getWidth(), scrollPane.getHeight());
+            setPreferredSize(null);
+        }
+        else
+        {
+            setPreferredSize(new Dimension(scrollPane.getWidth(),
+                    fm.getHeight() * nameHash.size()));
+            draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
+        }
 
-    FontMetrics fm = g.getFontMetrics(font);
+        scrollPane.revalidate();
+    }
 
-    if (nameHash.size() == 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getFontSize()
     {
-      repaint();
+        return fontSize;
     }
 
-    if (fitToWindow ||
-        (!fitToWindow &&
-         (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +
-                                    offy))))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param fontSize DOCUMENT ME!
+     */
+    public void setFontSize(int fontSize)
     {
-      draw(g, scrollPane.getWidth(), scrollPane.getHeight());
-      setPreferredSize(null);
+        this.fontSize = fontSize;
+        repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public void draw(Graphics g1, int width, int height)
     {
-      setPreferredSize(new Dimension(scrollPane.getWidth(),
-                                     fm.getHeight() * nameHash.size()));
-      draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
-    }
+        Graphics2D g2 = (Graphics2D) g1;
+        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
+        g2.setColor(Color.white);
+        g2.fillRect(0, 0, width, height);
 
-    scrollPane.revalidate();
-  }
+        labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
 
-  public int getFontSize()
-  {
-    return fontSize;
-  }
+        float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();
 
-  public void setFontSize(int fontSize)
-  {
-    this.fontSize = fontSize;
-    repaint();
-  }
+        SequenceNode top = tree.getTopNode();
 
-  public void draw(Graphics g1, int width, int height)
-  {
-    Graphics2D g2 = (Graphics2D) g1;
-    g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
-    g2.setColor(Color.white);
-    g2.fillRect(0, 0, width, height);
+        if (top.count == 0)
+        {
+            top.count = ((SequenceNode) top.left()).count +
+                ((SequenceNode) top.right()).count;
+        }
 
-    labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
+        float chunk = (float) (height - (offy * 2)) / top.count;
 
-    float wscale = (float) (width - labelLength - (offx * 2)) /
-        tree.getMaxHeight();
+        drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
 
-    SequenceNode top = tree.getTopNode();
+        if (threshold != 0)
+        {
+            if (av.getCurrentTree() == tree)
+            {
+                g2.setColor(Color.red);
+            }
+            else
+            {
+                g2.setColor(Color.gray);
+            }
+
+            int x = (int) ((threshold * (float) (getWidth() - labelLength -
+                (2 * offx))) + offx);
+
+            g2.drawLine(x, 0, x, getHeight());
+        }
+    }
 
-    if (top.count == 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent e)
     {
-      top.count = ( (SequenceNode) top.left()).count +
-          ( (SequenceNode) top.right()).count;
     }
 
-    float chunk = (float) (height - (offy * 2)) / top.count;
-
-    drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
-
-    if (threshold != 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent e)
     {
-      if (av.getCurrentTree() == tree)
-      {
-        g2.setColor(Color.red);
-      }
-      else
-      {
-        g2.setColor(Color.gray);
-      }
-
-      int x = (int) ( (threshold * (float) (getWidth() - labelLength -
-                                            (2 * offx))) + offx);
-
-      g2.drawLine(x, 0, x, getHeight());
     }
-  }
-
-  public void mouseReleased(MouseEvent e)
-  {
-  }
-
-  public void mouseEntered(MouseEvent e)
-  {
-  }
-
-  public void mouseExited(MouseEvent e)
-  {
-  }
-
-  public void mouseClicked(MouseEvent e)
-  {
-  }
 
-  public void mousePressed(MouseEvent e)
-  {
-    av.setCurrentTree(tree);
-
-    int x = e.getX();
-    int y = e.getY();
-
-    Object ob = findElement(x, y);
-
-    if (ob instanceof SequenceI)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent e)
     {
-      TreeSelectionChanged( (Sequence) ob);
-      repaint();
-
-      return;
     }
-    else if (ob instanceof SequenceNode)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent e)
     {
-      SequenceNode tmpnode = (SequenceNode) ob;
-      tree.swapNodes(tmpnode);
-      tree.reCount(tree.getTopNode());
-      tree.findHeight(tree.getTopNode());
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent e)
     {
-      // Find threshold
-      if (tree.getMaxHeight() != 0)
-      {
-        threshold = (float) (x - offx) / (float) (getWidth() -
-                                                  labelLength - (2 * offx));
+        av.setCurrentTree(tree);
 
-        tree.getGroups().removeAllElements();
-        tree.groupNodes(tree.getTopNode(), threshold);
-        setColor(tree.getTopNode(), Color.black);
+        int x = e.getX();
+        int y = e.getY();
 
-        av.setSelectionGroup(null);
-        av.alignment.deleteAllGroups();
+        Object ob = findElement(x, y);
 
-        for (int i = 0; i < tree.getGroups().size(); i++)
+        if (ob instanceof SequenceI)
         {
-          Color col = new Color( (int) (Math.random() * 255),
-                                (int) (Math.random() * 255),
-                                (int) (Math.random() * 255));
-          setColor( (SequenceNode) tree.getGroups().elementAt(i),
-                   col.brighter());
-
-          Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()
-                                     .elementAt(i),
-                                     new Vector());
-
-         Vector sequences = new Vector();
-         for (int j = 0; j < l.size(); j++)
-         {
-           SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
-           if (!sequences.contains(s1))
-             sequences.addElement(s1);
-
-          }
+            TreeSelectionChanged((Sequence) ob);
+            repaint();
 
-          ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),
-              ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));
-
-          SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
-                           cs, true, true,
-                           false, 0, av.alignment.getWidth());
-
-          if(sg.cs !=null)
-           ( (ResidueColourScheme) sg.cs).setThreshold(25);
-
-
-          if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
-          {
-            ConservationColourScheme ccs = (ConservationColourScheme) av.
-                getGlobalColourScheme();
-            Conservation c = new Conservation("Group",
-                                              ResidueProperties.propHash, 3,
-                                              sg.sequences,
-                                              sg.getStartRes(), sg.getEndRes());
+            return;
+        }
+        else if (ob instanceof SequenceNode)
+        {
+            SequenceNode tmpnode = (SequenceNode) ob;
+            tree.swapNodes(tmpnode);
+            tree.reCount(tree.getTopNode());
+            tree.findHeight(tree.getTopNode());
+        }
+        else
+        {
+            // Find threshold
+            if (tree.getMaxHeight() != 0)
+            {
+                threshold = (float) (x - offx) / (float) (getWidth() -
+                    labelLength - (2 * offx));
+
+                tree.getGroups().removeAllElements();
+                tree.groupNodes(tree.getTopNode(), threshold);
+                setColor(tree.getTopNode(), Color.black);
+
+                av.setSelectionGroup(null);
+                av.alignment.deleteAllGroups();
+
+                for (int i = 0; i < tree.getGroups().size(); i++)
+                {
+                    Color col = new Color((int) (Math.random() * 255),
+                            (int) (Math.random() * 255),
+                            (int) (Math.random() * 255));
+                    setColor((SequenceNode) tree.getGroups().elementAt(i),
+                        col.brighter());
+
+                    Vector l = tree.findLeaves((SequenceNode) tree.getGroups()
+                                                                  .elementAt(i),
+                            new Vector());
+
+                    Vector sequences = new Vector();
+
+                    for (int j = 0; j < l.size(); j++)
+                    {
+                        SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)).element();
+
+                        if (!sequences.contains(s1))
+                        {
+                            sequences.addElement(s1);
+                        }
+                    }
+
+                    ColourSchemeI cs = ColourSchemeProperty.getColour(sequences,
+                            av.alignment.getWidth(),
+                            ColourSchemeProperty.getColourName(
+                                av.getGlobalColourScheme()));
+
+                    SequenceGroup sg = new SequenceGroup(sequences,
+                            "TreeGroup", cs, true, true, false, 0,
+                            av.alignment.getWidth());
+
+                    if (sg.cs != null)
+                    {
+                        ((ResidueColourScheme) sg.cs).setThreshold(25);
+                    }
+
+                    if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
+                    {
+                        ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();
+                        Conservation c = new Conservation("Group",
+                                ResidueProperties.propHash, 3, sg.sequences,
+                                sg.getStartRes(), sg.getEndRes());
+
+                        c.calculate();
+                        c.verdict(false, av.ConsPercGaps);
+                        ccs = new ConservationColourScheme(c, ccs.cs);
+
+                        sg.cs = ccs;
+                    }
+
+                    av.alignment.addGroup(sg);
+                }
+            }
+        }
 
-            c.calculate();
-            c.verdict(false, av.ConsPercGaps);
-            ccs = new ConservationColourScheme(c, ccs.cs);
+        PaintRefresher.Refresh(this, av.alignment);
+        repaint();
+    }
 
-            sg.cs = ccs;
-          }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowDistances(boolean state)
+    {
+        this.showDistances = state;
+        repaint();
+    }
 
-          av.alignment.addGroup(sg);
-        }
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowBootstrap(boolean state)
+    {
+        this.showBootstrap = state;
+        repaint();
     }
 
-    PaintRefresher.Refresh(this, av.alignment);
-    repaint();
-  }
-
-  public void setShowDistances(boolean state)
-  {
-    this.showDistances = state;
-    repaint();
-  }
-
-  public void setShowBootstrap(boolean state)
-  {
-    this.showBootstrap = state;
-    repaint();
-  }
-
-  public void setMarkPlaceholders(boolean state)
-  {
-    this.markPlaceholders = state;
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setMarkPlaceholders(boolean state)
+    {
+        this.markPlaceholders = state;
+        repaint();
+    }
 }
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 3ba9cdd..ff02d49 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -18,350 +18,439 @@
  */
 package jalview.gui;
 
-import java.io.*;
-import java.util.*;
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import org.jibble.epsgraphics.*;
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
+
 import jalview.io.*;
+
 import jalview.jbgui.*;
 
-public class TreePanel
-    extends GTreePanel
-{
-  SequenceI[] seq;
-  String type;
-  String pwtype;
-  int start;
-  int end;
-  TreeCanvas treeCanvas;
-  NJTree tree;
+import org.jibble.epsgraphics.*;
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type,
-                   String pwtype, int s, int e)
-  {
-    super();
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
 
-    this.type = type;
-    this.pwtype = pwtype;
+import java.io.*;
 
-    start = s;
-    end = e;
+import java.util.*;
 
-    String longestName = "";
-    seq = new Sequence[seqVector.size()];
+import javax.imageio.*;
+
+import javax.swing.*;
 
-    for (int i = 0; i < seqVector.size(); i++)
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreePanel extends GTreePanel
+{
+    SequenceI[] seq;
+    String type;
+    String pwtype;
+    int start;
+    int end;
+    TreeCanvas treeCanvas;
+    NJTree tree;
+
+    /**
+     * Creates a new TreePanel object.
+     *
+     * @param av DOCUMENT ME!
+     * @param seqVector DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     * @param pwtype DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     * @param e DOCUMENT ME!
+     */
+    public TreePanel(AlignViewport av, Vector seqVector, String type,
+        String pwtype, int s, int e)
     {
-      seq[i] = (Sequence) seqVector.elementAt(i);
+        super();
 
-      if (seq[i].getName().length() > longestName.length())
-      {
-        longestName = seq[i].getName();
-      }
-    }
+        this.type = type;
+        this.pwtype = pwtype;
 
-    tree = new NJTree(seq, type, pwtype, start, end);
+        start = s;
+        end = e;
 
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-    treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
-    setViewStateFromTreeCanvas(treeCanvas);
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
-    scrollPane.setViewportView(treeCanvas);
-  }
+        String longestName = "";
+        seq = new Sequence[seqVector.size()];
 
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
-  {
-    super();
+        for (int i = 0; i < seqVector.size(); i++)
+        {
+            seq[i] = (Sequence) seqVector.elementAt(i);
+
+            if (seq[i].getName().length() > longestName.length())
+            {
+                longestName = seq[i].getName();
+            }
+        }
+
+        tree = new NJTree(seq, type, pwtype, start, end);
+
+        treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+        treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+        setViewStateFromTreeCanvas(treeCanvas);
+        tree.reCount(tree.getTopNode());
+        tree.findHeight(tree.getTopNode());
+        scrollPane.setViewportView(treeCanvas);
+    }
 
-    // These are probably only  arbitrary strings reflecting source of tree
-    this.type = type;
-    this.pwtype = pwtype;
+    /**
+     * Creates a new TreePanel object.
+     *
+     * @param av DOCUMENT ME!
+     * @param seqVector DOCUMENT ME!
+     * @param newtree DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     * @param pwtype DOCUMENT ME!
+     */
+    public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
+        String type, String pwtype)
+    {
+        super();
 
-    start = 0;
-    end = seqVector.size();
+        // These are probably only  arbitrary strings reflecting source of tree
+        this.type = type;
+        this.pwtype = pwtype;
 
-    String longestName = "";
-    seq = new Sequence[seqVector.size()];
+        start = 0;
+        end = seqVector.size();
 
-    for (int i = 0; i < seqVector.size(); i++)
-    {
-      seq[i] = (Sequence) seqVector.elementAt(i);
-    }
+        String longestName = "";
+        seq = new Sequence[seqVector.size()];
 
-    // This constructor matches sequence names to treenodes and sets up the tree layouts.
-    tree = new NJTree(seq, newtree);
+        for (int i = 0; i < seqVector.size(); i++)
+        {
+            seq[i] = (Sequence) seqVector.elementAt(i);
+        }
 
-    // Now have to calculate longest name based on the leaves
-    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
-    boolean has_placeholders = false;
+        // This constructor matches sequence names to treenodes and sets up the tree layouts.
+        tree = new NJTree(seq, newtree);
 
-    for (int i = 0; i < leaves.size(); i++)
-    {
-      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
-
-      if (lf.isPlaceholder())
-      {
-        has_placeholders = true;
-      }
-
-      if (longestName.length() < ( (Sequence) lf.element()).getName()
-          .length())
-      {
-        longestName = TreeCanvas.PLACEHOLDER +
-            ( (Sequence) lf.element()).getName();
-      }
-    }
+        // Now have to calculate longest name based on the leaves
+        Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+        boolean has_placeholders = false;
 
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
-
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-    treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-    treeCanvas.setShowDistances(newtree.HasDistances());
-    scrollPane.setViewportView(treeCanvas);
-    treeCanvas.setMarkPlaceholders(has_placeholders);
-    setViewStateFromTreeCanvas(treeCanvas);
-
-    // JBPNote TODO: preference for always marking placeholders in new associated tree
-  }
-
-  public NJTree getTree()
-  {
-    return tree;
-  }
-
-  private void setViewStateFromTreeCanvas(TreeCanvas tree)
-  {
-    // update view menu state from treeCanvas render state
-    distanceMenu.setSelected(tree.showDistances);
-    bootstrapMenu.setSelected(tree.showBootstrap);
-    placeholdersMenu.setSelected(tree.markPlaceholders);
-  }
-
-  private void setTreeCanvasFromViewState(TreeCanvas tree)
-  {
-    // update view menu state from treeCanvas render state
-    tree.showDistances = distanceMenu.isSelected();
-    tree.showBootstrap = bootstrapMenu.isSelected();
-    tree.markPlaceholders = placeholdersMenu.isSelected();
-  }
-
-  public void textbox_actionPerformed(ActionEvent e)
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-
-    StringBuffer buffer = new StringBuffer();
-
-    if (type.equals("AV"))
-    {
-      buffer.append("Average distance tree using ");
+        for (int i = 0; i < leaves.size(); i++)
+        {
+            SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+
+            if (lf.isPlaceholder())
+            {
+                has_placeholders = true;
+            }
+
+            if (longestName.length() < ((Sequence) lf.element()).getName()
+                                            .length())
+            {
+                longestName = TreeCanvas.PLACEHOLDER +
+                    ((Sequence) lf.element()).getName();
+            }
+        }
+
+        tree.reCount(tree.getTopNode());
+        tree.findHeight(tree.getTopNode());
+
+        treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+        treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+        treeCanvas.setShowDistances(newtree.HasDistances());
+        scrollPane.setViewportView(treeCanvas);
+        treeCanvas.setMarkPlaceholders(has_placeholders);
+        setViewStateFromTreeCanvas(treeCanvas);
+
+        // JBPNote TODO: preference for always marking placeholders in new associated tree
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public NJTree getTree()
     {
-      buffer.append("Neighbour joining tree using ");
+        return tree;
     }
 
-    if (pwtype.equals("BL"))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tree DOCUMENT ME!
+     */
+    private void setViewStateFromTreeCanvas(TreeCanvas tree)
     {
-      buffer.append("BLOSUM62");
+        // update view menu state from treeCanvas render state
+        distanceMenu.setSelected(tree.showDistances);
+        bootstrapMenu.setSelected(tree.showBootstrap);
+        placeholdersMenu.setSelected(tree.markPlaceholders);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tree DOCUMENT ME!
+     */
+    private void setTreeCanvasFromViewState(TreeCanvas tree)
     {
-      buffer.append("PID");
+        // update view menu state from treeCanvas render state
+        tree.showDistances = distanceMenu.isSelected();
+        tree.showBootstrap = bootstrapMenu.isSelected();
+        tree.markPlaceholders = placeholdersMenu.isSelected();
     }
 
-    Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void textbox_actionPerformed(ActionEvent e)
+    {
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
 
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-    cap.setText(fout.print(false, true));
-  }
+        StringBuffer buffer = new StringBuffer();
 
-  public void saveAsNewick_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"));
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save tree as newick file");
-    chooser.setToolTipText("Save");
+        if (type.equals("AV"))
+        {
+            buffer.append("Average distance tree using ");
+        }
+        else
+        {
+            buffer.append("Neighbour joining tree using ");
+        }
 
-    int value = chooser.showSaveDialog(null);
+        if (pwtype.equals("BL"))
+        {
+            buffer.append("BLOSUM62");
+        }
+        else
+        {
+            buffer.append("PID");
+        }
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+        Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 
-      try
-      {
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-        String output = fout.print(false, true); // distances only
-        java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
-            FileWriter(
-                choice));
-        out.println(output);
-        out.close();
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+        cap.setText(fout.print(false, true));
     }
-  }
-
-  public void printMenu_actionPerformed(ActionEvent e)
-  {
-    //Putting in a thread avoids Swing painting problems
-    treeCanvas.startPrinting();
-  }
-
-  public void fitToWindow_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.fitToWindow = fitToWindow.isSelected();
-    repaint();
-  }
-
-  public void fontSize_actionPerformed(ActionEvent e)
-  {
-    if (treeCanvas == null)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveAsNewick_actionPerformed(ActionEvent e)
     {
-      return;
-    }
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save tree as newick file");
+        chooser.setToolTipText("Save");
 
-    String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
-                                               1);
+        int value = chooser.showSaveDialog(null);
 
-    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
-        "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,
-        null,
-        new String[]
+        if (value == JalviewFileChooser.APPROVE_OPTION)
         {
-        "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"
-    }, "Font Size - " + size);
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+
+            try
+            {
+                jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+                String output = fout.print(false, true); // distances only
+                java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+                            choice));
+                out.println(output);
+                out.close();
+            }
+            catch (Exception ex)
+            {
+                ex.printStackTrace();
+            }
+        }
+    }
 
-    if (selection != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void printMenu_actionPerformed(ActionEvent e)
     {
-      fontSize.setText("Font Size - " + selection);
+        //Putting in a thread avoids Swing painting problems
+        treeCanvas.startPrinting();
+    }
 
-      int i = Integer.parseInt(selection.toString());
-      treeCanvas.setFontSize(i);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fitToWindow_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.fitToWindow = fitToWindow.isSelected();
+        repaint();
     }
 
-    scrollPane.setViewportView(treeCanvas);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fontSize_actionPerformed(ActionEvent e)
+    {
+        if (treeCanvas == null)
+        {
+            return;
+        }
 
-  public void distanceMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowDistances(distanceMenu.isSelected());
-  }
+        String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
+                1);
 
-  public void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
-  }
+        Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
+                "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,
+                null,
+                new String[]
+                {
+                    "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"
+                }, "Font Size - " + size);
 
-  public void placeholdersMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
-  }
+        if (selection != null)
+        {
+            fontSize.setText("Font Size - " + selection);
+
+            int i = Integer.parseInt(selection.toString());
+            treeCanvas.setFontSize(i);
+        }
 
-  public void epsTree_actionPerformed(ActionEvent e)
-  {
-    int width = treeCanvas.getWidth();
-    int height = treeCanvas.getHeight();
+        scrollPane.setViewportView(treeCanvas);
+    }
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void distanceMenu_actionPerformed(ActionEvent e)
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-          jalview.bin.Cache.getProperty(
-              "LAST_DIRECTORY"), new String[]
-          {"eps"},
-          new String[]
-          {"Encapsulated Postscript"},
-          "Encapsulated Postscript");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from tree");
-      chooser.setToolTipText("Save");
-
-      int value = chooser.showSaveDialog(this);
-
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-      {
-        return;
-      }
-
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
-
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
-                                           height);
-
-      treeCanvas.draw(pg, width, height);
-
-      pg.flush();
-      pg.close();
+        treeCanvas.setShowDistances(distanceMenu.isSelected());
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void bootstrapMenu_actionPerformed(ActionEvent e)
     {
-      ex.printStackTrace();
+        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
     }
-  }
 
-  public void pngTree_actionPerformed(ActionEvent e)
-  {
-    int width = treeCanvas.getWidth();
-    int height = treeCanvas.getHeight();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void placeholdersMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+    }
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void epsTree_actionPerformed(ActionEvent e)
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-          jalview.bin.Cache.getProperty(
-              "LAST_DIRECTORY"), new String[]
-          {"png"},
-          new String[]
-          {"Portable network graphics"},
-          "Portable network graphics");
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
 
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create PNG image from tree");
-      chooser.setToolTipText("Save");
+        try
+        {
+            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+                        "LAST_DIRECTORY"), new String[] { "eps" },
+                    new String[] { "Encapsulated Postscript" },
+                    "Encapsulated Postscript");
+            chooser.setFileView(new jalview.io.JalviewFileView());
+            chooser.setDialogTitle("Create EPS file from tree");
+            chooser.setToolTipText("Save");
+
+            int value = chooser.showSaveDialog(this);
+
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
+
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+
+            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+                    height);
+
+            treeCanvas.draw(pg, width, height);
+
+            pg.flush();
+            pg.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
 
-      int value = chooser.showSaveDialog(this);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pngTree_actionPerformed(ActionEvent e)
+    {
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
 
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-      {
-        return;
-      }
+        try
+        {
+            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+                        "LAST_DIRECTORY"), new String[] { "png" },
+                    new String[] { "Portable network graphics" },
+                    "Portable network graphics");
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+            chooser.setFileView(new jalview.io.JalviewFileView());
+            chooser.setDialogTitle("Create PNG image from tree");
+            chooser.setToolTipText("Save");
 
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            int value = chooser.showSaveDialog(this);
 
-      BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
-      Graphics png = bi.getGraphics();
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
 
-      treeCanvas.draw(png, width, height);
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
 
-      ImageIO.write(bi, "png", out);
-      out.close();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
+            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+
+            BufferedImage bi = new BufferedImage(width, height,
+                    BufferedImage.TYPE_INT_RGB);
+            Graphics png = bi.getGraphics();
+
+            treeCanvas.draw(png, width, height);
+
+            ImageIO.write(bi, "png", out);
+            out.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 18382fb..651f40c 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -18,321 +18,451 @@
  */
 package jalview.gui;
 
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
+import java.io.*;
+
+import java.util.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
 
-public class UserDefinedColours
-    extends GUserDefinedColours implements ChangeListener
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class UserDefinedColours extends GUserDefinedColours
+    implements ChangeListener
 {
-  AlignmentPanel ap;
-  SequenceGroup seqGroup;
-  JButton selectedButton;
-  Vector oldColours = new Vector();
-  ColourSchemeI oldColourScheme;
-  JInternalFrame frame;
-
-  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
-  {
-    super();
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "User Defined Colours", 450, 530, false);
-
-    if (System.getProperty("os.name").startsWith("Mac"))
+    AlignmentPanel ap;
+    SequenceGroup seqGroup;
+    Vector selectedButtons;
+    Vector oldColours = new Vector();
+    ColourSchemeI oldColourScheme;
+    JInternalFrame frame;
+
+    /**
+     * Creates a new UserDefinedColours object.
+     *
+     * @param ap DOCUMENT ME!
+     * @param sg DOCUMENT ME!
+     */
+    public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
     {
-      frame.setSize(450, 560);
-    }
+        super();
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "User Defined Colours", 450, 530, false);
 
-    if (sg != null)
-    {
-      frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");
-    }
+        if (System.getProperty("os.name").startsWith("Mac"))
+        {
+            frame.setSize(450, 560);
+        }
 
-    colorChooser.getSelectionModel().addChangeListener(this);
+        if (sg != null)
+        {
+            frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");
+        }
 
-    this.ap = ap;
-    seqGroup = sg;
+        colorChooser.getSelectionModel().addChangeListener(this);
 
-    if (seqGroup != null)
-    {
-      oldColourScheme = seqGroup.cs;
-    }
-    else
-    {
-      oldColourScheme = ap.av.getGlobalColourScheme();
-    }
+        this.ap = ap;
+        seqGroup = sg;
 
-    for (int i = 0; i < 20; i++)
-    {
-      makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
-                 "", ResidueProperties.aa[i]);
-    }
+        if (seqGroup != null)
+        {
+            oldColourScheme = seqGroup.cs;
+        }
+        else
+        {
+            oldColourScheme = ap.av.getGlobalColourScheme();
+        }
+
+        for (int i = 0; i < 20; i++)
+        {
+            makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
+                "", ResidueProperties.aa[i]);
+        }
 
-    makeButton("B", "B");
-    makeButton("Z", "Z");
-    makeButton("X", "X");
-    makeButton("Gap", "'.','-',' '");
+        makeButton("B", "B");
+        makeButton("Z", "Z");
+        makeButton("X", "X");
+        makeButton("Gap", "'.','-',' '");
 
-    if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)
-    {
-      loadColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
+        if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)
+        {
+            loadColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
+        }
     }
-  }
 
-  public void stateChanged(ChangeEvent evt)
-  {
-    if (selectedButton != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void stateChanged(ChangeEvent evt)
     {
-      selectedButton.setBackground(colorChooser.getColor());
+        if (selectedButtons != null)
+        {
+          JButton button;
+          for(int i=0; i<selectedButtons.size(); i++)
+          {
+            button = (JButton)selectedButtons.elementAt(i);
+            button.setBackground(colorChooser.getColor());
+            button.setForeground( button.getBackground().brighter().brighter().brighter());
+          }
+        }
     }
-  }
-
-  public void colourButtonPressed(MouseEvent e)
-  {
-    selectedButton = (JButton) e.getSource();
-    colorChooser.setColor(selectedButton.getBackground());
-  }
 
-  void makeButton(String label, String aa)
-  {
-    final JButton button = new JButton();
-    Color col = Color.white;
-
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void colourButtonPressed(MouseEvent e)
     {
-      col = oldColourScheme.findColour(aa, -1);
-    }
-    catch (Exception ex)
-    {
-    }
+      if(selectedButtons == null)
+        selectedButtons = new Vector();
 
-    button.setBackground(col);
-    oldColours.addElement(col);
-    button.setText(label);
-    button.setForeground(col.darker().darker().darker());
-    button.setFont(new java.awt.Font("Verdana", 1, 10));
-    button.addMouseListener(new java.awt.event.MouseAdapter()
-    {
-      public void mouseClicked(MouseEvent e)
+      JButton pressed = (JButton) e.getSource();
+
+      if(e.isShiftDown())
       {
-        colourButtonPressed(e);
-      }
-    });
+        JButton start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
+        JButton end = (JButton) e.getSource();
+        int startIndex=0, endIndex=0;
+        for(int b=0; b<buttonPanel.getComponentCount(); b++)
+        {
+          if(buttonPanel.getComponent(b)==start)
+            startIndex = b;
+          if(buttonPanel.getComponent(b)==end)
+            endIndex = b;
+        }
+
+        if(startIndex > endIndex)
+        {
+          int temp = startIndex;
+          startIndex = endIndex;
+          endIndex = temp;
+        }
 
-    buttonPanel.add(button, null);
-  }
+        for(int b=startIndex; b<=endIndex; b++)
+        {
+          JButton button = (JButton)buttonPanel.getComponent(b);
+          if(!selectedButtons.contains(button))
+          {
+            button.setForeground(button.getBackground().brighter().brighter());
+            selectedButtons.add(button);
+          }
+        }
+      }
+      else if(!e.isControlDown())
+      {
+        for(int b=0; b<selectedButtons.size(); b++)
+        {
+          JButton button = (JButton)selectedButtons.elementAt(b);
+          button.setForeground(button.getBackground().darker().darker());
+        }
+        selectedButtons.clear();
+        pressed.setForeground( pressed.getBackground().brighter().brighter());
+        selectedButtons.addElement(pressed);
 
-  protected void okButton_actionPerformed(ActionEvent e)
-  {
-    applyButton_actionPerformed(null);
+      }
+      else if(e.isControlDown())
+      {
+        if(selectedButtons.contains(pressed))
+        {
+          pressed.setForeground(pressed.getBackground().darker().darker());
+          selectedButtons.remove(pressed);
+        }
+        else
+        {
+          pressed.setForeground( pressed.getBackground().brighter().brighter());
+          selectedButtons.addElement(pressed);
+        }
+      }
 
-    try
-    {
-      frame.setClosed(true);
+      if(selectedButtons.size()>0)
+      colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());
     }
-    catch (Exception ex)
-    {
-    }
-  }
 
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-    Color[] newColours = new Color[24];
-
-    for (int i = 0; i < 24; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param label DOCUMENT ME!
+     * @param aa DOCUMENT ME!
+     */
+    void makeButton(String label, String aa)
     {
-      JButton button = (JButton) buttonPanel.getComponent(i);
-      newColours[i] = button.getBackground();
-    }
+        final JButton button = new JButton();
+        Color col = Color.white;
 
-    UserColourScheme ucs = new UserColourScheme(newColours);
-    ucs.setThreshold(0);
+        try
+        {
+            col = oldColourScheme.findColour(aa, -1);
+        }
+        catch (Exception ex)
+        {
+        }
 
-    if (seqGroup != null)
-    {
-      seqGroup.cs = ucs;
-      ap.repaint();
+        button.setBackground(col);
+        oldColours.addElement(col);
+        button.setText(label);
+        button.setForeground(col.darker().darker().darker());
+        button.setFont(new java.awt.Font("Verdana", 1, 10));
+        button.addMouseListener(new java.awt.event.MouseAdapter()
+            {
+                public void mouseClicked(MouseEvent e)
+                {
+                    colourButtonPressed(e);
+                }
+            });
+
+        buttonPanel.add(button, null);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void okButton_actionPerformed(ActionEvent e)
     {
-      ap.alignFrame.changeColour(ucs);
+        applyButton_actionPerformed(null);
+
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
     }
-  }
-
-  protected void loadbutton_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"jc"},
-        new String[]
-        {"Jalview User Colours"}, "Jalview User Colours");
-    chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle("Load colour scheme");
-    chooser.setToolTipText("Load");
-
-    int value = chooser.showOpenDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void applyButton_actionPerformed(ActionEvent e)
     {
-      File choice = chooser.getSelectedFile();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR",
-                                    choice.getPath());
+        Color[] newColours = new Color[24];
 
-      Color[] colors = loadColours(choice.getAbsolutePath());
+        for (int i = 0; i < 24; i++)
+        {
+            JButton button = (JButton) buttonPanel.getComponent(i);
+            newColours[i] = button.getBackground();
+        }
 
-      for (int i = 0; i < colors.length; i++)
-      {
-        JButton button = (JButton) buttonPanel.getComponent(i);
-        button.setBackground(colors[i]);
-      }
-    }
-  }
+        UserColourScheme ucs = new UserColourScheme(newColours);
+        ucs.setThreshold(0);
 
-  public static UserColourScheme loadDefaultColours()
-  {
-    if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)
-    {
-      return loadDefaultColours(jalview.bin.Cache.getProperty(
-          "USER_DEFINED_COLOUR"));
-    }
-    else
-    {
-      return null;
+        if (seqGroup != null)
+        {
+            seqGroup.cs = ucs;
+            ap.repaint();
+        }
+        else
+        {
+            ap.alignFrame.changeColour(ucs);
+        }
     }
-  }
-
-  public static UserColourScheme loadDefaultColours(String file)
-  {
-    UserColourScheme ucs = null;
-    Color[] cols = loadColours(file);
 
-    if (cols != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void loadbutton_actionPerformed(ActionEvent e)
     {
-      ucs = new UserColourScheme(cols);
-      ucs.setThreshold(0);
-    }
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"), new String[] { "jc" },
+                new String[] { "Jalview User Colours" }, "Jalview User Colours");
+        chooser.setFileView(new jalview.io.JalviewFileView());
+        chooser.setDialogTitle("Load colour scheme");
+        chooser.setToolTipText("Load");
 
-    return ucs;
-  }
+        int value = chooser.showOpenDialog(this);
 
-  static Color[] loadColours(String file)
-  {
-    Color[] newColours = null;
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            File choice = chooser.getSelectedFile();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+            jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR",
+                choice.getPath());
+
+            Color[] colors = loadColours(choice.getAbsolutePath());
+
+            for (int i = 0; i < colors.length; i++)
+            {
+                JButton button = (JButton) buttonPanel.getComponent(i);
+                button.setBackground(colors[i]);
+            }
+        }
+    }
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static UserColourScheme loadDefaultColours()
     {
-      InputStreamReader in = new InputStreamReader(new FileInputStream(
-          file), "UTF-8");
+        if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)
+        {
+            return loadDefaultColours(jalview.bin.Cache.getProperty(
+                    "USER_DEFINED_COLOUR"));
+        }
+        else
+        {
+            return null;
+        }
+    }
 
-      jalview.binding.JalviewUserColours ucs = new jalview.binding.
-          JalviewUserColours();
-      ucs = (jalview.binding.JalviewUserColours) ucs.unmarshal(in);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static UserColourScheme loadDefaultColours(String file)
+    {
+        UserColourScheme ucs = null;
+        Color[] cols = loadColours(file);
 
-      newColours = new Color[ucs.getColourCount()];
+        if (cols != null)
+        {
+            ucs = new UserColourScheme(cols);
+            ucs.setThreshold(0);
+        }
 
-      for (int i = 0; i < 24; i++)
-      {
-        newColours[i] = new Color(Integer.parseInt(
-            ucs.getColour(i).getRGB(), 16));
-      }
+        return ucs;
     }
-    catch (Exception ex)
+
+    static Color[] loadColours(String file)
     {
-      System.out.println("Error loading UserColourFile " + file);
-    }
+        Color[] newColours = null;
+
+        try
+        {
+            InputStreamReader in = new InputStreamReader(new FileInputStream(
+                        file), "UTF-8");
 
-    return newColours;
-  }
+            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+            ucs = (jalview.binding.JalviewUserColours) ucs.unmarshal(in);
 
-  protected void savebutton_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"jc"},
-        new String[]
-        {"Jalview User Colours"}, "Jalview User Colours");
+            newColours = new Color[ucs.getColourCount()];
 
-    chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle("Save colour scheme");
-    chooser.setToolTipText("Save");
+            for (int i = 0; i < 24; i++)
+            {
+                newColours[i] = new Color(Integer.parseInt(
+                            ucs.getColour(i).getRGB(), 16));
+            }
+        }
+        catch (Exception ex)
+        {
+            System.out.println("Error loading UserColourFile " + file);
+        }
 
-    int value = chooser.showSaveDialog(this);
+        return newColours;
+    }
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void savebutton_actionPerformed(ActionEvent e)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"), new String[] { "jc" },
+                new String[] { "Jalview User Colours" }, "Jalview User Colours");
 
-      jalview.binding.JalviewUserColours ucs = new jalview.binding.
-          JalviewUserColours();
+        chooser.setFileView(new jalview.io.JalviewFileView());
+        chooser.setDialogTitle("Save colour scheme");
+        chooser.setToolTipText("Save");
 
-      try
-      {
-        PrintWriter out = new PrintWriter(new OutputStreamWriter(
-            new FileOutputStream(choice), "UTF-8"));
+        int value = chooser.showSaveDialog(this);
 
-        for (int i = 0; i < 24; i++)
+        if (value == JalviewFileChooser.APPROVE_OPTION)
         {
-          JButton button = (JButton) buttonPanel.getComponent(i);
-          jalview.binding.Colour col = new jalview.binding.Colour();
-          col.setName(button.getText());
-          col.setRGB(jalview.util.Format.getHexString(
-              button.getBackground()));
-          ucs.addColour(col);
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
+
+            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+
+            try
+            {
+                PrintWriter out = new PrintWriter(new OutputStreamWriter(
+                            new FileOutputStream(choice), "UTF-8"));
+
+                for (int i = 0; i < 24; i++)
+                {
+                    JButton button = (JButton) buttonPanel.getComponent(i);
+                    jalview.binding.Colour col = new jalview.binding.Colour();
+                    col.setName(button.getText());
+                    col.setRGB(jalview.util.Format.getHexString(
+                            button.getBackground()));
+                    ucs.addColour(col);
+                }
+
+                ucs.marshal(out);
+                out.close();
+            }
+            catch (Exception ex)
+            {
+                ex.printStackTrace();
+            }
         }
-
-        ucs.marshal(out);
-        out.close();
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
     }
-  }
-
-  protected void cancelButton_actionPerformed(ActionEvent e)
-  {
-    Color[] newColours = new Color[24];
 
-    for (int i = 0; i < 24; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cancelButton_actionPerformed(ActionEvent e)
     {
-      newColours[i] = (Color) oldColours.elementAt(i);
-      buttonPanel.getComponent(i).setBackground(newColours[i]);
-    }
+        Color[] newColours = new Color[24];
 
-    UserColourScheme ucs = new UserColourScheme(newColours);
+        for (int i = 0; i < 24; i++)
+        {
+            newColours[i] = (Color) oldColours.elementAt(i);
+            buttonPanel.getComponent(i).setBackground(newColours[i]);
+        }
 
-    if (seqGroup != null)
-    {
-      seqGroup.cs = ucs;
-    }
-    else
-    {
-      ap.av.setGlobalColourScheme(ucs);
-    }
+        UserColourScheme ucs = new UserColourScheme(newColours);
+
+        if (seqGroup != null)
+        {
+            seqGroup.cs = ucs;
+        }
+        else
+        {
+            ap.av.setGlobalColourScheme(ucs);
+        }
 
-    ap.repaint();
+        ap.repaint();
 
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
     }
-  }
 }
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 0a098e5..5241ec4 100755
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -18,209 +18,296 @@
  */
 package jalview.gui;
 
+import jalview.jbgui.*;
+
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-import jalview.jbgui.*;
 
-public class WebserviceInfo
-    extends GWebserviceInfo
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class WebserviceInfo extends GWebserviceInfo
 {
-  public static final int STATE_QUEUING = 0;
-  public static final int STATE_RUNNING = 1;
-  public static final int STATE_STOPPED_OK = 2;
-  public static final int STATE_CANCELLED_OK = 3;
-  public static final int STATE_STOPPED_ERROR = 4;
-  public static final int STATE_STOPPED_SERVERERROR = 5;
-  int currentStatus = STATE_QUEUING;
-  Image image;
-  int angle = 0;
-  String title = "";
-  jalview.ws.WSClientI thisService;
-  boolean serviceIsCancellable;
-
-  public WebserviceInfo(String title, String info)
-  {
-    init(title, info, 520, 500);
-  }
-
-  public WebserviceInfo(String title, String info, int width, int height)
-  {
-    init(title, info, width, height);
-  }
-
-  public jalview.ws.WSClientI getthisService()
-  {
-    return thisService;
-  }
-
-  public void setthisService(jalview.ws.WSClientI newservice)
-  {
-    thisService = newservice;
-    serviceIsCancellable = newservice.isCancellable();
-  }
-
-  void init(String title, String info, int width, int height)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, title, width, height);
-
-    this.title = title;
-    setInfoText(info);
-
-    java.net.URL url = getClass().getResource("/images/logo.gif");
-    image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-
-    MediaTracker mt = new MediaTracker(this);
-    mt.addImage(image, 0);
-
-    try
+    /** DOCUMENT ME!! */
+    public static final int STATE_QUEUING = 0;
+
+    /** DOCUMENT ME!! */
+    public static final int STATE_RUNNING = 1;
+
+    /** DOCUMENT ME!! */
+    public static final int STATE_STOPPED_OK = 2;
+
+    /** DOCUMENT ME!! */
+    public static final int STATE_CANCELLED_OK = 3;
+
+    /** DOCUMENT ME!! */
+    public static final int STATE_STOPPED_ERROR = 4;
+
+    /** DOCUMENT ME!! */
+    public static final int STATE_STOPPED_SERVERERROR = 5;
+    int currentStatus = STATE_QUEUING;
+    Image image;
+    int angle = 0;
+    String title = "";
+    jalview.ws.WSClientI thisService;
+    boolean serviceIsCancellable;
+
+    /**
+     * Creates a new WebserviceInfo object.
+     *
+     * @param title DOCUMENT ME!
+     * @param info DOCUMENT ME!
+     */
+    public WebserviceInfo(String title, String info)
     {
-      mt.waitForID(0);
+        init(title, info, 520, 500);
     }
-    catch (Exception ex)
+
+    /**
+     * Creates a new WebserviceInfo object.
+     *
+     * @param title DOCUMENT ME!
+     * @param info DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public WebserviceInfo(String title, String info, int width, int height)
     {
+        init(title, info, width, height);
     }
 
-    AnimatedPanel ap = new AnimatedPanel();
-    titlePanel.add(ap, BorderLayout.CENTER);
-
-    Thread thread = new Thread(ap);
-    thread.start();
-  }
-
-  public void setStatus(int status)
-  {
-    currentStatus = status;
-  }
-
-  public String getInfoText()
-  {
-    return infoText.getText();
-  }
-
-  public void setInfoText(String text)
-  {
-    infoText.setText(text);
-  }
-
-  public void appendInfoText(String text)
-  {
-    infoText.append(text);
-  }
-
-  public String getProgressText()
-  {
-    return progressText.getText();
-  }
-
-  public void setProgressText(String text)
-  {
-    progressText.setText(text);
-  }
-
-  public void appendProgressText(String text)
-  {
-    progressText.append(text);
-  }
-
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-    if (!serviceIsCancellable)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public jalview.ws.WSClientI getthisService()
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "This job cannot be cancelled.",
-                                            "Cancel job",
-                                            JOptionPane.WARNING_MESSAGE);
+        return thisService;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param newservice DOCUMENT ME!
+     */
+    public void setthisService(jalview.ws.WSClientI newservice)
     {
-      thisService.cancelJob();
+        thisService = newservice;
+        serviceIsCancellable = newservice.isCancellable();
     }
-  }
-
-  class AnimatedPanel
-      extends JPanel implements Runnable
-  {
-    long startTime = 0;
 
-    public void run()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param title DOCUMENT ME!
+     * @param info DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    void init(String title, String info, int width, int height)
     {
-      startTime = System.currentTimeMillis();
+        JInternalFrame frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, title, width, height);
 
-      while (currentStatus < STATE_STOPPED_OK)
-      {
+        this.title = title;
+        setInfoText(info);
+
+        java.net.URL url = getClass().getResource("/images/logo.gif");
+        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+
+        MediaTracker mt = new MediaTracker(this);
+        mt.addImage(image, 0);
 
         try
         {
-          Thread.sleep(50);
-
-          int units = (int) ( (System.currentTimeMillis() - startTime) / 10f);
-          angle += units;
-          angle %= 360;
-          startTime = System.currentTimeMillis();
-          repaint();
+            mt.waitForID(0);
         }
         catch (Exception ex)
         {
         }
-      }
 
-      angle = 0;
-      cancel.setEnabled(false);
+        AnimatedPanel ap = new AnimatedPanel();
+        titlePanel.add(ap, BorderLayout.CENTER);
+
+        Thread thread = new Thread(ap);
+        thread.start();
     }
 
-    synchronized public void paintComponent(Graphics g1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param status DOCUMENT ME!
+     */
+    public void setStatus(int status)
     {
-      Graphics2D g = (Graphics2D) g1;
-      g.setColor(Color.white);
-      g.fillRect(0, 0, getWidth(), getHeight());
+        currentStatus = status;
+    }
 
-      if (image != null)
-      {
-        g.rotate(Math.toRadians(angle), 28, 28);
-        g.drawImage(image, 10, 10, this);
-        g.rotate( -Math.toRadians(angle), 28, 28);
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getInfoText()
+    {
+        return infoText.getText();
+    }
 
-      g.setFont(new Font("Arial", Font.BOLD, 12));
-      g.setColor(Color.black);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void setInfoText(String text)
+    {
+        infoText.setText(text);
+    }
 
-      switch (currentStatus)
-      {
-        case STATE_QUEUING:
-          g.drawString(title.concat(" - queuing"), 60, 30);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void appendInfoText(String text)
+    {
+        infoText.append(text);
+    }
 
-          break;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getProgressText()
+    {
+        return progressText.getText();
+    }
 
-        case STATE_RUNNING:
-          g.drawString(title.concat(" - running"), 60, 30);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void setProgressText(String text)
+    {
+        progressText.setText(text);
+    }
 
-          break;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void appendProgressText(String text)
+    {
+        progressText.append(text);
+    }
 
-        case STATE_STOPPED_OK:
-          g.drawString(title.concat(" - complete"), 60, 30);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cancel_actionPerformed(ActionEvent e)
+    {
+        if (!serviceIsCancellable)
+        {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "This job cannot be cancelled.", "Cancel job",
+                JOptionPane.WARNING_MESSAGE);
+        }
+        else
+        {
+            thisService.cancelJob();
+        }
+    }
 
-          break;
+    class AnimatedPanel extends JPanel implements Runnable
+    {
+        long startTime = 0;
 
-        case STATE_CANCELLED_OK:
-          g.drawString(title.concat(" - job cancelled!"), 60, 30);
+        public void run()
+        {
+            startTime = System.currentTimeMillis();
+
+            while (currentStatus < STATE_STOPPED_OK)
+            {
+                try
+                {
+                    Thread.sleep(50);
+
+                    int units = (int) ((System.currentTimeMillis() - startTime) / 10f);
+                    angle += units;
+                    angle %= 360;
+                    startTime = System.currentTimeMillis();
+                    repaint();
+                }
+                catch (Exception ex)
+                {
+                }
+            }
+
+            angle = 0;
+            cancel.setEnabled(false);
+        }
 
-          break;
+        synchronized public void paintComponent(Graphics g1)
+        {
+            Graphics2D g = (Graphics2D) g1;
+            g.setColor(Color.white);
+            g.fillRect(0, 0, getWidth(), getHeight());
 
-        case STATE_STOPPED_ERROR:
-          g.drawString(title.concat(" - job error!"), 60, 30);
+            if (image != null)
+            {
+                g.rotate(Math.toRadians(angle), 28, 28);
+                g.drawImage(image, 10, 10, this);
+                g.rotate(-Math.toRadians(angle), 28, 28);
+            }
 
-          break;
+            g.setFont(new Font("Arial", Font.BOLD, 12));
+            g.setColor(Color.black);
 
-        case STATE_STOPPED_SERVERERROR:
-          g.drawString(title.concat(" - Server Error! (try later)"), 60,
-                       30);
+            switch (currentStatus)
+            {
+            case STATE_QUEUING:
+                g.drawString(title.concat(" - queuing"), 60, 30);
 
-          break;
-      }
+                break;
+
+            case STATE_RUNNING:
+                g.drawString(title.concat(" - running"), 60, 30);
+
+                break;
+
+            case STATE_STOPPED_OK:
+                g.drawString(title.concat(" - complete"), 60, 30);
+
+                break;
+
+            case STATE_CANCELLED_OK:
+                g.drawString(title.concat(" - job cancelled!"), 60, 30);
+
+                break;
+
+            case STATE_STOPPED_ERROR:
+                g.drawString(title.concat(" - job error!"), 60, 30);
+
+                break;
+
+            case STATE_STOPPED_SERVERERROR:
+                g.drawString(title.concat(" - Server Error! (try later)"), 60,
+                    30);
+
+                break;
+            }
+        }
     }
-  }
 }
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 04ddff3..d22dc12 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -25,7 +25,14 @@ import java.io.*;
 import java.util.*;
 
 
-public abstract class AlignFile extends FileParse {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public abstract class AlignFile extends FileParse
+{
     int noSeqs = 0;
     int maxLength = 0;
     Vector seqs;
@@ -33,16 +40,29 @@ public abstract class AlignFile extends FileParse {
     long start;
     long end;
 
-    public AlignFile() {
+    /**
+     * Creates a new AlignFile object.
+     */
+    public AlignFile()
+    {
     }
 
-    public AlignFile(String inStr) {
+    /**
+     * Creates a new AlignFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public AlignFile(String inStr)
+    {
         initData();
         System.out.println("is this ever called??");
 
-        try {
+        try
+        {
             parse();
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
         }
     }
 
@@ -51,7 +71,8 @@ public abstract class AlignFile extends FileParse {
      * @param inFile Filename to read from.
      * @param type   What type of file to read from (File, URL)
      */
-    public AlignFile(String inFile, String type) throws IOException {
+    public AlignFile(String inFile, String type) throws IOException
+    {
         super(inFile, type);
 
         initData();
@@ -62,17 +83,20 @@ public abstract class AlignFile extends FileParse {
     /**
      * Return the seqs Vector
      */
-    public Vector getSeqs() {
+    public Vector getSeqs()
+    {
         return seqs;
     }
 
     /**
      * Return the Sequences in the seqs Vector as an array of Sequences
      */
-    public SequenceI[] getSeqsAsArray() {
+    public SequenceI[] getSeqsAsArray()
+    {
         SequenceI[] s = new SequenceI[seqs.size()];
 
-        for (int i = 0; i < seqs.size(); i++) {
+        for (int i = 0; i < seqs.size(); i++)
+        {
             s[i] = (SequenceI) seqs.elementAt(i);
         }
 
@@ -82,24 +106,34 @@ public abstract class AlignFile extends FileParse {
     /**
      * Initialise objects to store sequence data in.
      */
-    protected void initData() {
+    protected void initData()
+    {
         seqs = new Vector();
         headers = new Vector();
     }
 
-    protected void setSeqs(SequenceI[] s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     */
+    protected void setSeqs(SequenceI[] s)
+    {
         seqs = new Vector();
 
-        for (int i = 0; i < s.length; i++) {
+        for (int i = 0; i < s.length; i++)
+        {
             seqs.addElement(s[i]);
         }
     }
 
     // Checks whether sequence is valid aa characters
-    protected boolean isValidProteinSequence(String sequence) {
+    protected boolean isValidProteinSequence(String sequence)
+    {
         for (int i = 0; i < sequence.length(); i++)
             if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
-                        String.valueOf(sequence.charAt(i)))) {
+                        String.valueOf(sequence.charAt(i))))
+            {
                 return false;
             }
 
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index e0750d5..074e6ce 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -25,26 +25,60 @@ import java.io.*;
 import java.util.*;
 
 
-public class BLCFile extends AlignFile {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BLCFile extends AlignFile
+{
     Vector titles;
 
-    public BLCFile() {
+    /**
+     * Creates a new BLCFile object.
+     */
+    public BLCFile()
+    {
     }
 
-    public BLCFile(String inStr) {
+    /**
+     * Creates a new BLCFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public BLCFile(String inStr)
+    {
         super(inStr);
     }
 
-    public BLCFile(String inFile, String type) throws IOException {
+    /**
+     * Creates a new BLCFile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public BLCFile(String inFile, String type) throws IOException
+    {
         super(inFile, type);
     }
 
-    public void initData() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void initData()
+    {
         super.initData();
         titles = new Vector();
     }
 
-    public void parse() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void parse()
+    {
         boolean idsFound = false;
         Vector ids = new Vector();
         StringBuffer[] seqstrings;
@@ -53,12 +87,15 @@ public class BLCFile extends AlignFile {
 
         String line = null;
 
-        try {
-            do {
+        try
+        {
+            do
+            {
                 line = nextLine();
 
                 // seek end of ids
-                if (line.indexOf("*") > -1) {
+                if (line.indexOf("*") > -1)
+                {
                     idsFound = true;
 
                     break;
@@ -66,14 +103,16 @@ public class BLCFile extends AlignFile {
 
                 int abracket = line.indexOf(">");
 
-                if (abracket > -1) {
+                if (abracket > -1)
+                {
                     if (line.indexOf(" ") > -1) //
-                     {
+                    {
                         ///Colur it be this format?
                         //>54402046         0             1   137   137:
                         // or this??
                         //     1   >L1H14       30539  343
-                        try {
+                        try
+                        {
                             ids.addElement(line.substring(abracket + 1,
                                     line.indexOf(" ", abracket + 1)));
 
@@ -92,75 +131,106 @@ public class BLCFile extends AlignFile {
                             value = Integer.parseInt(line.substring(0,
                                         line.indexOf(" ")));
                             ends.addElement(value + "");
-                        } catch (Exception ex) {
+                        }
+                        catch (Exception ex)
+                        {
                             System.err.println("Error during blockfile read.");
                             ex.printStackTrace();
                             starts.addElement("0");
                             ends.addElement("0");
                         }
-                    } else {
-                        if(line.indexOf("/")>-1)
+                    }
+                    else
+                    {
+                        if (line.indexOf("/") > -1)
                         {
-                          ids.addElement(line.substring(abracket + 1,
-                              line.indexOf("/")));
-                          line = line.substring(line.indexOf("/") + 1);
-                          starts.addElement(line.substring(0, line.indexOf("-")));
-                          ends.addElement(line.substring(line.indexOf("-") + 1));
+                            ids.addElement(line.substring(abracket + 1,
+                                    line.indexOf("/")));
+                            line = line.substring(line.indexOf("/") + 1);
+                            starts.addElement(line.substring(0,
+                                    line.indexOf("-")));
+                            ends.addElement(line.substring(line.indexOf("-") +
+                                    1));
                         }
-                        else{
-                          ids.addElement(line.substring(abracket+1));
-                          starts.addElement("0");
-                          ends.addElement("0");
+                        else
+                        {
+                            ids.addElement(line.substring(abracket + 1));
+                            starts.addElement("0");
+                            ends.addElement("0");
                         }
-
                     }
                 }
-            } while (!idsFound);
+            }
+            while (!idsFound);
 
             int starCol = line.indexOf("*");
             seqstrings = new StringBuffer[ids.size()];
 
-            for (int i = 0; i < ids.size(); i++) {
-                if (seqstrings[i] == null) {
+            for (int i = 0; i < ids.size(); i++)
+            {
+                if (seqstrings[i] == null)
+                {
                     seqstrings[i] = new StringBuffer();
                 }
             }
 
-            while ((line = nextLine()).indexOf("*") == -1) {
-                for (int i = 0; i < ids.size(); i++) {
-                    if (line.length() > (i + starCol)) {
+            while ((line = nextLine()).indexOf("*") == -1)
+            {
+                for (int i = 0; i < ids.size(); i++)
+                {
+                    if (line.length() > (i + starCol))
+                    {
                         seqstrings[i].append(line.charAt(i + starCol));
                     }
                 }
             }
 
-            for (int i = 0; i < ids.size(); i++) {
+            for (int i = 0; i < ids.size(); i++)
+            {
                 Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
                         seqstrings[i].toString(),
                         Integer.parseInt(starts.elementAt(i).toString()),
                         Integer.parseInt(ends.elementAt(i).toString()));
                 seqs.addElement(newSeq);
             }
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             ex.printStackTrace();
         }
     }
 
-    public String print() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
+    {
         return print(getSeqsAsArray());
     }
 
-    public static String print(SequenceI[] s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String print(SequenceI[] s)
+    {
         StringBuffer out = new StringBuffer();
 
         int i = 0;
         int max = -1;
 
-        while ((i < s.length) && (s[i] != null)) {
+        while ((i < s.length) && (s[i] != null))
+        {
             out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +
                 s[i].getEnd() + "\n");
 
-            if (s[i].getSequence().length() > max) {
+            if (s[i].getSequence().length() > max)
+            {
                 max = s[i].getSequence().length();
             }
 
@@ -169,13 +239,18 @@ public class BLCFile extends AlignFile {
 
         out.append("* iteration 1\n");
 
-        for (int j = 0; j < max; j++) {
+        for (int j = 0; j < max; j++)
+        {
             i = 0;
 
-            while ((i < s.length) && (s[i] != null)) {
-                if (s[i].getSequence().length() > j) {
+            while ((i < s.length) && (s[i] != null))
+            {
+                if (s[i].getSequence().length() > j)
+                {
                     out.append(s[i].getSequence().substring(j, j + 1));
-                } else {
+                }
+                else
+                {
                     out.append("-");
                 }
 
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index b0d46b2..74cb2d0 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,215 +1,261 @@
 /*
-* 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
-*/
+ * 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.io;
 
-import jalview.datamodel.*;
-
-import jalview.util.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.util.*;
 
-public class ClustalFile extends AlignFile {
-    Vector ids;
-
-    public ClustalFile() {
-    }
-
-    public ClustalFile(String inStr) {
-        super(inStr);
-    }
-
-    public ClustalFile(String inFile, String type) throws IOException {
-        super(inFile, type);
-    }
-
-    public void initData() {
-        super.initData();
-        ids = new Vector();
-    }
+public class ClustalFile
+    extends AlignFile
+{
+  Vector ids;
+
+  public ClustalFile()
+  {
+  }
+
+  public ClustalFile(String inStr)
+  {
+    super(inStr);
+  }
+
+  public ClustalFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  public void initData()
+  {
+    super.initData();
+    ids = new Vector();
+  }
+
+  public void parse()
+  {
+    int i = 0;
+    boolean flag = false;
+
+    Vector headers = new Vector();
+    Hashtable seqhash = new Hashtable();
+
+    String line;
+
+    try
+    {
+      while ( (line = nextLine()) != null)
+      {
+        if (line.indexOf(" ") != 0)
+        {
+          StringTokenizer str = new StringTokenizer(line, " ");
+          String id = "";
+
+          if (str.hasMoreTokens())
+          {
+            id = str.nextToken();
+
+            if (id.equals("CLUSTAL"))
+            {
+              flag = true;
+            }
+            else
+            {
+              if (flag)
+              {
+                StringBuffer tempseq;
+
+                if (seqhash.containsKey(id))
+                {
+                  tempseq = (StringBuffer) seqhash.get(id);
+                }
+                else
+                {
+                  tempseq = new StringBuffer();
+                  seqhash.put(id, tempseq);
+                }
 
-    public void parse() {
-        int i = 0;
-        boolean flag = false;
-
-        Vector headers = new Vector();
-        Hashtable seqhash = new Hashtable();
-
-        String line;
-
-        try {
-            while ((line = nextLine()) != null) {
-                if (line.indexOf(" ") != 0) {
-                    StringTokenizer str = new StringTokenizer(line, " ");
-                    String id = "";
-
-                    if (str.hasMoreTokens()) {
-                        id = str.nextToken();
-
-                        if (id.equals("CLUSTAL")) {
-                            flag = true;
-                        } else {
-                            if (flag) {
-                                StringBuffer tempseq;
-
-                                if (seqhash.containsKey(id)) {
-                                    tempseq = (StringBuffer) seqhash.get(id);
-                                } else {
-                                    tempseq = new StringBuffer();
-                                    seqhash.put(id, tempseq);
-                                }
-
-                                if (!(headers.contains(id))) {
-                                    headers.addElement(id);
-                                }
-
-                                if (str.hasMoreTokens()) {
-                                    tempseq.append(str.nextToken());
-                                }
-                            }
-                        }
-                    }
+                if (! (headers.contains(id)))
+                {
+                  headers.addElement(id);
                 }
-            }
-        } catch (IOException e) {
-            System.err.println("Exception parsing clustal file " + e);
-            e.printStackTrace();
-        }
 
-        if (flag) {
-            this.noSeqs = headers.size();
-
-            //Add sequences to the hash
-            for (i = 0; i < headers.size(); i++) {
-                int start = -1;
-                int end = -1;
-
-                if (seqhash.get(headers.elementAt(i)) != null) {
-                    if (maxLength < seqhash.get(headers.elementAt(i)).toString()
-                                               .length()) {
-                        maxLength = seqhash.get(headers.elementAt(i)).toString()
-                                           .length();
-                    }
-
-                    String head = headers.elementAt(i).toString();
-                    start = 1;
-                    end = seqhash.get(headers.elementAt(i)).toString().length();
-
-                    if (head.indexOf("/") > 0) {
-                        StringTokenizer st = new StringTokenizer(head, "/");
-
-                        if (st.countTokens() == 2) {
-                            ids.addElement(st.nextToken());
-
-                            String tmp = st.nextToken();
-                            st = new StringTokenizer(tmp, "-");
-
-                            if (st.countTokens() == 2) {
-                                start = Integer.valueOf(st.nextToken())
-                                               .intValue();
-                                end = Integer.valueOf(st.nextToken()).intValue();
-                            }
-                        } else {
-                            ids.addElement(headers.elementAt(i));
-                        }
-                    } else {
-                        ids.addElement(headers.elementAt(i));
-                    }
-
-                    Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-                            seqhash.get(headers.elementAt(i).toString())
-                                   .toString(), start, end);
-
-                    seqs.addElement(newSeq);
-                } else {
-                    System.err.println(
-                        "Clustal File Reader: Can't find sequence for " +
-                        headers.elementAt(i));
+                if (str.hasMoreTokens())
+                {
+                  tempseq.append(str.nextToken());
                 }
+              }
             }
+          }
         }
+      }
     }
-
-    public String print() {
-        return print(getSeqsAsArray());
+    catch (IOException e)
+    {
+      System.err.println("Exception parsing clustal file " + e);
+      e.printStackTrace();
     }
 
-    public static String print(SequenceI[] s) {
-        StringBuffer out = new StringBuffer("CLUSTAL\n\n");
+    if (flag)
+    {
+      this.noSeqs = headers.size();
+
+      //Add sequences to the hash
+      for (i = 0; i < headers.size(); i++)
+      {
+        int start = -1;
+        int end = -1;
+
+        if (seqhash.get(headers.elementAt(i)) != null)
+        {
+          if (maxLength < seqhash.get(headers.elementAt(i)).toString()
+              .length())
+          {
+            maxLength = seqhash.get(headers.elementAt(i)).toString()
+                .length();
+          }
+
+          String head = headers.elementAt(i).toString();
+          start = 1;
+          end = seqhash.get(headers.elementAt(i)).toString().length();
+
+          if (head.indexOf("/") > 0)
+          {
+            StringTokenizer st = new StringTokenizer(head, "/");
+
+            if (st.countTokens() == 2)
+            {
+              ids.addElement(st.nextToken());
+
+              String tmp = st.nextToken();
+              st = new StringTokenizer(tmp, "-");
+
+              if (st.countTokens() == 2)
+              {
+                start = Integer.valueOf(st.nextToken())
+                    .intValue();
+                end = Integer.valueOf(st.nextToken()).intValue();
+              }
+            }
+            else
+            {
+              ids.addElement(headers.elementAt(i));
+            }
+          }
+          else
+          {
+            ids.addElement(headers.elementAt(i));
+          }
+
+          Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
+                                         seqhash.get(headers.elementAt(i).
+              toString())
+                                         .toString(), start, end);
+
+          seqs.addElement(newSeq);
+        }
+        else
+        {
+          System.err.println(
+              "Clustal File Reader: Can't find sequence for " +
+              headers.elementAt(i));
+        }
+      }
+    }
+  }
 
-        int max = 0;
-        int maxid = 0;
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
 
-        int i = 0;
+  public static String print(SequenceI[] s)
+  {
+    StringBuffer out = new StringBuffer("CLUSTAL\n\n");
 
-        while ((i < s.length) && (s[i] != null)) {
-            String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
-                s[i].getEnd();
+    int max = 0;
+    int maxid = 0;
 
-            if (s[i].getSequence().length() > max) {
-                max = s[i].getSequence().length();
-            }
+    int i = 0;
 
-            if (tmp.length() > maxid) {
-                maxid = tmp.length();
-            }
+    while ( (i < s.length) && (s[i] != null))
+    {
+      String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
+          s[i].getEnd();
 
-            i++;
-        }
+      if (s[i].getSequence().length() > max)
+      {
+        max = s[i].getSequence().length();
+      }
 
-        if (maxid < 15) {
-            maxid = 15;
-        }
+      if (tmp.length() > maxid)
+      {
+        maxid = tmp.length();
+      }
 
-        maxid++;
+      i++;
+    }
 
-        int len = 60;
-        int nochunks = (max / len) + 1;
+    if (maxid < 15)
+    {
+      maxid = 15;
+    }
 
-        for (i = 0; i < nochunks; i++) {
-            int j = 0;
+    maxid++;
 
-            while ((j < s.length) && (s[j] != null)) {
-                out.append(new Format("%-" + maxid + "s").form(s[j].getName() +
-                        "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
+    int len = 60;
+    int nochunks = (max / len) + 1;
 
-                int start = i * len;
-                int end = start + len;
+    for (i = 0; i < nochunks; i++)
+    {
+      int j = 0;
 
-                if ((end < s[j].getSequence().length()) &&
-                        (start < s[j].getSequence().length())) {
-                    out.append(s[j].getSequence().substring(start, end));
-                } else {
-                    if (start < s[j].getSequence().length()) {
-                        out.append(s[j].getSequence().substring(start));
-                    }
-                }
+      while ( (j < s.length) && (s[j] != null))
+      {
+        out.append(new Format("%-" + maxid + "s").form(s[j].getName() +
+            "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
 
-                out.append("\n");
-                j++;
-            }
+        int start = i * len;
+        int end = start + len;
 
-            out.append("\n");
+        if ( (end < s[j].getSequence().length()) &&
+            (start < s[j].getSequence().length()))
+        {
+          out.append(s[j].getSequence().substring(start, end));
+        }
+        else
+        {
+          if (start < s[j].getSequence().length())
+          {
+            out.append(s[j].getSequence().substring(start));
+          }
         }
 
-        return out.toString();
+        out.append("\n");
+        j++;
+      }
+
+      out.append("\n");
     }
+
+    return out.toString();
+  }
 }
diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index 5b21bfe..2c829ff 100755
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -32,83 +32,151 @@ import javax.xml.namespace.QName;
 import javax.xml.rpc.ParameterMode;
 
 
-public class EBIFetchClient {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
     Call call;
     String format = "default";
     String style = "raw";
 
-    public EBIFetchClient() {
-        try {
+    /**
+     * Creates a new EBIFetchClient object.
+     */
+    public EBIFetchClient()
+    {
+        try
+        {
             call = (Call) new Service().createCall();
             call.setTargetEndpointAddress(new java.net.URL(
                     "http://www.ebi.ac.uk/ws/services/Dbfetch"));
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
         }
     }
 
-    public String[] getSupportedDBs() {
-        try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String[] getSupportedDBs()
+    {
+        try
+        {
             call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
             call.setReturnType(XMLType.SOAP_ARRAY);
 
             return (String[]) call.invoke(new Object[] {  });
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             return null;
         }
     }
 
-    public String[] getSupportedFormats() {
-        try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String[] getSupportedFormats()
+    {
+        try
+        {
             call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
             call.setReturnType(XMLType.SOAP_ARRAY);
 
             return (String[]) call.invoke(new Object[] {  });
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             return null;
         }
     }
 
-    public String[] getSupportedStyles() {
-        try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String[] getSupportedStyles()
+    {
+        try
+        {
             call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
             call.setReturnType(XMLType.SOAP_ARRAY);
 
             return (String[]) call.invoke(new Object[] {  });
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             return null;
         }
     }
 
-    public String[] fetchData(String ids, String f, String s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ids DOCUMENT ME!
+     * @param f DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String[] fetchData(String ids, String f, String s)
+    {
         // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;
         // max 50 ids can be added at one time
-        try {
+        try
+        {
             call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
             call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);
             call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
             call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
             call.setReturnType(XMLType.SOAP_ARRAY);
 
-            if (f != null) {
+            if (f != null)
+            {
                 format = f;
             }
 
-            if (s != null) {
+            if (s != null)
+            {
                 style = s;
             }
 
             return (String[]) call.invoke(new Object[] { ids, format, style });
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             return null;
         }
     }
 
-    public String fetchDataFile(String arg, String f, String s) {
-        if (f != null) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param arg DOCUMENT ME!
+     * @param f DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String fetchDataFile(String arg, String f, String s)
+    {
+        if (f != null)
+        {
             format = f;
         }
 
-        if (s != null) {
+        if (s != null)
+        {
             style = s;
         }
 
@@ -124,21 +192,25 @@ public class EBIFetchClient {
 
         call.setReturnType(qnameAttachment);
 
-        try {
+        try
+        {
             Object ret = call.invoke(new Object[] { arg, format, style });
 
-            if (null == ret) {
+            if (null == ret)
+            {
                 System.err.println("Received null ");
                 throw new AxisFault("", "Received null", null, null);
             }
 
-            if (ret instanceof String) {
+            if (ret instanceof String)
+            {
                 System.err.println("Received problem response from server: " +
                     ret);
                 throw new AxisFault("", (String) ret, null, null);
             }
 
-            if (!(ret instanceof DataHandler)) {
+            if (!(ret instanceof DataHandler))
+            {
                 //The wrong type of object that what was expected.
                 System.err.println("Received problem response from server:" +
                     ret.getClass().getName());
@@ -153,20 +225,28 @@ public class EBIFetchClient {
             //From here we'll just treat the data resource as file.
             String receivedfileName = rdh.getName(); //Get the filename.
 
-            if (receivedfileName == null) {
+            if (receivedfileName == null)
+            {
                 System.err.println("Could not get the file name.");
                 throw new AxisFault("", "Could not get the file name.", null,
                     null);
             }
 
-            if (arg.equalsIgnoreCase("medline")) {
+            if (arg.equalsIgnoreCase("medline"))
+            {
                 return receivedfileName;
-            } else if (arg.equalsIgnoreCase("interpro")) {
+            }
+            else if (arg.equalsIgnoreCase("interpro"))
+            {
                 return receivedfileName;
-            } else {
+            }
+            else
+            {
                 System.err.println(receivedfileName);
             }
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             ex.printStackTrace();
         }
 
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 458465e..757bb57 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -27,19 +27,51 @@ import java.io.*;
 import java.util.*;
 
 
-public class FastaFile extends AlignFile {
-    public FastaFile() {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FastaFile extends AlignFile
+{
+    /**
+     * Creates a new FastaFile object.
+     */
+    public FastaFile()
+    {
     }
 
-    public FastaFile(String inStr) {
+    /**
+     * Creates a new FastaFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public FastaFile(String inStr)
+    {
         super(inStr);
     }
 
-    public FastaFile(String inFile, String type) throws IOException {
+    /**
+     * Creates a new FastaFile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public FastaFile(String inFile, String type) throws IOException
+    {
         super(inFile, type);
     }
 
-    public void parse() throws IOException {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public void parse() throws IOException
+    {
         String id = "";
         StringBuffer seq = new StringBuffer();
         int count = 0;
@@ -49,20 +81,25 @@ public class FastaFile extends AlignFile {
 
         String line;
 
-        while ((line = nextLine()) != null) {
-            if (line.length() > 0) {
+        while ((line = nextLine()) != null)
+        {
+            if (line.length() > 0)
+            {
                 // Do we have an id line?
                 // JBPNote - this code needs to be standardised to EBI/whatever for the
                 // >dbref/dbref/dbref|refid1|refid2|refid3 'human-readable' style of naming (should it really exist)
-
-                if (line.substring(0, 1).equals(">")) {
-                    if (count != 0) {
-                        if (sstart != 0) {
-                            seqs.addElement(new Sequence(id,
-                                    seq.toString(), sstart, send));
-                        } else {
-                            seqs.addElement(new Sequence(id,
-                                    seq.toString(), 1,
+                if (line.substring(0, 1).equals(">"))
+                {
+                    if (count != 0)
+                    {
+                        if (sstart != 0)
+                        {
+                            seqs.addElement(new Sequence(id, seq.toString(),
+                                    sstart, send));
+                        }
+                        else
+                        {
+                            seqs.addElement(new Sequence(id, seq.toString(), 1,
                                     seq.length()));
                         }
                     }
@@ -76,31 +113,39 @@ public class FastaFile extends AlignFile {
 
                     com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(
                             "[A-Za-z-]+/?[A-Za-z-]+\\|(\\w+)\\|(.+)");
+
                     // JBPNote At the moment - we don't get rid of the friendly names but this
                     // behaviour is probably wrong in the long run.
-                    if (dbId.search(id)) {
+                    if (dbId.search(id))
+                    {
                         String dbid = dbId.stringMatched(1);
                         String idname = dbId.stringMatched(2);
-                        if ( (idname.length() > 0) &&
-                             (idname.indexOf("_") > -1)) {
-                          id = idname; // use the friendly name - apparently no dbid
-                        } else
-                        if (dbid.length()>1) {
+
+                        if ((idname.length() > 0) &&
+                                (idname.indexOf("_") > -1))
+                        {
+                            id = idname; // use the friendly name - apparently no dbid
+                        }
+                        else if (dbid.length() > 1)
+                        {
                             id = dbid; // ignore the friendly name - we lose uniprot accession ID otherwise
                         }
                     }
 
-                    if (id.indexOf("/") > 0) {
+                    if (id.indexOf("/") > 0)
+                    {
                         StringTokenizer st = new StringTokenizer(id, "/");
 
-                        if (st.countTokens() == 2) {
+                        if (st.countTokens() == 2)
+                        {
                             id = st.nextToken();
 
                             String tmp = st.nextToken();
 
                             st = new StringTokenizer(tmp, "-");
 
-                            if (st.countTokens() == 2) {
+                            if (st.countTokens() == 2)
+                            {
                                 sstart = Integer.valueOf(st.nextToken())
                                                 .intValue();
                                 send = Integer.valueOf(st.nextToken()).intValue();
@@ -109,50 +154,99 @@ public class FastaFile extends AlignFile {
                     }
 
                     seq = new StringBuffer();
-                } else {
+                }
+                else
+                {
                     seq = seq.append(line);
                 }
             }
         }
 
-        if (count > 0) {
-            if (!isValidProteinSequence(seq.toString().toUpperCase())) {
+        if (count > 0)
+        {
+            if (!isValidProteinSequence(seq.toString().toUpperCase()))
+            {
                 throw new IOException("Invalid protein sequence");
             }
 
-            if (sstart != 0) {
+            if (sstart != 0)
+            {
                 seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),
                         sstart, send));
-            } else {
+            }
+            else
+            {
                 seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),
                         1, seq.length()));
             }
         }
     }
 
-    public static String print(SequenceI[] s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String print(SequenceI[] s)
+    {
         return print(s, 72);
     }
 
-    public static String print(SequenceI[] s, int len) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param len DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String print(SequenceI[] s, int len)
+    {
         return print(s, len, true);
     }
 
-    public static String print(SequenceI[] s, int len, boolean gaps) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param len DOCUMENT ME!
+     * @param gaps DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String print(SequenceI[] s, int len, boolean gaps)
+    {
         return print(s, len, gaps, true);
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param len DOCUMENT ME!
+     * @param gaps DOCUMENT ME!
+     * @param displayId DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public static String print(SequenceI[] s, int len, boolean gaps,
-        boolean displayId) {
+        boolean displayId)
+    {
         StringBuffer out = new StringBuffer();
         int i = 0;
 
-        while ((i < s.length) && (s[i] != null)) {
+        while ((i < s.length) && (s[i] != null))
+        {
             String seq = "";
 
-            if (gaps) {
+            if (gaps)
+            {
                 seq = s[i].getSequence();
-            } else {
+            }
+            else
+            {
                 seq = AlignSeq.extractGaps("-. ", s[i].getSequence());
             }
 
@@ -162,13 +256,17 @@ public class FastaFile extends AlignFile {
 
             int nochunks = (seq.length() / len) + 1;
 
-            for (int j = 0; j < nochunks; j++) {
+            for (int j = 0; j < nochunks; j++)
+            {
                 int start = j * len;
                 int end = start + len;
 
-                if (end < seq.length()) {
+                if (end < seq.length())
+                {
                     out.append(seq.substring(start, end) + "\n");
-                } else if (start < seq.length()) {
+                }
+                else if (start < seq.length())
+                {
                     out.append(seq.substring(start) + "\n");
                 }
             }
@@ -179,7 +277,13 @@ public class FastaFile extends AlignFile {
         return out.toString();
     }
 
-    public String print() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
+    {
         return print(getSeqsAsArray());
     }
 }
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 0c46a17..af3bbec 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,63 +1,72 @@
 /*
-* 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
-*/
+ * 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.io;
 
 import java.io.*;
-
 import java.net.*;
 
+public class FileParse
+{
+  public File inFile;
+  public int fileSize;
+  public int noLines;
+  protected String type;
+  protected BufferedReader dataIn;
 
-public class FileParse {
-    public File inFile;
-    public int fileSize;
-    public int noLines;
-    protected String type;
-    protected BufferedReader dataIn;
+  public FileParse()
+  {
+  }
 
-    public FileParse() {
-    }
+  public FileParse(String fileStr, String type)
+      throws MalformedURLException, IOException
+  {
+    this.type = type;
 
-    public FileParse(String fileStr, String type)
-        throws MalformedURLException, IOException {
-        this.type = type;
-
-        if (type.equals("File")) {
-            this.inFile = new File(fileStr);
-            this.fileSize = (int) inFile.length();
-
-            dataIn = new BufferedReader(new FileReader(fileStr));
-        } else if (type.equals("URL")) {
-            URL url = new URL(fileStr);
-            this.fileSize = 0;
-            dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-        } else if (type.equals("Paste")) {
-            dataIn = new BufferedReader(new StringReader(fileStr));
-        }
-    }
+    if (type.equals("File"))
+    {
+      this.inFile = new File(fileStr);
+      this.fileSize = (int) inFile.length();
 
-    public String nextLine() throws IOException {
-        String next = dataIn.readLine();
+      dataIn = new BufferedReader(new FileReader(fileStr));
+    }
+    else if (type.equals("URL"))
+    {
+      URL url = new URL(fileStr);
+      this.fileSize = 0;
+      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    }
+    else if (type.equals("Paste"))
+    {
+      dataIn = new BufferedReader(new StringReader(fileStr));
+    }
+  }
 
-        if (next != null) {
-            noLines++;
-        }
+  public String nextLine()
+      throws IOException
+  {
+    String next = dataIn.readLine();
 
-        return next;
+    if (next != null)
+    {
+      noLines++;
     }
+
+    return next;
+  }
 }
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index e59c191..6ac110d 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -23,10 +23,19 @@ import jalview.datamodel.*;
 import java.util.Vector;
 
 
-public class FormatAdapter {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FormatAdapter
+{
+    /** DOCUMENT ME!! */
     public static Vector formats = new Vector();
 
-    static {
+    static
+    {
         formats.addElement("FASTA");
         formats.addElement("MSF");
         formats.addElement("PileUp");
@@ -36,28 +45,54 @@ public class FormatAdapter {
         formats.addElement("PFAM");
     }
 
-    public static SequenceI[] readFile(String inFile, String type, String format) {
-        try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     * @param format DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static SequenceI[] readFile(String inFile, String type, String format)
+    {
+        try
+        {
             AlignFile afile = null;
 
-            if (format.equals("FASTA")) {
+            if (format.equals("FASTA"))
+            {
                 afile = new FastaFile(inFile, type);
-            } else if (format.equals("MSF")) {
+            }
+            else if (format.equals("MSF"))
+            {
                 afile = new MSFfile(inFile, type);
-            } else if (format.equals("PileUp")) {
+            }
+            else if (format.equals("PileUp"))
+            {
                 afile = new PileUpfile(inFile, type);
-            } else if (format.equals("CLUSTAL")) {
+            }
+            else if (format.equals("CLUSTAL"))
+            {
                 afile = new ClustalFile(inFile, type);
-            } else if (format.equals("BLC")) {
+            }
+            else if (format.equals("BLC"))
+            {
                 afile = new BLCFile(inFile, type);
-            } else if (format.equals("PIR")) {
+            }
+            else if (format.equals("PIR"))
+            {
                 afile = new PIRFile(inFile, type);
-            } else if (format.equals("PFAM")) {
+            }
+            else if (format.equals("PFAM"))
+            {
                 afile = new PfamFile(inFile, type);
             }
 
             return afile.getSeqsAsArray();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             System.err.println("Failed to read alignment using the '" + format +
                 "' reader.");
             e.printStackTrace();
@@ -66,35 +101,60 @@ public class FormatAdapter {
         return null;
     }
 
-    public static String formatSequences(String format, Vector seqs) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param format DOCUMENT ME!
+     * @param seqs DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String formatSequences(String format, Vector seqs)
+    {
         SequenceI[] s = new SequenceI[seqs.size()];
 
         for (int i = 0; i < seqs.size(); i++)
             s[i] = (SequenceI) seqs.elementAt(i);
 
-        try {
+        try
+        {
             AlignFile afile = null;
 
-            if (format.equals("FASTA")) {
+            if (format.equalsIgnoreCase("FASTA"))
+            {
                 afile = new FastaFile();
-            } else if (format.equals("MSF")) {
+            }
+            else if (format.equalsIgnoreCase("MSF"))
+            {
                 afile = new MSFfile();
-            } else if (format.equals("PileUp")) {
+            }
+            else if (format.equalsIgnoreCase("PileUp"))
+            {
                 afile = new PileUpfile();
-            } else if (format.equals("CLUSTAL")) {
+            }
+            else if (format.equalsIgnoreCase("CLUSTAL"))
+            {
                 afile = new ClustalFile();
-            } else if (format.equals("BLC")) {
+            }
+            else if (format.equalsIgnoreCase("BLC"))
+            {
                 afile = new BLCFile();
-            } else if (format.equals("PIR")) {
+            }
+            else if (format.equalsIgnoreCase("PIR"))
+            {
                 afile = new PIRFile();
-            } else if (format.equals("PFAM")) {
+            }
+            else if (format.equalsIgnoreCase("PFAM"))
+            {
                 afile = new PfamFile();
             }
 
             afile.setSeqs(s);
 
             return afile.print();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             System.err.println("Failed to write alignment as a '" + format +
                 "' file\n");
             e.printStackTrace();
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 54b9595..e4dc83e 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,267 +1,398 @@
 /*
-* 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
-*/
+ * 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.io;
 
-import jalview.datamodel.*;
-
-import jalview.gui.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-
 import java.io.*;
 
-import java.util.*;
-
-import javax.swing.*;
-
-
-public class HTMLOutput {
-    AlignViewport av;
-    SequenceRenderer sr;
-    Color color;
-
-    public HTMLOutput(AlignViewport av) {
-        this.av = av;
-        sr = new SequenceRenderer(av);
-
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
-                    "LAST_DIRECTORY"), new String[] { "html" },
-                new String[] { "HTML files" }, "HTML files");
-
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Save as HTML");
-        chooser.setToolTipText("Save");
-
-        int value = chooser.showSaveDialog(null);
-
-        if (value == JalviewFileChooser.APPROVE_OPTION) {
-            String choice = chooser.getSelectedFile().getPath();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
-
-            try {
-                PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-                            choice));
-                out.println("<HTML>");
-                out.println("<style type=\"text/css\">");
-                out.println("<!--");
-                out.print("td {font-family: \"" + av.getFont().getFamily() +
-                    "\", \"" + av.getFont().getName() + "\", mono; " +
-                    "font-size: " + av.getFont().getSize() + "px; ");
-
-                if (av.getFont().getStyle() == Font.BOLD) {
-                    out.print("font-weight: BOLD; ");
-                }
-
-                if (av.getFont().getStyle() == Font.ITALIC) {
-                    out.print("font-style: italic; ");
-                }
-
-                out.println("text-align: center; }");
-
-                out.println("-->");
-                out.println("</style>");
-                out.println("<BODY>");
+import java.awt.*;
 
-                if (av.getWrapAlignment()) {
-                    drawWrappedAlignment(out);
-                } else {
-                    drawUnwrappedAlignment(out);
-                }
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.schemes.*;
 
-                out.println("\n</body>\n</html>");
-                out.close();
-                jalview.util.BrowserLauncher.openURL("file:///" + choice);
-            } catch (Exception ex) {
-                ex.printStackTrace();
-            }
+public class HTMLOutput
+{
+  AlignViewport av;
+  SequenceRenderer sr;
+  Color color;
+
+  public HTMLOutput(AlignViewport av)
+  {
+    this.av = av;
+    sr = new SequenceRenderer(av);
+
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"), new String[]
+        {"html"},
+        new String[]
+        {"HTML files"}, "HTML files");
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save as HTML");
+    chooser.setToolTipText("Save");
+
+    int value = chooser.showSaveDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
+
+      try
+      {
+        PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+            choice));
+        out.println("<HTML>");
+        out.println("<style type=\"text/css\">");
+        out.println("<!--");
+        out.print("td {font-family: \"" + av.getFont().getFamily() +
+                  "\", \"" + av.getFont().getName() + "\", mono; " +
+                  "font-size: " + av.getFont().getSize() + "px; ");
+
+        if (av.getFont().getStyle() == Font.BOLD)
+        {
+          out.print("font-weight: BOLD; ");
         }
-    }
 
-    void drawUnwrappedAlignment(PrintWriter out) {
-        out.println("<table border=\"1\"><tr><td>\n");
-        out.println(
-            "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+        if (av.getFont().getStyle() == Font.ITALIC)
+        {
+          out.print("font-style: italic; ");
+        }
 
-        //////////////
-        SequenceGroup[] groups;
-        SequenceI seq;
-        ColourSchemeI cs = null;
-        AlignmentI alignment = av.getAlignment();
-        String r;
-        String g;
-        String b;
+        out.println("text-align: center; }");
 
-        // draws the top row, the measure rule
-        out.println("<tr><td colspan=\"6\"></td>");
+        out.println("-->");
+        out.println("</style>");
+        out.println("<BODY>");
 
-        int i = 0;
+        if (av.getWrapAlignment())
+        {
+          drawWrappedAlignment(out);
+        }
+        else
+        {
+          drawUnwrappedAlignment(out);
+        }
 
-        for (i = 10; i < (alignment.getWidth() - 10); i += 10)
-            out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+        out.println("\n</body>\n</html>");
+        out.close();
+        jalview.util.BrowserLauncher.openURL("file:///" + choice);
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+  }
+
+  void drawUnwrappedAlignment(PrintWriter out)
+  {
+    out.println("<table border=\"1\"><tr><td>\n");
+    out.println(
+        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+
+    //////////////
+    SequenceGroup[] groups;
+    SequenceI seq;
+    ColourSchemeI cs = null;
+    AlignmentI alignment = av.getAlignment();
+    String r;
+    String g;
+    String b;
+
+    // draws the top row, the measure rule
+    out.println("<tr><td colspan=\"6\"></td>");
+
+    int i = 0;
+
+    for (i = 10; i < (alignment.getWidth() - 10); i += 10)
+    {
+      out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+    }
 
-        out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
-            "<br>|</td>");
-        out.println("</tr>");
+    out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
+                "<br>|</td>");
+    out.println("</tr>");
 
-        for (i = 0; i < alignment.getHeight(); i++) {
-            seq = alignment.getSequenceAt(i);
-            groups = alignment.findAllGroups(seq);
+    for (i = 0; i < alignment.getHeight(); i++)
+    {
+      seq = alignment.getSequenceAt(i);
+      groups = alignment.findAllGroups(seq);
 
-            if (av.getShowFullId()) {
-                out.println("<tr><td nowrap>" + seq.getDisplayId() +
+      if (av.getShowFullId())
+      {
+        out.println("<tr><td nowrap>" + seq.getDisplayId() +
                     "&nbsp;&nbsp;</td>");
-            } else {
-                out.println("<tr><td nowrap>" + seq.getName() +
+      }
+      else
+      {
+        out.println("<tr><td nowrap>" + seq.getName() +
                     "&nbsp;&nbsp;</td>");
+      }
+
+      for (int res = 0; res < seq.getLength(); res++)
+      {
+        cs = av.getGlobalColourScheme();
+
+        if (groups != null)
+        {
+          for (int k = 0; k < groups.length; k++)
+          {
+            if ( (groups[k].getStartRes() <= res) &&
+                (groups[k].getEndRes() >= res))
+            {
+              cs = groups[k].cs;
+
+              break;
             }
+          }
+        }
 
-            for (int res = 0; res < seq.getLength(); res++) {
-                cs = av.getGlobalColourScheme();
-
-                if (groups != null) {
-                    for (int k = 0; k < groups.length; k++)
-                        if ((groups[k].getStartRes() <= res) &&
-                                (groups[k].getEndRes() >= res)) {
-                            cs = groups[k].cs;
-
-                            break;
-                        }
-                }
-
-                color = sr.getResidueBoxColour(cs, seq, res);
+        color = sr.getResidueBoxColour(cs, seq, res);
 
-                if (color.getRGB() < -1) {
-                    out.println("<td bgcolor=\"#" +
-                        jalview.util.Format.getHexString(color) + "\">" +
-                        seq.getCharAt(res) + "</td>");
-                } else {
-                    out.println("<td>" + seq.getCharAt(res) + "</td>");
-                }
-            }
-
-            out.println("</tr>");
+        if (color.getRGB() < -1)
+        {
+          out.println("<td bgcolor=\"#" +
+                      jalview.util.Format.getHexString(color) + "\">" +
+                      seq.getCharAt(res) + "</td>");
+        }
+        else
+        {
+          out.println("<td>" + seq.getCharAt(res) + "</td>");
         }
+      }
 
-        //////////////
-        out.println("</table>");
-        out.println("</td></tr></table>");
+      out.println("</tr>");
     }
 
-    void drawWrappedAlignment(PrintWriter out) {
-        ////////////////////////////////////
-        /// How many sequences and residues can we fit on a printable page?
-        AlignmentI al = av.getAlignment();
-        SequenceGroup[] groups;
-        SequenceI seq;
-        ColourSchemeI cs = null;
-        String r;
-        String g;
-        String b;
-
-        out.println("<table border=\"1\"><tr><td>\n");
-        out.println(
-            "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
-
-        for (int startRes = 0; startRes < al.getWidth();
-                startRes += av.getChunkWidth()) {
-            int endRes = startRes + av.getChunkWidth();
-
-            if (endRes > al.getWidth()) {
-                endRes = al.getWidth();
-            }
-
-            out.println("<tr>");
-            out.println("<td colspan=\"6\">&nbsp;</td>");
-
-            for (int i = startRes + 10; i < endRes; i += 10)
-                out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
-
-            // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
-            //             "<br>|</td>");
-            out.println("</tr>");
-
-            for (int s = 0; s < al.getHeight(); s++) {
-                out.println("<tr>");
-                seq = al.getSequenceAt(s);
-                groups = al.findAllGroups(seq);
-
-                if (av.getShowFullId()) {
-                    out.println("<td nowrap>" + seq.getDisplayId() +
-                        "&nbsp;&nbsp;</td>");
-                } else {
-                    out.println("<td nowrap>" + seq.getName() +
-                        "&nbsp;&nbsp;</td>");
-                }
-
-                for (int res = startRes; res < endRes; res++) {
-                    cs = av.getGlobalColourScheme();
-
-                    if (groups != null) {
-                        for (int k = 0; k < groups.length; k++)
-                            if ((groups[k].getStartRes() <= res) &&
-                                    (groups[k].getEndRes() >= res)) {
-                                cs = groups[k].cs;
-
-                                break;
-                            }
-                    }
-
-                    color = sr.getResidueBoxColour(cs, seq, res);
+    //////////////
+    out.println("</table>");
+    out.println("</td></tr></table>");
+  }
+
+  void drawWrappedAlignment(PrintWriter out)
+  {
+    ////////////////////////////////////
+    /// How many sequences and residues can we fit on a printable page?
+    AlignmentI al = av.getAlignment();
+    SequenceGroup[] groups;
+    SequenceI seq;
+    ColourSchemeI cs = null;
+    String r;
+    String g;
+    String b;
+
+    out.println("<table border=\"1\"><tr><td>\n");
+    out.println(
+        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+
+    for (int startRes = 0; startRes < al.getWidth();
+         startRes += av.getChunkWidth())
+    {
+      int endRes = startRes + av.getChunkWidth();
+
+      if (endRes > al.getWidth())
+      {
+        endRes = al.getWidth();
+      }
+
+      out.println("<tr>");
+      out.println("<td colspan=\"6\">&nbsp;</td>");
+
+      for (int i = startRes + 10; i < endRes; i += 10)
+      {
+        out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+      }
+
+      // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
+      //             "<br>|</td>");
+      out.println("</tr>");
+
+      for (int s = 0; s < al.getHeight(); s++)
+      {
+        out.println("<tr>");
+        seq = al.getSequenceAt(s);
+        groups = al.findAllGroups(seq);
+
+        if (av.getShowFullId())
+        {
+          out.println("<td nowrap>" + seq.getDisplayId() +
+                      "&nbsp;&nbsp;</td>");
+        }
+        else
+        {
+          out.println("<td nowrap>" + seq.getName() +
+                      "&nbsp;&nbsp;</td>");
+        }
 
-                    if (color.getRGB() < -1) {
-                        r = Integer.toHexString(color.getRed());
+        for (int res = startRes; res < endRes; res++)
+        {
+          cs = av.getGlobalColourScheme();
+
+          if (groups != null)
+          {
+            for (int k = 0; k < groups.length; k++)
+            {
+              if ( (groups[k].getStartRes() <= res) &&
+                  (groups[k].getEndRes() >= res))
+              {
+                cs = groups[k].cs;
+
+                break;
+              }
+            }
+          }
 
-                        if (r.length() < 2) {
-                            r = "0" + r;
-                        }
+          color = sr.getResidueBoxColour(cs, seq, res);
 
-                        g = Integer.toHexString(color.getGreen());
+          if (color.getRGB() < -1)
+          {
+            r = Integer.toHexString(color.getRed());
 
-                        if (g.length() < 2) {
-                            g = "0" + g;
-                        }
+            if (r.length() < 2)
+            {
+              r = "0" + r;
+            }
 
-                        b = Integer.toHexString(color.getBlue());
+            g = Integer.toHexString(color.getGreen());
 
-                        if (b.length() < 2) {
-                            b = "0" + b;
-                        }
+            if (g.length() < 2)
+            {
+              g = "0" + g;
+            }
 
-                        out.println("<td bgcolor=\"#" + r + g + b + "\">" +
-                            seq.getCharAt(res) + "</td>");
-                    } else {
-                        out.println("<td>" + seq.getCharAt(res) + "</td>");
-                    }
-                }
+            b = Integer.toHexString(color.getBlue());
 
-                out.println("</tr>");
+            if (b.length() < 2)
+            {
+              b = "0" + b;
             }
 
-            if (endRes < al.getWidth()) {
-                out.println("<tr><td height=\"5\"></td></tr>");
-            }
+            out.println("<td bgcolor=\"#" + r + g + b + "\">" +
+                        seq.getCharAt(res) + "</td>");
+          }
+          else
+          {
+            out.println("<td>" + seq.getCharAt(res) + "</td>");
+          }
         }
 
-        out.println("</table>");
-        out.println("</table>");
+        out.println("</tr>");
+      }
+
+      if (endRes < al.getWidth())
+      {
+        out.println("<tr><td height=\"5\"></td></tr>");
+      }
     }
+
+    out.println("</table>");
+    out.println("</table>");
+  }
+
+  public static String getImageMapHTML()
+  {
+    return new String(
+      "<html>\n"
+      +"<head>\n"
+      +"<script language=\"JavaScript\">\n"
+      +"var ns4 = document.layers;\n"
+      +"var ns6 = document.getElementById && !document.all;\n"
+      +"var ie4 = document.all;\n"
+      +"offsetX = 0;\n"
+      +"offsetY = 20;\n"
+      +"var toolTipSTYLE=\"\";\n"
+      +"function initToolTips()\n"
+      +"{\n"
+      +"  if(ns4||ns6||ie4)\n"
+      +"  {\n"
+      +"    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+      +"    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+      +"    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+      +"    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+      +"    else\n"
+      +"    {\n"
+      +"      toolTipSTYLE.visibility = \"visible\";\n"
+      +"      toolTipSTYLE.display = \"none\";\n"
+      +"    }\n"
+      +"    document.onmousemove = moveToMouseLoc;\n"
+      +"  }\n"
+      +"}\n"
+      +"function toolTip(msg, fg, bg)\n"
+      +"{\n"
+      +"  if(toolTip.arguments.length < 1) // hide\n"
+      +"  {\n"
+      +"    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+      +"    else toolTipSTYLE.display = \"none\";\n"
+      +"  }\n"
+      +"  else // show\n"
+      +"  {\n"
+      +"    if(!fg) fg = \"#555555\";\n"
+      +"    if(!bg) bg = \"#FFFFFF\";\n"
+      +"    var content =\n"
+      +"    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+      +"    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+      +"    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+      +"    '\" size=\"-2\">&nbsp;' + msg +\n"
+      +"    '&nbsp;</font></td></table></td></table>';\n"
+      +"    if(ns4)\n"
+      +"    {\n"
+      +"      toolTipSTYLE.document.write(content);\n"
+      +"      toolTipSTYLE.document.close();\n"
+      +"      toolTipSTYLE.visibility = \"visible\";\n"
+      +"    }\n"
+      +"    if(ns6)\n"
+      +"    {\n"
+      +"      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+      +"      toolTipSTYLE.display='block'\n"
+      +"    }\n"
+      +"    if(ie4)\n"
+      +"    {\n"
+      +"      document.all(\"toolTipLayer\").innerHTML=content;\n"
+      +"      toolTipSTYLE.display='block'\n"
+      +"    }\n"
+      +"  }\n"
+      +"}\n"
+      +"function moveToMouseLoc(e)\n"
+      +"{\n"
+      +"  if(ns4||ns6)\n"
+      +"  {\n"
+      +"    x = e.pageX;\n"
+      +"    y = e.pageY;\n"
+      +"  }\n"
+      +"  else\n"
+      +"  {\n"
+      +"    x = event.x + document.body.scrollLeft;\n"
+      +"    y = event.y + document.body.scrollTop;\n"
+      +"  }\n"
+      +"  toolTipSTYLE.left = x + offsetX;\n"
+      +"  toolTipSTYLE.top = y + offsetY;\n"
+      +"  return true;\n"
+      +"}\n"
+      +"</script>\n"
+      +"</head>\n"
+      +"<body>\n"
+      +"<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+      +"<script language=\"JavaScript\"><!--\n"
+      +"initToolTips(); //--></script>\n");
+
+  }
 }
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 2442b4b..dbee007 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -23,37 +23,61 @@ import java.io.*;
 import java.net.*;
 
 
-public class IdentifyFile {
-    public static String Identify(String file, String protocol) {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdentifyFile
+{
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     * @param protocol DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String Identify(String file, String protocol)
+    {
         String reply = "PFAM";
 
-        try {
+        try
+        {
             BufferedReader reader = null;
 
-            if (protocol.equals("File")) {
+            if (protocol.equals("File"))
+            {
                 reader = new BufferedReader(new FileReader(file));
             }
-            else if (protocol.equals("URL")) {
+            else if (protocol.equals("URL"))
+            {
                 reply = "URL NOT FOUND";
 
                 URL url = new URL(file);
                 reader = new BufferedReader(new InputStreamReader(
                             url.openStream()));
                 reply = "error";
-            } else if (protocol.equals("Paste")) {
+            }
+            else if (protocol.equals("Paste"))
+            {
                 reader = new BufferedReader(new StringReader(file));
             }
 
             String data;
 
-            while ((data = reader.readLine()) != null) {
+            while ((data = reader.readLine()) != null)
+            {
                 data = data.toUpperCase();
 
-                if ((data.indexOf("#") == 0) || (data.length() < 1)) {
+                if ((data.indexOf("#") == 0) || (data.length() < 1))
+                {
                     continue;
                 }
 
-                if (data.indexOf("PILEUP") > -1) {
+                if (data.indexOf("PILEUP") > -1)
+                {
                     reply = "PileUp";
 
                     break;
@@ -62,26 +86,36 @@ public class IdentifyFile {
                 if ((data.indexOf("//") == 0) ||
                         ((data.indexOf("!!") > -1) &&
                         (data.indexOf("!!") < data.indexOf(
-                            "_MULTIPLE_ALIGNMENT ")))) {
+                            "_MULTIPLE_ALIGNMENT "))))
+                {
                     reply = "MSF";
 
                     break;
-                } else if (data.indexOf("CLUSTAL") > -1) {
+                }
+                else if (data.indexOf("CLUSTAL") > -1)
+                {
                     reply = "CLUSTAL";
 
                     break;
-                } else if ((data.indexOf(">P1;") > -1) ||
-                        (data.indexOf(">DL;") > -1)) {
+                }
+                else if ((data.indexOf(">P1;") > -1) ||
+                        (data.indexOf(">DL;") > -1))
+                {
                     reply = "PIR";
 
                     break;
-                } else if (data.indexOf(">") > -1) {
+                }
+                else if (data.indexOf(">") > -1)
+                {
                     // could be BLC file, read next line to confirm
                     data = reader.readLine();
 
-                    if (data.indexOf(">") > -1) {
+                    if (data.indexOf(">") > -1)
+                    {
                         reply = "BLC";
-                    } else {
+                    }
+                    else
+                    {
                         reply = "FASTA";
                     }
 
@@ -90,7 +124,9 @@ public class IdentifyFile {
             }
 
             reader.close();
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             System.err.println("File Identification failed!\n" + ex);
         }
 
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 12be9de..901c204 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -33,38 +33,88 @@ import java.io.*;
 import java.util.*;
 
 
-public class JPredFile extends AlignFile {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class JPredFile extends AlignFile
+{
     Vector ids;
     Vector conf;
     Hashtable Scores; // Hash of names and score vectors
     Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
     private int QuerySeqPosition;
 
-    public JPredFile(String inStr) {
+    /**
+     * Creates a new JPredFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public JPredFile(String inStr)
+    {
         super(inStr);
     }
 
-    public JPredFile(String inFile, String type) throws IOException {
+    /**
+     * Creates a new JPredFile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public JPredFile(String inFile, String type) throws IOException
+    {
         super(inFile, type);
     }
 
-    public void setQuerySeqPosition(int QuerySeqPosition) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param QuerySeqPosition DOCUMENT ME!
+     */
+    public void setQuerySeqPosition(int QuerySeqPosition)
+    {
         this.QuerySeqPosition = QuerySeqPosition;
     }
 
-    public int getQuerySeqPosition() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getQuerySeqPosition()
+    {
         return QuerySeqPosition;
     }
 
-    public Hashtable getScores() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Hashtable getScores()
+    {
         return Scores;
     }
 
-    public Hashtable getSymscores() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Hashtable getSymscores()
+    {
         return Symscores;
     }
 
-    public void initData() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void initData()
+    {
         super.initData();
         Scores = new Hashtable();
         ids = null;
@@ -74,7 +124,8 @@ public class JPredFile extends AlignFile {
     /**
  * parse a JPred concise file into a sequence-alignment like object.
  */
-    public void parse() throws IOException {
+    public void parse() throws IOException
+    {
         // JBPNote log.System.out.println("all read in ");
         String line;
         QuerySeqPosition = -1;
@@ -84,12 +135,14 @@ public class JPredFile extends AlignFile {
         Vector ids = new Vector();
         Hashtable Symscores = new Hashtable();
 
-        while ((line = nextLine()) != null) {
+        while ((line = nextLine()) != null)
+        {
             // Concise format allows no comments or non comma-formatted data
             StringTokenizer str = new StringTokenizer(line, ":");
             String id = "";
 
-            if (!str.hasMoreTokens()) {
+            if (!str.hasMoreTokens())
+            {
                 continue;
             }
 
@@ -101,16 +154,20 @@ public class JPredFile extends AlignFile {
             // decide if we have more than just alphanumeric symbols
             int numSymbols = symbols.countTokens();
 
-            if (numSymbols == 0) {
+            if (numSymbols == 0)
+            {
                 continue;
             }
 
-            if (seqsym.length() != (2 * numSymbols)) {
+            if (seqsym.length() != (2 * numSymbols))
+            {
                 // Set of scalars for some property
-                if (Scores.containsKey(id)) {
+                if (Scores.containsKey(id))
+                {
                     int i = 1;
 
-                    while (Scores.containsKey(id + "_" + i)) {
+                    while (Scores.containsKey(id + "_" + i))
+                    {
                         i++;
                     }
 
@@ -123,9 +180,11 @@ public class JPredFile extends AlignFile {
                 int i = 0;
                 String ascore = "dead";
 
-                try {
+                try
+                {
                     // store elements as floats...
-                    while (symbols.hasMoreTokens()) {
+                    while (symbols.hasMoreTokens())
+                    {
                         ascore = symbols.nextToken();
 
                         Float score = new Float(ascore);
@@ -133,55 +192,70 @@ public class JPredFile extends AlignFile {
                     }
 
                     Scores.put(id, scores);
-                } catch (Exception e) {
+                }
+                catch (Exception e)
+                {
                     // or just keep them as strings
                     i = scores.size();
 
-                    for (int j = 0; j < i; j++) {
+                    for (int j = 0; j < i; j++)
+                    {
                         scores.set(j,
                             (Object) ((Float) scores.get(j)).toString());
                     }
 
                     scores.addElement((Object) ascore);
 
-                    while (symbols.hasMoreTokens()) {
+                    while (symbols.hasMoreTokens())
+                    {
                         ascore = symbols.nextToken();
                         scores.addElement((Object) ascore);
                     }
 
                     Scores.put(id, scores);
                 }
-            } else if (id.equals("jnetconf")) {
+            }
+            else if (id.equals("jnetconf"))
+            {
                 // log.debug System.out.println("here");
                 id = "Prediction Confidence";
                 this.conf = new Vector(numSymbols);
 
-                for (int i = 0; i < numSymbols; i++) {
+                for (int i = 0; i < numSymbols; i++)
+                {
                     conf.set(i, (Object) symbols.nextToken());
                 }
-            } else {
+            }
+            else
+            {
                 // Sequence or a prediction string (rendered as sequence)
                 StringBuffer newseq = new StringBuffer();
 
-                for (int i = 0; i < numSymbols; i++) {
+                for (int i = 0; i < numSymbols; i++)
+                {
                     newseq.append(symbols.nextToken());
                 }
 
-                if (id.indexOf(";") > -1) {
+                if (id.indexOf(";") > -1)
+                {
                     seq_entries.addElement(newseq);
 
                     int i = 1;
                     String name = id.substring(id.indexOf(";") + 1);
 
-                    while (ids.lastIndexOf(name) > -1) {
+                    while (ids.lastIndexOf(name) > -1)
+                    {
                         name = id.substring(id.indexOf(";") + 1) + "_" + 1;
                     }
 
                     ids.addElement(name);
 
                     noSeqs++;
-                } else {
-                    if (id.equals("JNETPRED")) {
+                }
+                else
+                {
+                    if (id.equals("JNETPRED"))
+                    {
                         id = "Predicted Secondary Structure";
                     }
 
@@ -193,34 +267,39 @@ public class JPredFile extends AlignFile {
             }
         }
 
-        if (noSeqs < 1) {
+        if (noSeqs < 1)
+        {
             throw new IOException(
                 "JpredFile Parser: No sequence in the prediction!");
         }
 
         maxLength = seq_entries.elementAt(0).toString().length();
 
-        for (int i = 0; i < ids.size(); i++) {
+        for (int i = 0; i < ids.size(); i++)
+        {
             // Add all sequence like objects
             Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
                     seq_entries.elementAt(i).toString(), 1,
                     seq_entries.elementAt(i).toString().length());
 
             if (!Symscores.containsKey(ids.elementAt(i)) &&
-                    !isValidProteinSequence(newSeq.getSequence())) {
+                    !isValidProteinSequence(newSeq.getSequence()))
+            {
                 throw new IOException(
                     "JPredConcise: Not a valid protein sequence - (" +
                     ids.elementAt(i).toString() + ")");
             }
 
-            if (maxLength != seq_entries.elementAt(i).toString().length()) {
+            if (maxLength != seq_entries.elementAt(i).toString().length())
+            {
                 throw new IOException("JPredConcise: Entry (" +
                     ids.elementAt(i).toString() +
                     ") has an unexpected number of columns");
             }
 
             if (newSeq.getName().startsWith("QUERY") &&
-                    (QuerySeqPosition == -1)) {
+                    (QuerySeqPosition == -1))
+            {
                 QuerySeqPosition = seqs.size();
             }
 
@@ -233,20 +312,31 @@ public class JPredFile extends AlignFile {
  *
  * @return String
    */
-    public String print() {
+    public String print()
+    {
         return "Not Supported";
     }
 
-    public static void main(String[] args) {
-        try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param args DOCUMENT ME!
+     */
+    public static void main(String[] args)
+    {
+        try
+        {
             JPredFile blc = new JPredFile(args[0], "File");
 
-            for (int i = 0; i < blc.seqs.size(); i++) {
+            for (int i = 0; i < blc.seqs.size(); i++)
+            {
                 System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() +
                     "\n" + ((Sequence) blc.seqs.elementAt(i)).getSequence() +
                     "\n");
             }
-        } catch (java.io.IOException e) {
+        }
+        catch (java.io.IOException e)
+        {
             System.err.println("Exception " + e);
             e.printStackTrace();
         }
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index d44275a..585ed4f 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -1,21 +1,21 @@
 /*
-* 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
-*/
+ * 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
+ */
 /*///////////////////////////////////////////////////////////////////
 // This file was taken from java forum
 // Re: JFileChooser functioning like normal Windows Apps FileChooser
@@ -26,380 +26,442 @@
 //////////////////////////////////////////////////////////////////
 package jalview.io;
 
-import java.awt.*;
-import java.awt.event.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import java.awt.*;
+import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.plaf.*;
 import javax.swing.plaf.basic.*;
 import javax.swing.plaf.metal.*;
 import javax.swing.table.*;
 
+public class JalviewFileChooser
+    extends JFileChooser
+{
 
-public class JalviewFileChooser extends JFileChooser {
-    private static final int COLUMN_FILENAME = 0;
-    private static final int COLUMN_FILESIZE = 1;
-    private static final int COLUMN_FILETYPE = 2;
-    private static final int COLUMN_FILEDATE = 3;
-    private static final int COLUMN_FILEATTR = 4;
-    private static final int COLUMN_COLCOUNT = 5;
-    private static String[] COLUMNS = null;
-
-    public JalviewFileChooser(String dir, String[] suffix, String[] desc,
-        String selected) {
-        super(dir);
 
-        JalviewFileFilter chosen = null;
+  public JalviewFileChooser(String dir, String[] suffix, String[] desc,
+                            String selected)
+  {
+    super(dir);
 
-        for (int i = 0; i < suffix.length; i++) {
-            JalviewFileFilter jvf = new JalviewFileFilter(suffix[i], desc[i]);
-            addChoosableFileFilter(jvf);
-
-            if ((selected != null) && selected.equalsIgnoreCase(desc[i])) {
-                chosen = jvf;
-            }
-        }
+    JalviewFileFilter chosen = null;
 
-        if (chosen != null) {
-            setFileFilter(chosen);
-        }
+    for (int i = 0; i < suffix.length; i++)
+    {
+      JalviewFileFilter jvf = new JalviewFileFilter(suffix[i], desc[i]);
+      addChoosableFileFilter(jvf);
 
-        initColumns();
+      if ( (selected != null) && selected.equalsIgnoreCase(desc[i]))
+      {
+        chosen = jvf;
+      }
     }
 
-    public JalviewFileChooser(String dir) {
-        super(dir);
-        initColumns();
+    if (chosen != null)
+    {
+      setFileFilter(chosen);
     }
 
-    public String getSelectedFormat() {
-        String format = getFileFilter().getDescription();
-
-        if (format.toUpperCase().startsWith("JALVIEW")) {
-            format = "Jalview";
-        } else if (format.toUpperCase().startsWith("FASTA")) {
-            format = "FASTA";
-        } else if (format.toUpperCase().startsWith("MSF")) {
-            format = "MSF";
-        } else if (format.toUpperCase().startsWith("CLUSTAL")) {
-            format = "CLUSTAL";
-        } else if (format.toUpperCase().startsWith("BLC")) {
-            format = "BLC";
-        } else if (format.toUpperCase().startsWith("PIR")) {
-            format = "PIR";
-        } else if (format.toUpperCase().startsWith("PFAM")) {
-            format = "PFAM";
-        }
+  }
+
+
+  public void setFileFilter(javax.swing.filechooser.FileFilter filter)
+ {
+   super.setFileFilter(filter);
+
+   if (!(getUI() instanceof BasicFileChooserUI)) {
+           return;
+   }
+
+   final BasicFileChooserUI ui = (BasicFileChooserUI) getUI();
+   final String name = ui.getFileName().trim();
+
+   if ((name == null) || (name.length() == 0)) {
+           return;
+   }
+
+   EventQueue.invokeLater(new Thread() {
+           public void run() {
+                   String currentName = ui.getFileName();
+                   if ((currentName == null) || (currentName.length() == 0)) {
+                           ui.setFileName(name);
+                   }
+           }
+	});
+ }
+
 
-        return format;
+  public JalviewFileChooser(String dir)
+  {
+    super(dir);
+  }
+
+  public String getSelectedFormat()
+  {
+    String format = getFileFilter().getDescription();
+
+    if (format.toUpperCase().startsWith("JALVIEW"))
+    {
+      format = "Jalview";
+    }
+    else if (format.toUpperCase().startsWith("FASTA"))
+    {
+      format = "FASTA";
+    }
+    else if (format.toUpperCase().startsWith("MSF"))
+    {
+      format = "MSF";
+    }
+    else if (format.toUpperCase().startsWith("CLUSTAL"))
+    {
+      format = "CLUSTAL";
+    }
+    else if (format.toUpperCase().startsWith("BLC"))
+    {
+      format = "BLC";
+    }
+    else if (format.toUpperCase().startsWith("PIR"))
+    {
+      format = "PIR";
+    }
+    else if (format.toUpperCase().startsWith("PFAM"))
+    {
+      format = "PFAM";
     }
 
-    public int showSaveDialog(Component parent) throws HeadlessException {
-        setDialogType(SAVE_DIALOG);
+    return format;
+  }
 
-        int ret = showDialog(parent, null);
+  public int showSaveDialog(Component parent)
+      throws HeadlessException
+  {
+    setDialogType(SAVE_DIALOG);
 
-        if (getFileFilter() instanceof JalviewFileFilter) {
-            JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
+    int ret = showDialog(parent, null);
 
-            if (!jvf.accept(getSelectedFile())) {
-                String withExtension = getSelectedFile() + "." +
-                    jvf.getAcceptableExtension();
-                setSelectedFile(new File(withExtension));
-            }
-        }
+    if (getFileFilter() instanceof JalviewFileFilter)
+    {
+      JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
 
-        if ((ret == JalviewFileChooser.APPROVE_OPTION) &&
-                getSelectedFile().exists()) {
-            int confirm = JOptionPane.showConfirmDialog(parent,
-                    "Overwrite existing file?", "File exists",
-                    JOptionPane.YES_NO_OPTION);
+      if (!jvf.accept(getSelectedFile()))
+      {
+        String withExtension = getSelectedFile() + "." +
+            jvf.getAcceptableExtension();
+        setSelectedFile(new File(withExtension));
+      }
+    }
 
-            if (confirm != JOptionPane.YES_OPTION) {
-                ret = this.CANCEL_OPTION;
-            }
-        }
+    if ( (ret == JalviewFileChooser.APPROVE_OPTION) &&
+        getSelectedFile().exists())
+    {
+      int confirm = JOptionPane.showConfirmDialog(parent,
+                                                  "Overwrite existing file?",
+                                                  "File exists",
+                                                  JOptionPane.YES_NO_OPTION);
+
+      if (confirm != JOptionPane.YES_OPTION)
+      {
+        ret = this.CANCEL_OPTION;
+      }
+    }
+
+    return ret;
+  }
+
+  /**************************************************************************
+   * Always create the local UI
+   * @param comp
+   *************************************************************************/
+  public final void setUI(ComponentUI comp)
+  {
+    super.setUI(new UI(this));
+  }
+
+  /**************************************************************************
+   * Internal implementation of Metal LookAndFeel to create the table sorting
+   * ability.
+   *************************************************************************/
+  private class UI
+      extends MetalFileChooserUI
+  {
+    private DirectoryModel model;
 
-        return ret;
+    /**************************************************************************
+     * Must be overridden to extend
+     * @param e
+     *************************************************************************/
+    public UI(JFileChooser e)
+    {
+      super(e);
     }
 
-    void initColumns() {
-        if (COLUMNS == null) {
-            Locale l = getLocale();
-            COLUMNS = new String[] {
-                    UIManager.getString("FileChooser.fileNameHeaderText", l),
-                    UIManager.getString("FileChooser.fileSizeHeaderText", l),
-                    UIManager.getString("FileChooser.fileTypeHeaderText", l),
-                    UIManager.getString("FileChooser.fileDateHeaderText", l),
-                    UIManager.getString("FileChooser.fileAttrHeaderText", l)
-                };
-        }
+    /**************************************************************************
+     * Overridden to create our own model
+     *************************************************************************/
+    protected final void createModel()
+    {
+      model = new DirectoryModel(getFileChooser());
     }
 
     /**************************************************************************
-     * Always create the local UI
-     * @param comp
+     * Overridden to get our own model
+     * @return
      *************************************************************************/
-    public final void setUI(ComponentUI comp) {
-        super.setUI(new UI(this));
+    public final BasicDirectoryModel getModel()
+    {
+      return model;
     }
 
     /**************************************************************************
-     * Internal implementation of Metal LookAndFeel to create the table sorting
-     * ability.
+     * Calls the default method then adds a MouseListener to the JTable
+     * @param chooser
+     * @return
      *************************************************************************/
-    private final static class UI extends MetalFileChooserUI {
-        private DirectoryModel model;
-
-        /**************************************************************************
-         * Must be overridden to extend
-         * @param e
-         *************************************************************************/
-        public UI(JFileChooser e) {
-            super(e);
-        }
+    protected final JPanel createDetailsView(JFileChooser chooser)
+    {
+      final JPanel panel = super.createDetailsView(chooser);
 
-        /**************************************************************************
-         * Overridden to create our own model
-         *************************************************************************/
-        protected final void createModel() {
-            model = new DirectoryModel(getFileChooser());
-        }
+      //Since we can't access MetalFileChooserUI's private member detailsTable
+      //directly, we have to find it in the JPanel
+      final JTable tbl = findJTable(panel.getComponents());
 
-        /**************************************************************************
-         * Overridden to get our own model
-         * @return
-         *************************************************************************/
-        public final BasicDirectoryModel getModel() {
-            return model;
-        }
+      if (tbl != null)
+      {
+        //Add a mouselistener to listen for presses on column headers
+        tbl.getTableHeader().addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent e)
+          {
 
-        /**************************************************************************
-         * Calls the default method then adds a MouseListener to the JTable
-         * @param chooser
-         * @return
-         *************************************************************************/
-        protected final JPanel createDetailsView(JFileChooser chooser) {
-            final JPanel panel = super.createDetailsView(chooser);
-
-            //Since we can't access MetalFileChooserUI's private member detailsTable
-            //directly, we have to find it in the JPanel
-            final JTable tbl = findJTable(panel.getComponents());
-
-            if (tbl != null) {
-                //Fix the columns so they can't be rearranged, if we don't do this
-                //we would need to keep track when each column is moved
-                tbl.getTableHeader().setReorderingAllowed(false);
-
-                //Add a mouselistener to listen for clicks on column headers
-                tbl.getTableHeader().addMouseListener(new MouseAdapter() {
-                        public void mouseClicked(MouseEvent e) {
-                            //Only process single clicks
-                            if (e.getClickCount() > 1) {
-                                return;
-                            }
-
-                            e.consume();
-
-                            final int col = tbl.getTableHeader().columnAtPoint(e.getPoint());
-
-                            if ((col == COLUMN_FILENAME) ||
-                                    (col == COLUMN_FILESIZE) ||
-                                    (col == COLUMN_FILEDATE)) {
-                                model.sort(col, tbl);
-                            }
-                        }
-                    });
-            }
+            e.consume();
 
-            return panel;
-        }
+            final int col = tbl.getTableHeader().columnAtPoint(e.getPoint());
+            model.sort(col, tbl);
 
-        /**************************************************************************
-         * Finds the JTable in the panel so we can add MouseListener
-         * @param comp
-         * @return
-         *************************************************************************/
-        private final static JTable findJTable(Component[] comp) {
-            for (int i = 0; i < comp.length; i++) {
-                if (comp[i] instanceof JTable) {
-                    return (JTable) comp[i];
-                }
-
-                if (comp[i] instanceof Container) {
-                    JTable tbl = findJTable(((Container) comp[i]).getComponents());
-
-                    if (tbl != null) {
-                        return tbl;
-                    }
-                }
-            }
+          }
+        });
+      }
 
-            return null;
-        }
+      return panel;
     }
 
-    /***************************************************************************
-     * Implementation of BasicDirectoryModel that sorts the Files by column
-     **************************************************************************/
-    private final static class DirectoryModel extends BasicDirectoryModel {
-        int col = 0;
-        boolean ascending;
-
-        /**************************************************************************
-         * Must be overridden to extend BasicDirectoryModel
-         * @param chooser
-         *************************************************************************/
-        DirectoryModel(JFileChooser chooser) {
-            super(chooser);
+    /**************************************************************************
+     * Finds the JTable in the panel so we can add MouseListener
+     * @param comp
+     * @return
+     *************************************************************************/
+    private JTable findJTable(Component[] comp)
+    {
+      for (int i = 0; i < comp.length; i++)
+      {
+        if (comp[i] instanceof JTable)
+        {
+          return (JTable) comp[i];
         }
 
-        /**************************************************************************
-         * Supposedly this is not used anymore, hopefully not.  We implemented
-         * some basic attempt at sorting just in case
-         * @param a
-         * @param b
-         * @return
-         *************************************************************************/
-        protected final boolean lt(File a, File b) {
-            System.out.println("DEBUG:LT called?");
-
-            boolean less = false;
+        if (comp[i] instanceof Container)
+        {
+          JTable tbl = findJTable( ( (Container) comp[i]).getComponents());
 
-            switch (col) {
-            case COLUMN_FILEDATE:
-                less = a.lastModified() > b.lastModified();
-
-                break;
+          if (tbl != null)
+          {
+            return tbl;
+          }
+        }
+      }
 
-            case COLUMN_FILESIZE:
-                less = a.length() > b.length();
+      return null;
+    }
+  }
+
+  /***************************************************************************
+   * Implementation of BasicDirectoryModel that sorts the Files by column
+   **************************************************************************/
+  private final  class DirectoryModel
+      extends BasicDirectoryModel
+  {
+    String sortingColumnName=null;
+    int col = 0;
+    boolean ascending;
 
-                break;
+    /**************************************************************************
+     * Must be overridden to extend BasicDirectoryModel
+     * @param chooser
+     *************************************************************************/
+    DirectoryModel(JFileChooser chooser)
+    {
+      super(chooser);
+    }
 
-            default:
-                less = a.getName().compareToIgnoreCase(b.getName()) > 0;
 
-                break;
-            }
+    /**************************************************************************
+     * Resorts the JFileChooser table based on new column
+     * @param c
+     *************************************************************************/
+    protected final void sort(int c, JTable tbl)
+    {
 
-            if (ascending) {
-                return less = !less;
-            }
 
-            return less;
-        }
+      //Set column and order
+      col = c;
+      ascending = !ascending;
 
-        /**************************************************************************
-         * Resorts the JFileChooser table based on new column
-         * @param c
-         *************************************************************************/
-        protected final void sort(int c, JTable tbl) {
-            //Set column and order
-            col = c;
-            ascending = !ascending;
+      String indicator = " (^)";
 
-            String indicator = " (^)";
+      if (ascending)
+      {
+        indicator = " (v)";
+      }
 
-            if (ascending) {
-                indicator = " (v)";
-            }
+      final JTableHeader th = tbl.getTableHeader();
+      final TableColumnModel tcm = th.getColumnModel();
+      TableColumn tc = null;
+      String title = null;
 
-            final JTableHeader th = tbl.getTableHeader();
-            final TableColumnModel tcm = th.getColumnModel();
 
-            for (int i = 0; i < JalviewFileChooser.COLUMN_COLCOUNT; i++) {
-                final TableColumn tc = tcm.getColumn(i); // the column to change
-                tc.setHeaderValue(COLUMNS[i]);
-            }
+      //Remove indicator from old sort, and add to new
+      for(int i=0; i<tcm.getColumnCount(); i++)
+      {
+        tc = tcm.getColumn(i);
+        title = tc.getHeaderValue().toString();
+        if (title.endsWith(" (^)") || title.endsWith(" (v)"))
+        {
+          title = title.substring(0, title.length() - 4);
+        }
 
-            final TableColumn tc = tcm.getColumn(col); // the column to change
-            tc.setHeaderValue(COLUMNS[col] + indicator);
+        if(i==col)
+        {
+          sortingColumnName = title;
+          title = title + indicator;
+        }
 
-            th.repaint();
+        tc.setHeaderValue(title);
+      }
 
-            //Requery the file listing
-            validateFileCache();
-        }
+      //Requery the file listing
+      validateFileCache();
+    }
 
-        /**************************************************************************
-         * Sorts the data based on current column setting
-         * @param data
-         *************************************************************************/
-        protected final void sort(Vector data) {
-            switch (col) {
-            case COLUMN_FILEDATE:
-                Collections.sort(data,
-                    new Comparator() {
-                        public int compare(Object o1, Object o2) {
-                            int ret = 1;
-                            final File a = (File) o1;
-                            final File b = (File) o2;
-
-                            if (a.lastModified() > b.lastModified()) {
-                                ret = -1;
-                            } else if (a.lastModified() == b.lastModified()) {
-                                ret = 0;
-                            }
-
-                            if (ascending) {
-                                ret *= -1;
-                            }
-
-                            return ret;
-                        }
-                    });
-
-
-                break;
-
-            case COLUMN_FILESIZE:
-                Collections.sort(data,
-                    new Comparator() {
-                        public int compare(Object o1, Object o2) {
-                            int ret = 1;
-                            final File a = (File) o1;
-                            final File b = (File) o2;
-
-                            if (a.length() > b.length()) {
-                                ret = -1;
-                            } else if (a.length() == b.length()) {
-                                ret = 0;
-                            }
-
-                            if (ascending) {
-                                ret *= -1;
-                            }
-
-                            return ret;
-                        }
-                    });
-
-
-                break;
-
-            case COLUMN_FILENAME:
-                Collections.sort(data,
-                    new Comparator() {
-                        public int compare(Object o1, Object o2) {
-                            final File a = (File) o1;
-                            final File b = (File) o2;
-
-                            if (ascending) {
-                                return a.getName().compareToIgnoreCase(b.getName());
-                            } else {
-                                return -1 * a.getName().compareToIgnoreCase(b.getName());
-                            }
-                        }
-                    });
-
-
-                break;
+    /**************************************************************************
+     * Sorts the data based on current column setting
+     * @param data
+     *************************************************************************/
+    protected final void sort(Vector data)
+    {
+        /*
+                        UIManager.getString("FileChooser.fileTypeHeaderText", l),
+                        UIManager.getString("FileChooser.fileAttrHeaderText", l)
+*/
+    if(sortingColumnName==null)
+      return;
+
+
+    if(sortingColumnName.equals(UIManager.getString("FileChooser.fileDateHeaderText")))
+    {
+      Collections.sort(data,
+                           new Comparator()
+          {
+
+            public int compare(Object o1, Object o2)
+            {
+              int ret = 1;
+              final File a = (File) o1;
+              final File b = (File) o2;
+
+              if (a.lastModified() > b.lastModified())
+              {
+                ret = -1;
+              }
+              else if (a.lastModified() == b.lastModified())
+              {
+                ret = 0;
+              }
+
+              if (ascending)
+              {
+                ret *= -1;
+              }
+
+              return ret;
             }
+          });
+    }
+    else if(sortingColumnName.equals(UIManager.getString("FileChooser.fileSizeHeaderText")))
+    {
+
+         Collections.sort(data,
+                           new Comparator()
+          {
+
+            public int compare(Object o1, Object o2)
+            {
+              int ret = 1;
+              final File a = (File) o1;
+              final File b = (File) o2;
+
+              if (a.length() > b.length())
+              {
+                ret = -1;
+              }
+              else if (a.length() == b.length())
+              {
+                ret = 0;
+              }
+
+              if (ascending)
+              {
+                ret *= -1;
+              }
+
+              return ret;
+            }
+          });
+    }
+    else if(sortingColumnName.equals(UIManager.getString("FileChooser.fileTypeHeaderText")))
+    {
+          Collections.sort(data,
+                           new Comparator()
+          {
+            public int compare(Object o1, Object o2)
+            {
+              final String a = getFileSystemView().getSystemTypeDescription( (File)o1 );
+              final String b = getFileSystemView().getSystemTypeDescription( (File)o2 );
+              if (ascending)
+              {
+                return a.compareToIgnoreCase(b);
+              }
+              else
+              {
+                return -1 * a.compareToIgnoreCase(b);
+              }
+            }
+          });
+      }
+      else if(sortingColumnName.equals(UIManager.getString("FileChooser.fileNameHeaderText")))
+{
+      Collections.sort(data,
+                       new Comparator()
+      {
+        public int compare(Object o1, Object o2)
+        {
+          final String a = ((File) o1).getName();
+          final String b = ((File) o2).getName();
+
+          if (ascending)
+          {
+            return a.compareToIgnoreCase(b);
+          }
+          else
+          {
+            return -1 * a.compareToIgnoreCase(b);
+          }
         }
+      });
+  }
+
     }
+  }
 }
diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index e2692e2..907b1b3 100755
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -1,154 +1,184 @@
 /*
-* 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
-*/
+ * 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.io;
 
-import java.io.File;
-
+import java.io.*;
 import java.util.*;
 
-import javax.swing.filechooser.*;
-
-
-public class JalviewFileFilter extends FileFilter {
-    private static String TYPE_UNKNOWN = "Type Unknown";
-    private static String HIDDEN_FILE = "Hidden File";
-    public static Hashtable suffixHash = new Hashtable();
-    private Hashtable filters = null;
-    private String description = "no description";
-    private String fullDescription = "full description";
-    private boolean useExtensionsInDescription = true;
-
-    public JalviewFileFilter(String extension, String description) {
-        StringTokenizer st = new StringTokenizer(extension, ",");
-
-        while (st.hasMoreElements()) {
-            addExtension(st.nextToken().trim());
-        }
-
-        setDescription(description);
+import javax.swing.filechooser.FileFilter;
+
+public class JalviewFileFilter
+    extends FileFilter
+{
+  private static String TYPE_UNKNOWN = "Type Unknown";
+  private static String HIDDEN_FILE = "Hidden File";
+  public static Hashtable suffixHash = new Hashtable();
+  private Hashtable filters = null;
+  private String description = "no description";
+  private String fullDescription = "full description";
+  private boolean useExtensionsInDescription = true;
+
+  public JalviewFileFilter(String extension, String description)
+  {
+    StringTokenizer st = new StringTokenizer(extension, ",");
+
+    while (st.hasMoreElements())
+    {
+      addExtension(st.nextToken().trim());
     }
 
-    public JalviewFileFilter(String[] filts) {
-        this(filts, null);
-    }
+    setDescription(description);
+  }
 
-    public JalviewFileFilter(String[] filts, String description) {
-        for (int i = 0; i < filts.length; i++) {
-            // add filters one by one
-            addExtension(filts[i]);
-        }
+  public JalviewFileFilter(String[] filts)
+  {
+    this(filts, null);
+  }
 
-        if (description != null) {
-            setDescription(description);
-        }
+  public JalviewFileFilter(String[] filts, String description)
+  {
+    for (int i = 0; i < filts.length; i++)
+    {
+      // add filters one by one
+      addExtension(filts[i]);
     }
 
-    public String getAcceptableExtension() {
-        return filters.keys().nextElement().toString();
+    if (description != null)
+    {
+      setDescription(description);
     }
-
-    // takes account of the fact that database is a directory
-    public boolean accept(File f) {
-        if (f != null) {
-            String extension = getExtension(f);
-
-            if (f.isDirectory()) {
-                if ((extension == null) || extension.equals("")) {
-                    return true;
-                } else {
-                    if (filters.get(getExtension(f)) != null) {
-                        return true;
-                    }
-                }
-            }
-
-            if ((extension != null) && (filters.get(getExtension(f)) != null)) {
-                return true;
-            }
+  }
+
+  public String getAcceptableExtension()
+  {
+    return filters.keys().nextElement().toString();
+  }
+
+  // takes account of the fact that database is a directory
+  public boolean accept(File f)
+  {
+    if (f != null)
+    {
+      String extension = getExtension(f);
+
+      if (f.isDirectory())
+      {
+        if ( (extension == null) || extension.equals(""))
+        {
+          return true;
+        }
+        else
+        {
+          if (filters.get(getExtension(f)) != null)
+          {
+            return true;
+          }
         }
+      }
 
-        return false;
+      if ( (extension != null) && (filters.get(getExtension(f)) != null))
+      {
+        return true;
+      }
     }
 
-    public String getExtension(File f) {
-        if (f != null) {
-            String filename = f.getName();
-            int i = filename.lastIndexOf('.');
+    return false;
+  }
 
-            if ((i > 0) && (i < (filename.length() - 1))) {
-                return filename.substring(i + 1).toLowerCase();
-            }
+  public String getExtension(File f)
+  {
+    if (f != null)
+    {
+      String filename = f.getName();
+      int i = filename.lastIndexOf('.');
 
-            ;
-        }
+      if ( (i > 0) && (i < (filename.length() - 1)))
+      {
+        return filename.substring(i + 1).toLowerCase();
+      }
 
-        return "";
+      ;
     }
 
-    public void addExtension(String extension) {
-        if (filters == null) {
-            filters = new Hashtable(5);
-        }
+    return "";
+  }
 
-        filters.put(extension.toLowerCase(), this);
-        fullDescription = null;
+  public void addExtension(String extension)
+  {
+    if (filters == null)
+    {
+      filters = new Hashtable(5);
     }
 
-    public String getDescription() {
-        if (fullDescription == null) {
-            if ((description == null) || isExtensionListInDescription()) {
-                fullDescription = (description == null) ? "(" : (description +
-                    " (");
-
-                // build the description from the extension list
-                Enumeration extensions = filters.keys();
-
-                if (extensions != null) {
-                    fullDescription += ("." +
-                    (String) extensions.nextElement());
-
-                    while (extensions.hasMoreElements()) {
-                        fullDescription += (", " +
-                        (String) extensions.nextElement());
-                    }
-                }
-
-                fullDescription += ")";
-            } else {
-                fullDescription = description;
-            }
+    filters.put(extension.toLowerCase(), this);
+    fullDescription = null;
+  }
+
+  public String getDescription()
+  {
+    if (fullDescription == null)
+    {
+      if ( (description == null) || isExtensionListInDescription())
+      {
+        fullDescription = (description == null) ? "(" : (description +
+            " (");
+
+        // build the description from the extension list
+        Enumeration extensions = filters.keys();
+
+        if (extensions != null)
+        {
+          fullDescription += ("." +
+                              (String) extensions.nextElement());
+
+          while (extensions.hasMoreElements())
+          {
+            fullDescription += (", " +
+                                (String) extensions.nextElement());
+          }
         }
 
-        return fullDescription;
+        fullDescription += ")";
+      }
+      else
+      {
+        fullDescription = description;
+      }
     }
 
-    public void setDescription(String description) {
-        this.description = description;
-        fullDescription = null;
-    }
-
-    public void setExtensionListInDescription(boolean b) {
-        useExtensionsInDescription = b;
-        fullDescription = null;
-    }
-
-    public boolean isExtensionListInDescription() {
-        return useExtensionsInDescription;
-    }
+    return fullDescription;
+  }
+
+  public void setDescription(String description)
+  {
+    this.description = description;
+    fullDescription = null;
+  }
+
+  public void setExtensionListInDescription(boolean b)
+  {
+    useExtensionsInDescription = b;
+    fullDescription = null;
+  }
+
+  public boolean isExtensionListInDescription()
+  {
+    return useExtensionsInDescription;
+  }
 }
diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java
index f4c7f23..04189e1 100755
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -1,97 +1,111 @@
 /*
-* 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
-*/
+ * 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.io;
 
 import java.io.*;
-
 import java.util.*;
 
 import javax.swing.*;
-import javax.swing.filechooser.FileView;
-
-
-public class JalviewFileView extends FileView {
-    static Hashtable alignSuffix = new Hashtable();
-
-    static {
-        alignSuffix.put("fasta", "Fasta file");
-        alignSuffix.put("fa", "Fasta file");
-        alignSuffix.put("fastq", "Fasta file");
-        alignSuffix.put("blc", "BLC file");
-        alignSuffix.put("msf", "MSF file");
-        alignSuffix.put("pfam", "PFAM file");
-        alignSuffix.put("aln", "Clustal file");
-        alignSuffix.put("pir", "PIR file");
+import javax.swing.filechooser.*;
+
+public class JalviewFileView
+    extends FileView
+{
+  static Hashtable alignSuffix = new Hashtable();
+
+  static
+  {
+    alignSuffix.put("fasta", "Fasta file");
+    alignSuffix.put("fa", "Fasta file");
+    alignSuffix.put("fastq", "Fasta file");
+    alignSuffix.put("blc", "BLC file");
+    alignSuffix.put("msf", "MSF file");
+    alignSuffix.put("pfam", "PFAM file");
+    alignSuffix.put("aln", "Clustal file");
+    alignSuffix.put("pir", "PIR file");
+    alignSuffix.put("jar", "Jalview file");
+  }
+
+  public String getTypeDescription(File f)
+  {
+    String extension = getExtension(f);
+    String type = null;
+
+    if (extension != null)
+    {
+      if (alignSuffix.containsKey(extension))
+      {
+        type = alignSuffix.get(extension).toString();
+      }
     }
 
-    public String getTypeDescription(File f) {
-        String extension = getExtension(f);
-        String type = null;
+    return type;
+  }
 
-        if (extension != null) {
-            if (alignSuffix.containsKey(extension)) {
-                type = alignSuffix.get(extension).toString();
-            }
-        }
+  public Icon getIcon(File f)
+  {
+    String extension = getExtension(f);
+    Icon icon = null;
 
-        return type;
+    if (extension != null)
+    {
+      if (alignSuffix.containsKey(extension))
+      {
+        icon = createImageIcon("/images/file.png");
+      }
     }
 
-    public Icon getIcon(File f) {
-        String extension = getExtension(f);
-        Icon icon = null;
-
-        if (extension != null) {
-            if (alignSuffix.containsKey(extension)) {
-                icon = createImageIcon("/images/file.png");
-            }
-        }
-
-        return icon;
+    return icon;
+  }
+
+  /*
+   * Get the extension of a file.
+   */
+  public static String getExtension(File f)
+  {
+    String ext = null;
+    String s = f.getName();
+    int i = s.lastIndexOf('.');
+
+    if ( (i > 0) && (i < (s.length() - 1)))
+    {
+      ext = s.substring(i + 1).toLowerCase();
     }
 
-    /*
-     * Get the extension of a file.
-     */
-    public static String getExtension(File f) {
-        String ext = null;
-        String s = f.getName();
-        int i = s.lastIndexOf('.');
+    return ext;
+  }
 
-        if ((i > 0) && (i < (s.length() - 1))) {
-            ext = s.substring(i + 1).toLowerCase();
-        }
+  /** Returns an ImageIcon, or null if the path was invalid. */
+  protected static ImageIcon createImageIcon(String path)
+  {
+    java.net.URL imgURL = JalviewFileView.class.getResource(path);
 
-        return ext;
+    if (imgURL != null)
+    {
+      return new ImageIcon(imgURL);
     }
+    else
+    {
+      System.err.println(
+          "JalviewFileView.createImageIcon: Couldn't find file: " + path);
 
-    /** Returns an ImageIcon, or null if the path was invalid. */
-    protected static ImageIcon createImageIcon(String path) {
-        java.net.URL imgURL = JalviewFileView.class.getResource(path);
-
-        if (imgURL != null) {
-            return new ImageIcon(imgURL);
-        } else {
-            System.err.println(
-                "JalviewFileView.createImageIcon: Couldn't find file: " + path);
-
-            return null;
-        }
+      return null;
     }
+  }
 }
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 2a6e10f..5f81215 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -27,24 +27,54 @@ import java.io.*;
 import java.util.*;
 
 
-public class MSFfile extends AlignFile {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class MSFfile extends AlignFile
+{
     private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",
             "-");
     private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(
             "[" + jalview.util.Comparison.GapChars + "]", "\\~");
 
-    public MSFfile() {
+    /**
+     * Creates a new MSFfile object.
+     */
+    public MSFfile()
+    {
     }
 
-    public MSFfile(String inStr) {
+    /**
+     * Creates a new MSFfile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public MSFfile(String inStr)
+    {
         super(inStr);
     }
 
-    public MSFfile(String inFile, String type) throws IOException {
+    /**
+     * Creates a new MSFfile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public MSFfile(String inFile, String type) throws IOException
+    {
         super(inFile, type);
     }
 
-    public void parse() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void parse()
+    {
         int i = 0;
         boolean seqFlag = false;
         String key = new String();
@@ -52,48 +82,60 @@ public class MSFfile extends AlignFile {
         Hashtable seqhash = new Hashtable();
         String line;
 
-        try {
-            while ((line = nextLine()) != null) {
+        try
+        {
+            while ((line = nextLine()) != null)
+            {
                 StringTokenizer str = new StringTokenizer(line);
 
-                while (str.hasMoreTokens()) {
+                while (str.hasMoreTokens())
+                {
                     String inStr = str.nextToken();
 
                     //If line has header information add to the headers vector
-                    if (inStr.indexOf("Name:") != -1) {
+                    if (inStr.indexOf("Name:") != -1)
+                    {
                         key = str.nextToken();
                         headers.addElement(key);
                     }
 
                     //if line has // set SeqFlag to 1 so we know sequences are coming
-                    if (inStr.indexOf("//") != -1) {
+                    if (inStr.indexOf("//") != -1)
+                    {
                         seqFlag = true;
                     }
 
                     //Process lines as sequence lines if seqFlag is set
-                    if ((inStr.indexOf("//") == -1) && (seqFlag == true)) {
+                    if ((inStr.indexOf("//") == -1) && (seqFlag == true))
+                    {
                         //seqeunce id is the first field
                         key = inStr;
 
                         StringBuffer tempseq;
 
                         //Get sequence from hash if it exists
-                        if (seqhash.containsKey(key)) {
+                        if (seqhash.containsKey(key))
+                        {
                             tempseq = (StringBuffer) seqhash.get(key);
-                        } else {
+                        }
+                        else
+                        {
                             tempseq = new StringBuffer();
                             seqhash.put(key, tempseq);
                         }
 
                         //loop through the rest of the words
-                        while (str.hasMoreTokens()) {
+                        while (str.hasMoreTokens())
+                        {
                             //append the word to the sequence
                             tempseq.append(str.nextToken());
                         }
                     }
                 }
             }
-        } catch (IOException e) {
+        }
+        catch (IOException e)
+        {
             System.err.println("Exception parsing MSFFile " + e);
             e.printStackTrace();
         }
@@ -101,28 +143,34 @@ public class MSFfile extends AlignFile {
         this.noSeqs = headers.size();
 
         //Add sequences to the hash
-        for (i = 0; i < headers.size(); i++) {
-            if (seqhash.get(headers.elementAt(i)) != null) {
+        for (i = 0; i < headers.size(); i++)
+        {
+            if (seqhash.get(headers.elementAt(i)) != null)
+            {
                 String head = headers.elementAt(i).toString();
                 String seq = seqhash.get(head).toString();
 
                 int start = 1;
                 int end = seq.length();
 
-                if (maxLength < head.length()) {
+                if (maxLength < head.length())
+                {
                     maxLength = head.length();
                 }
 
-                if (head.indexOf("/") > 0) {
+                if (head.indexOf("/") > 0)
+                {
                     StringTokenizer st = new StringTokenizer(head, "/");
 
-                    if (st.countTokens() == 2) {
+                    if (st.countTokens() == 2)
+                    {
                         head = st.nextToken();
 
                         String tmp = st.nextToken();
                         st = new StringTokenizer(tmp, "-");
 
-                        if (st.countTokens() == 2) {
+                        if (st.countTokens() == 2)
+                        {
                             start = Integer.valueOf(st.nextToken()).intValue();
                             end = Integer.valueOf(st.nextToken()).intValue();
                         }
@@ -135,30 +183,44 @@ public class MSFfile extends AlignFile {
                 Sequence newSeq = new Sequence(head, seq, start, end);
 
                 seqs.addElement(newSeq);
-            } else {
+            }
+            else
+            {
                 System.err.println("MSFFile Parser: Can't find sequence for " +
                     headers.elementAt(i));
             }
         }
     }
 
-    public static int checkSum(String seq) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static int checkSum(String seq)
+    {
         //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
         int check = 0;
+        String sequence = seq.toUpperCase();
 
         String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
-        index += "--------------------------------------------------------------------------------------------------------------------------------";
+        index +=       "--------------------------------------------------------------------------------------------------------------------------------";
 
-        for (int i = 0; i < seq.length(); i++) {
-            try {
-                if (i < seq.length()) {
-                    int pos = index.indexOf(seq.substring(i, i + 1));
+        for (int i = 0; i < sequence.length(); i++)
+        {
+            try
+            {
+                    int pos = index.indexOf(sequence.charAt(i));
 
-                    if (!index.substring(pos, pos + 1).equals("_")) {
+                    if (index.charAt(pos)!='_')
+                    {
                         check += (((i % 57) + 1) * pos);
                     }
-                }
-            } catch (Exception e) {
+            }
+            catch (Exception e)
+            {
                 System.err.println("Exception during MSF Checksum calculation");
                 e.printStackTrace();
             }
@@ -167,11 +229,28 @@ public class MSFfile extends AlignFile {
         return check % 10000;
     }
 
-    public static String print(SequenceI[] s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String print(SequenceI[] s)
+    {
         return print(s, false);
     }
 
-    public static String print(SequenceI[] s, boolean is_NA) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param is_NA DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String print(SequenceI[] s, boolean is_NA)
+    {
         StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
                 "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
 
@@ -180,11 +259,13 @@ public class MSFfile extends AlignFile {
         int i = 0;
         String big = "";
 
-        while ((i < s.length) && (s[i] != null)) {
+        while ((i < s.length) && (s[i] != null))
+        {
             String sq;
             big += (sq = s[i].getSequence());
 
-            if (sq.length() > max) {
+            if (sq.length() > max)
+            {
                 max = sq.length();
             }
 
@@ -205,8 +286,8 @@ public class MSFfile extends AlignFile {
         String[] nameBlock = new String[s.length];
         String[] idBlock = new String[s.length];
 
-        while ((i < s.length) && (s[i] != null)) {
-            String seq = s[i].getSequence();
+        while ((i < s.length) && (s[i] != null))
+        {
             String name = s[i].getName() + "/" + s[i].getStart() + "-" +
                 s[i].getEnd();
             int check = checkSum(s[i].getSequence());
@@ -215,28 +296,33 @@ public class MSFfile extends AlignFile {
                     maxLenpad.form(s[i].getSequence().length()) + "  Check:" +
                     maxChkpad.form(check) + "  Weight: 1.00\n");
 
-            if (name.length() > maxid) {
+            if (name.length() > maxid)
+            {
                 maxid = name.length();
             }
 
-            if (nameBlock[i].length() > maxNB) {
+            if (nameBlock[i].length() > maxNB)
+            {
                 maxNB = nameBlock[i].length();
             }
 
             i++;
         }
 
-        if (maxid < 10) {
+        if (maxid < 10)
+        {
             maxid = 10;
         }
 
-        if (maxNB < 15) {
+        if (maxNB < 15)
+        {
             maxNB = 15;
         }
 
         Format nbFormat = new Format("%-" + maxNB + "s");
 
-        for (i = 0; (i < s.length) && (s[i] != null); i++) {
+        for (i = 0; (i < s.length) && (s[i] != null); i++)
+        {
             out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);
         }
 
@@ -247,39 +333,53 @@ public class MSFfile extends AlignFile {
 
         int nochunks = (max / len) + 1;
 
-        if ((max % len) == 0) {
+        if ((max % len) == 0)
+        {
             nochunks--;
         }
 
-        for (i = 0; i < nochunks; i++) {
+        for (i = 0; i < nochunks; i++)
+        {
             int j = 0;
 
-            while ((j < s.length) && (s[j] != null)) {
+            while ((j < s.length) && (s[j] != null))
+            {
                 String name = s[j].getName();
                 out.append(new Format("%-" + maxid + "s").form(name + "/" +
                         s[j].getStart() + "-" + s[j].getEnd()) + " ");
 
-                for (int k = 0; k < 5; k++) {
+                for (int k = 0; k < 5; k++)
+                {
                     int start = (i * 50) + (k * 10);
                     int end = start + 10;
 
                     if ((end < s[j].getSequence().length()) &&
-                            (start < s[j].getSequence().length())) {
+                            (start < s[j].getSequence().length()))
+                    {
                         out.append(re2gap.replaceAll(s[j].getSequence()
                                                          .substring(start, end)));
 
-                        if (k < 4) {
+                        if (k < 4)
+                        {
                             // out.append(" ");
-                        } else {
+                        }
+                        else
+                        {
                             out.append("\n");
                         }
-                    } else {
-                        if (start < s[j].getSequence().length()) {
+                    }
+                    else
+                    {
+                        if (start < s[j].getSequence().length())
+                        {
                             out.append(re2gap.replaceAll(
                                     s[j].getSequence().substring(start)));
                             out.append("\n");
-                        } else {
-                            if (k == 0) {
+                        }
+                        else
+                        {
+                            if (k == 0)
+                            {
                                 out.append("\n");
                             }
                         }
@@ -295,7 +395,13 @@ public class MSFfile extends AlignFile {
         return out.toString();
     }
 
-    public String print() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
+    {
         return print(getSeqsAsArray());
     }
 }
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index a6f1580..c1ef5b6 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -29,7 +29,14 @@ import java.io.*;
 import java.util.*;
 
 
-public class NewickFile extends FileParse {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NewickFile extends FileParse
+{
     SequenceNode root;
     private boolean HasBootstrap = false;
     private boolean HasDistances = false;
@@ -38,46 +45,106 @@ public class NewickFile extends FileParse {
     // File IO Flags
     boolean ReplaceUnderscores = false;
     boolean printRootInfo = false;
-    private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] {
+    private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
+        {
             new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes
             new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters
             new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation
         };
     char QuoteChar = '\'';
 
-    public NewickFile(String inStr) throws IOException {
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public NewickFile(String inStr) throws IOException
+    {
         super(inStr, "Paste");
     }
 
-    public NewickFile(String inFile, String type) throws IOException {
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public NewickFile(String inFile, String type) throws IOException
+    {
         super(inFile, type);
     }
 
-    public NewickFile(SequenceNode newtree) {
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param newtree DOCUMENT ME!
+     */
+    public NewickFile(SequenceNode newtree)
+    {
         root = newtree;
     }
 
-    public NewickFile(SequenceNode newtree, boolean bootstrap) {
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param newtree DOCUMENT ME!
+     * @param bootstrap DOCUMENT ME!
+     */
+    public NewickFile(SequenceNode newtree, boolean bootstrap)
+    {
         HasBootstrap = bootstrap;
         root = newtree;
     }
 
-    public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances) {
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param newtree DOCUMENT ME!
+     * @param bootstrap DOCUMENT ME!
+     * @param distances DOCUMENT ME!
+     */
+    public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)
+    {
         root = newtree;
         HasBootstrap = bootstrap;
         HasDistances = distances;
     }
 
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param newtree DOCUMENT ME!
+     * @param bootstrap DOCUMENT ME!
+     * @param distances DOCUMENT ME!
+     * @param rootdistance DOCUMENT ME!
+     */
     public NewickFile(SequenceNode newtree, boolean bootstrap,
-        boolean distances, boolean rootdistance) {
+        boolean distances, boolean rootdistance)
+    {
         root = newtree;
         HasBootstrap = bootstrap;
         HasDistances = distances;
         RootHasDistance = rootdistance;
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Error DOCUMENT ME!
+     * @param Er DOCUMENT ME!
+     * @param r DOCUMENT ME!
+     * @param p DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     private String ErrorStringrange(String Error, String Er, int r, int p,
-        String s) {
+        String s)
+    {
         return ((Error == null) ? "" : Error) + Er + " at position " + p +
         " ( " +
         s.substring(((p - r) < 0) ? 0 : (p - r),
@@ -86,22 +153,36 @@ public class NewickFile extends FileParse {
 
     // @tree annotations
     // These are set automatically by the reader
-    public boolean HasBootstrap() {
+    public boolean HasBootstrap()
+    {
         return HasBootstrap;
     }
 
-    public boolean HasDistances() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean HasDistances()
+    {
         return HasDistances;
     }
 
-    public void parse() throws IOException {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public void parse() throws IOException
+    {
         String nf;
 
         { // fill nf with complete tree file
 
             StringBuffer file = new StringBuffer();
 
-            while ((nf = nextLine()) != null) {
+            while ((nf = nextLine()) != null)
+            {
                 file.append(nf);
             }
 
@@ -131,19 +212,24 @@ public class NewickFile extends FileParse {
         com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
                 "[(\\['),;]");
 
-        while (majorsyms.searchFrom(nf, cp) && (Error == null)) {
+        while (majorsyms.searchFrom(nf, cp) && (Error == null))
+        {
             int fcp = majorsyms.matchedFrom();
 
-            switch (nf.charAt(fcp)) {
+            switch (nf.charAt(fcp))
+            {
             case '[': // Comment or structured/extended NH format info
 
                 com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(
                         "]");
 
-                if (comment.searchFrom(nf, fcp)) {
+                if (comment.searchFrom(nf, fcp))
+                {
                     // Skip the comment field
                     cp = 1 + comment.matchedFrom();
-                } else {
+                }
+                else
+                {
                     Error = ErrorStringrange(Error, "Unterminated comment", 3,
                             fcp, nf);
                 }
@@ -156,7 +242,8 @@ public class NewickFile extends FileParse {
 
                 // ascending should not be set
                 // New Internal node
-                if (ascending) {
+                if (ascending)
+                {
                     Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
 
                     continue;
@@ -165,12 +252,16 @@ public class NewickFile extends FileParse {
                 ;
                 d++;
 
-                if (c.right() == null) {
+                if (c.right() == null)
+                {
                     c.setRight(new SequenceNode(null, c, null, DefDistance,
                             DefBootstrap, false));
                     c = (SequenceNode) c.right();
-                } else {
-                    if (c.left() != null) {
+                }
+                else
+                {
+                    if (c.left() != null)
+                    {
                         // Dummy node for polytomy - keeps c.left free for new node
                         SequenceNode tmpn = new SequenceNode(null, c, null, 0,
                                 0, true);
@@ -183,7 +274,8 @@ public class NewickFile extends FileParse {
                     c = (SequenceNode) c.left();
                 }
 
-                if (realroot == null) {
+                if (realroot == null)
+                {
                     realroot = c;
                 }
 
@@ -200,12 +292,15 @@ public class NewickFile extends FileParse {
                 com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
                         "([^']|'')+'");
 
-                if (qnodename.searchFrom(nf, fcp)) {
+                if (qnodename.searchFrom(nf, fcp))
+                {
                     int nl = qnodename.stringMatched().length();
                     nodename = new String(qnodename.stringMatched().substring(0,
                                 nl - 1));
                     cp = fcp + nl + 1;
-                } else {
+                }
+                else
+                {
                     Error = ErrorStringrange(Error,
                             "Unterminated quotes for nodename", 7, fcp, nf);
                 }
@@ -214,7 +309,8 @@ public class NewickFile extends FileParse {
 
             case ';':
 
-                if (d != -1) {
+                if (d != -1)
+                {
                     Error = ErrorStringrange(Error,
                             "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
                 }
@@ -234,15 +330,21 @@ public class NewickFile extends FileParse {
                 if (uqnodename.search(fstring) &&
                         ((uqnodename.matchedFrom(1) == 0) ||
                         (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!
-                 {
-                    if (nodename == null) {
-                        if (ReplaceUnderscores) {
+                {
+                    if (nodename == null)
+                    {
+                        if (ReplaceUnderscores)
+                        {
                             nodename = uqnodename.stringMatched(1).replace('_',
                                     ' ');
-                        } else {
+                        }
+                        else
+                        {
                             nodename = uqnodename.stringMatched(1);
                         }
-                    } else {
+                    }
+                    else
+                    {
                         Error = ErrorStringrange(Error,
                                 "File has broken algorithm - overwritten nodename",
                                 10, fcp, nf);
@@ -251,11 +353,15 @@ public class NewickFile extends FileParse {
 
                 if (nbootstrap.search(fstring) &&
                         (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +
-                        uqnodename.stringMatched().length()))) {
-                    try {
+                        uqnodename.stringMatched().length())))
+                {
+                    try
+                    {
                         bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
                         HasBootstrap = true;
-                    } catch (Exception e) {
+                    }
+                    catch (Exception e)
+                    {
                         Error = ErrorStringrange(Error,
                                 "Can't parse bootstrap value", 4,
                                 cp + nbootstrap.matchedFrom(), nf);
@@ -264,39 +370,53 @@ public class NewickFile extends FileParse {
 
                 boolean nodehasdistance = false;
 
-                if (ndist.search(fstring)) {
-                    try {
+                if (ndist.search(fstring))
+                {
+                    try
+                    {
                         distance = (new Float(ndist.stringMatched(1))).floatValue();
                         HasDistances = true;
                         nodehasdistance = true;
-                    } catch (Exception e) {
+                    }
+                    catch (Exception e)
+                    {
                         Error = ErrorStringrange(Error,
                                 "Can't parse node distance value", 7,
                                 cp + ndist.matchedFrom(), nf);
                     }
                 }
 
-                if (ascending) {
+                if (ascending)
+                {
                     // Write node info here
                     c.setName(nodename);
                     c.dist = (HasDistances) ? distance : 0;
                     c.setBootstrap((HasBootstrap) ? bootstrap : 0);
 
-                    if (c == realroot) {
+                    if (c == realroot)
+                    {
                         RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!
                     }
-                } else {
+                }
+                else
+                {
                     // Find a place to put the leaf
                     SequenceNode newnode = new SequenceNode(null, c, nodename,
                             (HasDistances) ? distance : DefDistance,
                             (HasBootstrap) ? bootstrap : DefBootstrap, false);
 
-                    if (c.right() == null) {
+                    if (c.right() == null)
+                    {
                         c.setRight(newnode);
-                    } else {
-                        if (c.left() == null) {
+                    }
+                    else
+                    {
+                        if (c.left() == null)
+                        {
                             c.setLeft(newnode);
-                        } else {
+                        }
+                        else
+                        {
                             // Insert a dummy node for polytomy
                             SequenceNode newdummy = new SequenceNode(null, c,
                                     null, 0, 0, true);
@@ -306,32 +426,43 @@ public class NewickFile extends FileParse {
                     }
                 }
 
-                if (ascending) {
+                if (ascending)
+                {
                     // move back up the tree from preceding closure
                     c = c.AscendTree();
 
-                    if ((d > -1) && (c == null)) {
+                    if ((d > -1) && (c == null))
+                    {
                         Error = ErrorStringrange(Error,
                                 "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
                                 7, fcp, nf);
                     }
                 }
 
-                if (nf.charAt(fcp) == ')') {
+                if (nf.charAt(fcp) == ')')
+                {
                     d--;
                     ascending = true;
-                } else {
-                    if (nf.charAt(fcp) == ',') {
-                        if (ascending) {
+                }
+                else
+                {
+                    if (nf.charAt(fcp) == ',')
+                    {
+                        if (ascending)
+                        {
                             ascending = false;
-                        } else {
+                        }
+                        else
+                        {
                             // Just advance focus, if we need to
-                            if ((c.left() != null) && (!c.left().isLeaf())) {
+                            if ((c.left() != null) && (!c.left().isLeaf()))
+                            {
                                 c = (SequenceNode) c.left();
                             }
                         }
                     }
-                     // else : We do nothing if ';' is encountered.
+
+                    // else : We do nothing if ';' is encountered.
                 }
 
                 // Reset new node properties to obvious fakes
@@ -343,23 +474,38 @@ public class NewickFile extends FileParse {
             }
         }
 
-        if (Error != null) {
+        if (Error != null)
+        {
             throw (new IOException("NewickFile: " + Error + "\n"));
         }
 
         root = (SequenceNode) root.right().detach(); // remove the imaginary root.
 
-        if (!RootHasDistance) {
+        if (!RootHasDistance)
+        {
             root.dist = 0;
         }
     }
 
-    public SequenceNode getTree() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceNode getTree()
+    {
         return root;
     }
 
-    public String print() {
-        synchronized (this) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
+    {
+        synchronized (this)
+        {
             StringBuffer tf = new StringBuffer();
             print(tf, root);
 
@@ -367,8 +513,17 @@ public class NewickFile extends FileParse {
         }
     }
 
-    public String print(boolean withbootstraps) {
-        synchronized (this) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param withbootstraps DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print(boolean withbootstraps)
+    {
+        synchronized (this)
+        {
             boolean boots = this.HasBootstrap;
             this.HasBootstrap = withbootstraps;
 
@@ -379,8 +534,18 @@ public class NewickFile extends FileParse {
         }
     }
 
-    public String print(boolean withbootstraps, boolean withdists) {
-        synchronized (this) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param withbootstraps DOCUMENT ME!
+     * @param withdists DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print(boolean withbootstraps, boolean withdists)
+    {
+        synchronized (this)
+        {
             boolean dists = this.HasDistances;
             this.HasDistances = withdists;
 
@@ -391,9 +556,20 @@ public class NewickFile extends FileParse {
         }
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param withbootstraps DOCUMENT ME!
+     * @param withdists DOCUMENT ME!
+     * @param printRootInfo DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public String print(boolean withbootstraps, boolean withdists,
-        boolean printRootInfo) {
-        synchronized (this) {
+        boolean printRootInfo)
+    {
+        synchronized (this)
+        {
             boolean rootinfo = printRootInfo;
             this.printRootInfo = printRootInfo;
 
@@ -404,33 +580,74 @@ public class NewickFile extends FileParse {
         }
     }
 
-    char getQuoteChar() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    char getQuoteChar()
+    {
         return QuoteChar;
     }
 
-    char setQuoteChar(char c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    char setQuoteChar(char c)
+    {
         char old = QuoteChar;
         QuoteChar = c;
 
         return old;
     }
 
-    private String nodeName(String name) {
-        if (NodeSafeName[0].search(name)) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String nodeName(String name)
+    {
+        if (NodeSafeName[0].search(name))
+        {
             return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
-        } else {
+        }
+        else
+        {
             return NodeSafeName[2].replaceAll(name);
         }
     }
 
-    private String printNodeField(SequenceNode c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String printNodeField(SequenceNode c)
+    {
         return ((c.getName() == null) ? "" : nodeName(c.getName())) +
         ((HasBootstrap)
         ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +
         ((HasDistances) ? (":" + c.dist) : "");
     }
 
-    private String printRootField(SequenceNode root) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param root DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String printRootField(SequenceNode root)
+    {
         return (printRootInfo)
         ? (((root.getName() == null) ? "" : nodeName(root.getName())) +
         ((HasBootstrap)
@@ -439,19 +656,28 @@ public class NewickFile extends FileParse {
     }
 
     // Non recursive call deals with root node properties
-    public void print(StringBuffer tf, SequenceNode root) {
-        if (root != null) {
-            if (root.isLeaf() && printRootInfo) {
+    public void print(StringBuffer tf, SequenceNode root)
+    {
+        if (root != null)
+        {
+            if (root.isLeaf() && printRootInfo)
+            {
                 tf.append(printRootField(root));
-            } else {
-                if (root.isDummy()) {
+            }
+            else
+            {
+                if (root.isDummy())
+                {
                     _print(tf, (SequenceNode) root.right());
                     _print(tf, (SequenceNode) root.left());
-                } else {
+                }
+                else
+                {
                     tf.append("(");
                     _print(tf, (SequenceNode) root.right());
 
-                    if (root.left() != null) {
+                    if (root.left() != null)
+                    {
                         tf.append(",");
                     }
 
@@ -463,19 +689,28 @@ public class NewickFile extends FileParse {
     }
 
     // Recursive call for non-root nodes
-    public void _print(StringBuffer tf, SequenceNode c) {
-        if (c != null) {
-            if (c.isLeaf()) {
+    public void _print(StringBuffer tf, SequenceNode c)
+    {
+        if (c != null)
+        {
+            if (c.isLeaf())
+            {
                 tf.append(printNodeField(c));
-            } else {
-                if (c.isDummy()) {
+            }
+            else
+            {
+                if (c.isDummy())
+                {
                     _print(tf, (SequenceNode) c.right());
                     _print(tf, (SequenceNode) c.left());
-                } else {
+                }
+                else
+                {
                     tf.append("(");
                     _print(tf, (SequenceNode) c.right());
 
-                    if (c.left() != null) {
+                    if (c.left() != null)
+                    {
                         tf.append(",");
                     }
 
@@ -487,15 +722,18 @@ public class NewickFile extends FileParse {
     }
 
     // Test
-    public static void main(String[] args) {
-        try {
+    public static void main(String[] args)
+    {
+        try
+        {
             File fn = new File(args[0]);
 
             StringBuffer newickfile = new StringBuffer();
             BufferedReader treefile = new BufferedReader(new FileReader(fn));
             String l;
 
-            while ((l = treefile.readLine()) != null) {
+            while ((l = treefile.readLine()) != null)
+            {
                 newickfile.append(l);
             }
 
@@ -522,7 +760,9 @@ public class NewickFile extends FileParse {
             System.out.println(trf.print(false, false));
             System.out.println("With bootstraps and with distances.\n");
             System.out.println(trf.print(true, true));
-        } catch (java.io.IOException e) {
+        }
+        catch (java.io.IOException e)
+        {
             System.err.println("Exception\n" + e);
             e.printStackTrace();
         }
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 42334e3..a15a4cb 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,145 +1,173 @@
 /*
-* 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
-*/
+ * 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.io;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+
+public class PIRFile
+    extends AlignFile
+{
+  Vector words = new Vector(); //Stores the words in a line after splitting
+
+  public PIRFile()
+  {
+  }
+
+  public PIRFile(String inStr)
+  {
+    super(inStr);
+  }
+
+  public PIRFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  public void parse()
+  {
+    try
+    {
+      String id;
+      String start;
+      String end;
+      StringBuffer sequence;
+      String line = null;
+
+      while ( (line = nextLine()) != null)
+      {
+        try
+        {
+          id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));
+          line = line.substring(line.indexOf("/") + 1);
+          start = line.substring(0, line.indexOf("-"));
+          end = line.substring(line.indexOf("-") + 1);
+        }
+        catch (Exception ex)
+        {
+          id = "No id";
+          start = "0";
+          end = "0";
+        }
 
-public class PIRFile extends AlignFile {
-    Vector words = new Vector(); //Stores the words in a line after splitting
+        sequence = new StringBuffer();
 
-    public PIRFile() {
-    }
+        line = nextLine(); // this is the title line
 
-    public PIRFile(String inStr) {
-        super(inStr);
-    }
+        boolean starFound = false;
 
-    public PIRFile(String inFile, String type) throws IOException {
-        super(inFile, type);
-    }
+        do
+        {
+          line = nextLine();
+          sequence.append(line);
 
-    public void parse() {
-        try {
-            String id;
-            String start;
-            String end;
-            StringBuffer sequence;
-            String line = null;
-
-            while ((line = nextLine()) != null) {
-                try {
-                    id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));
-                    line = line.substring(line.indexOf("/") + 1);
-                    start = line.substring(0, line.indexOf("-"));
-                    end = line.substring(line.indexOf("-") + 1);
-                } catch (Exception ex) {
-                    id = "No id";
-                    start = "0";
-                    end = "0";
-                }
-
-                sequence = new StringBuffer();
-
-                line = nextLine(); // this is the title line
-
-                boolean starFound = false;
-
-                do {
-                    line = nextLine();
-                    sequence.append(line);
-
-                    if (line.indexOf("*") > -1) {
-                        starFound = true;
-                    }
-                } while (!starFound);
-
-                sequence.setLength(sequence.length() - 1);
-
-                Sequence newSeq = new Sequence(id, sequence.toString(),
-                        Integer.parseInt(start), Integer.parseInt(end));
-                seqs.addElement(newSeq);
-            }
-        } catch (Exception ex) {
-            ex.printStackTrace();
+          if (line.indexOf("*") > -1)
+          {
+            starFound = true;
+          }
         }
-    }
+        while (!starFound);
 
-    public String print() {
-        return print(getSeqsAsArray());
-    }
+        sequence.setLength(sequence.length() - 1);
 
-    public static String print(SequenceI[] s) {
-        return print(s, 72, true);
+        Sequence newSeq = new Sequence(id, sequence.toString(),
+                                       Integer.parseInt(start),
+                                       Integer.parseInt(end));
+        seqs.addElement(newSeq);
+      }
     }
-
-    public static String print(SequenceI[] s, int len) {
-        return print(s, len, true);
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
     }
-
-    public static String print(SequenceI[] s, int len, boolean gaps) {
-        StringBuffer out = new StringBuffer();
-        int i = 0;
-
-        while ((i < s.length) && (s[i] != null)) {
-            String seq = "";
-
-            if (gaps) {
-                seq = s[i].getSequence() + "*";
-            } else {
-                seq = AlignSeq.extractGaps(s[i].getSequence(), "-");
-                seq = AlignSeq.extractGaps(seq, ".");
-                seq = AlignSeq.extractGaps(seq, " ");
-                seq = seq + "*";
-            }
-
-            out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +
-                s[i].getEnd() + "\n");
-            out.append(" Dummy title\n");
-
-            int nochunks = (seq.length() / len) + 1;
-
-            for (int j = 0; j < nochunks; j++) {
-                int start = j * len;
-                int end = start + len;
-
-                if (end < seq.length()) {
-                    out.append(seq.substring(start, end) + "\n");
-                } else if (start < seq.length()) {
-                    out.append(seq.substring(start) + "\n");
-                }
-            }
-
-            i++;
+  }
+
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
+
+  public static String print(SequenceI[] s)
+  {
+    return print(s, 72, true);
+  }
+
+  public static String print(SequenceI[] s, int len)
+  {
+    return print(s, len, true);
+  }
+
+  public static String print(SequenceI[] s, int len, boolean gaps)
+  {
+    StringBuffer out = new StringBuffer();
+    int i = 0;
+
+    while ( (i < s.length) && (s[i] != null))
+    {
+      String seq = "";
+
+      if (gaps)
+      {
+        seq = s[i].getSequence() + "*";
+      }
+      else
+      {
+        seq = AlignSeq.extractGaps(s[i].getSequence(), "-");
+        seq = AlignSeq.extractGaps(seq, ".");
+        seq = AlignSeq.extractGaps(seq, " ");
+        seq = seq + "*";
+      }
+
+      out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +
+                 s[i].getEnd() + "\n");
+      out.append(" Dummy title\n");
+
+      int nochunks = (seq.length() / len) + 1;
+
+      for (int j = 0; j < nochunks; j++)
+      {
+        int start = j * len;
+        int end = start + len;
+
+        if (end < seq.length())
+        {
+          out.append(seq.substring(start, end) + "\n");
         }
+        else if (start < seq.length())
+        {
+          out.append(seq.substring(start) + "\n");
+        }
+      }
 
-        return out.toString();
+      i++;
     }
 
-    public static void main(String[] args) {
-        String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";
-        PIRFile fa = new PIRFile(inStr);
-    }
+    return out.toString();
+  }
+
+  public static void main(String[] args)
+  {
+    String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";
+    PIRFile fa = new PIRFile(inStr);
+  }
 }
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index b31a148..a6c7a4f 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,197 +1,237 @@
 /*
-* 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
-*/
+ * 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.io;
 
-import jalview.datamodel.*;
-
-import jalview.util.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.util.*;
 
-public class PfamFile extends AlignFile {
-    Vector ids;
+public class PfamFile
+    extends AlignFile
+{
+  Vector ids;
+
+  public PfamFile()
+  {
+  }
+
+  public PfamFile(String inStr)
+  {
+    super(inStr);
+  }
+
+  public PfamFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  public void initData()
+  {
+    super.initData();
+    ids = new Vector();
+  }
+
+  public void parse()
+      throws IOException
+  {
+    int i = 0;
+    String line;
+
+    Hashtable seqhash = new Hashtable();
+    Vector headers = new Vector();
+
+    while ( (line = nextLine()) != null)
+    {
+      if (line.indexOf(" ") != 0)
+      {
+        if (line.indexOf("#") != 0)
+        {
+          StringTokenizer str = new StringTokenizer(line, " ");
+          String id = "";
+
+          if (str.hasMoreTokens())
+          {
+            id = str.nextToken();
+
+            StringBuffer tempseq;
+
+            if (seqhash.containsKey(id))
+            {
+              tempseq = (StringBuffer) seqhash.get(id);
+            }
+            else
+            {
+              tempseq = new StringBuffer();
+              seqhash.put(id, tempseq);
+            }
 
-    public PfamFile() {
-    }
+            if (! (headers.contains(id)))
+            {
+              headers.addElement(id);
+            }
 
-    public PfamFile(String inStr) {
-        super(inStr);
+            tempseq.append(str.nextToken());
+          }
+        }
+      }
     }
 
-    public PfamFile(String inFile, String type) throws IOException {
-        super(inFile, type);
-    }
+    this.noSeqs = headers.size();
 
-    public void initData() {
-        super.initData();
-        ids = new Vector();
+    if (noSeqs < 1)
+    {
+      throw new IOException("No sequences found (PFAM input)");
     }
 
-    public void parse() throws IOException {
-        int i = 0;
-        String line;
-
-        Hashtable seqhash = new Hashtable();
-        Vector headers = new Vector();
-
-        while ((line = nextLine()) != null) {
-            if (line.indexOf(" ") != 0) {
-                if (line.indexOf("#") != 0) {
-                    StringTokenizer str = new StringTokenizer(line, " ");
-                    String id = "";
+    for (i = 0; i < headers.size(); i++)
+    {
+      if (seqhash.get(headers.elementAt(i)) != null)
+      {
+        if (maxLength < seqhash.get(headers.elementAt(i)).toString()
+            .length())
+        {
+          maxLength = seqhash.get(headers.elementAt(i)).toString()
+              .length();
+        }
 
-                    if (str.hasMoreTokens()) {
-                        id = str.nextToken();
+        String head = headers.elementAt(i).toString();
+        int start = 1;
+        int end = seqhash.get(headers.elementAt(i)).toString().length();
 
-                        StringBuffer tempseq;
+        if (head.indexOf("/") > 0)
+        {
+          StringTokenizer st = new StringTokenizer(head, "/");
 
-                        if (seqhash.containsKey(id)) {
-                            tempseq = (StringBuffer) seqhash.get(id);
-                        } else {
-                            tempseq = new StringBuffer();
-                            seqhash.put(id, tempseq);
-                        }
+          if (st.countTokens() == 2)
+          {
+            ids.addElement(st.nextToken());
 
-                        if (!(headers.contains(id))) {
-                            headers.addElement(id);
-                        }
+            String tmp = st.nextToken();
+            st = new StringTokenizer(tmp, "-");
 
-                        tempseq.append(str.nextToken());
-                    }
-                }
+            if (st.countTokens() == 2)
+            {
+              start = Integer.valueOf(st.nextToken()).intValue();
+              end = Integer.valueOf(st.nextToken()).intValue();
+            }
+            else
+            {
+              start = -1;
+              end = -1;
             }
+          }
+          else
+          {
+            ids.addElement(headers.elementAt(i));
+          }
+        }
+        else
+        {
+          ids.addElement(headers.elementAt(i));
         }
 
-        this.noSeqs = headers.size();
+        Sequence newSeq = null;
 
-        if (noSeqs < 1) {
-            throw new IOException("No sequences found (PFAM input)");
+        if ( (start != -1) && (end != -1))
+        {
+          newSeq = new Sequence(ids.elementAt(i).toString(),
+                                seqhash.get(headers.elementAt(i).toString())
+                                .toString(), start, end);
+          seqs.addElement(newSeq);
+        }
+        else
+        {
+          newSeq = new Sequence(ids.elementAt(i).toString(),
+                                seqhash.get(headers.elementAt(i).toString())
+                                .toString(), 1,
+                                seqhash.get(headers.elementAt(i).toString())
+                                .toString().length());
+          seqs.addElement(newSeq);
         }
 
-        for (i = 0; i < headers.size(); i++) {
-            if (seqhash.get(headers.elementAt(i)) != null) {
-                if (maxLength < seqhash.get(headers.elementAt(i)).toString()
-                                           .length()) {
-                    maxLength = seqhash.get(headers.elementAt(i)).toString()
-                                       .length();
-                }
-
-                String head = headers.elementAt(i).toString();
-                int start = 1;
-                int end = seqhash.get(headers.elementAt(i)).toString().length();
-
-                if (head.indexOf("/") > 0) {
-                    StringTokenizer st = new StringTokenizer(head, "/");
-
-                    if (st.countTokens() == 2) {
-                        ids.addElement(st.nextToken());
-
-                        String tmp = st.nextToken();
-                        st = new StringTokenizer(tmp, "-");
-
-                        if (st.countTokens() == 2) {
-                            start = Integer.valueOf(st.nextToken()).intValue();
-                            end = Integer.valueOf(st.nextToken()).intValue();
-                        } else {
-                            start = -1;
-                            end = -1;
-                        }
-                    } else {
-                        ids.addElement(headers.elementAt(i));
-                    }
-                } else {
-                    ids.addElement(headers.elementAt(i));
-                }
-
-                Sequence newSeq = null;
-
-                if ((start != -1) && (end != -1)) {
-                    newSeq = new Sequence(ids.elementAt(i).toString(),
-                            seqhash.get(headers.elementAt(i).toString())
-                                   .toString(), start, end);
-                    seqs.addElement(newSeq);
-                } else {
-                    newSeq = new Sequence(ids.elementAt(i).toString(),
-                            seqhash.get(headers.elementAt(i).toString())
-                                   .toString(), 1,
-                            seqhash.get(headers.elementAt(i).toString())
-                                   .toString().length());
-                    seqs.addElement(newSeq);
-                }
-
-                if (!isValidProteinSequence(newSeq.getSequence())) {
-                    throw new IOException(
-                        "Not a valid protein sequence - (PFAM input)");
-                }
-            } else {
-                System.err.println("PFAM File reader: Can't find sequence for " +
-                    headers.elementAt(i));
-            }
+        if (!isValidProteinSequence(newSeq.getSequence()))
+        {
+          throw new IOException(
+              "Not a valid protein sequence - (PFAM input)");
         }
+      }
+      else
+      {
+        System.err.println("PFAM File reader: Can't find sequence for " +
+                           headers.elementAt(i));
+      }
     }
+  }
 
-    public static String print(SequenceI[] s) {
-        StringBuffer out = new StringBuffer("");
+  public static String print(SequenceI[] s)
+  {
+    StringBuffer out = new StringBuffer("");
 
-        int max = 0;
-        int maxid = 0;
+    int max = 0;
+    int maxid = 0;
 
-        int i = 0;
+    int i = 0;
 
-        while ((i < s.length) && (s[i] != null)) {
-            String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
-                s[i].getEnd();
+    while ( (i < s.length) && (s[i] != null))
+    {
+      String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
+          s[i].getEnd();
 
-            if (s[i].getSequence().length() > max) {
-                max = s[i].getSequence().length();
-            }
+      if (s[i].getSequence().length() > max)
+      {
+        max = s[i].getSequence().length();
+      }
 
-            if (tmp.length() > maxid) {
-                maxid = tmp.length();
-            }
+      if (tmp.length() > maxid)
+      {
+        maxid = tmp.length();
+      }
 
-            i++;
-        }
+      i++;
+    }
 
-        if (maxid < 15) {
-            maxid = 15;
-        }
+    if (maxid < 15)
+    {
+      maxid = 15;
+    }
 
-        int j = 0;
+    int j = 0;
 
-        while ((j < s.length) && (s[j] != null)) {
-            out.append(new Format("%-" + maxid + "s").form(s[j].getName() +
-                    "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
+    while ( (j < s.length) && (s[j] != null))
+    {
+      out.append(new Format("%-" + maxid + "s").form(s[j].getName() +
+          "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
 
-            out.append(s[j].getSequence() + "\n");
-            j++;
-        }
+      out.append(s[j].getSequence() + "\n");
+      j++;
+    }
 
-        out.append("\n");
+    out.append("\n");
 
-        return out.toString();
-    }
+    return out.toString();
+  }
 
-    public String print() {
-        return print(getSeqsAsArray());
-    }
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
 }
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 9f879c0..1cb5b43 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,276 +1,327 @@
-/*
-* 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
-*/
+/*
+ * 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.io;
 
-
-/**
- * <p>Title: </p>
- *  PileUpfile
- * <p>Description: </p>
- *
- *  Read and write PileUp style MSF Files.
- *  This used to be the MSFFile class, and was written according to the EBI's idea
- *  of a subset of the MSF alignment format. But, that was updated to reflect current
- *  GCG style IO fashion, as found in Emboss (thanks David Martin!)
- *
+/**
+ * <p>Title: </p>
+ *  PileUpfile
+ * <p>Description: </p>
+ *
+ *  Read and write PileUp style MSF Files.
+ *  This used to be the MSFFile class, and was written according to the EBI's idea
+ *  of a subset of the MSF alignment format. But, that was updated to reflect current
+ *  GCG style IO fashion, as found in Emboss (thanks David Martin!)
+ *
  **/
-import jalview.datamodel.*;
-
-import jalview.util.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.util.*;
 
-public class PileUpfile extends AlignFile {
-    public PileUpfile() {
-    }
-
-    public PileUpfile(String inStr) {
-        super(inStr);
-    }
-
-    public PileUpfile(String inFile, String type) throws IOException {
-        super(inFile, type);
-    }
+public class PileUpfile
+    extends AlignFile
+{
+  public PileUpfile()
+  {
+  }
+
+  public PileUpfile(String inStr)
+  {
+    super(inStr);
+  }
+
+  public PileUpfile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  public void parse()
+  {
+    int i = 0;
+    boolean seqFlag = false;
+    String key = new String();
+    Vector headers = new Vector();
+    Hashtable seqhash = new Hashtable();
+    String line;
+
+    try
+    {
+      while ( (line = nextLine()) != null)
+      {
+        StringTokenizer str = new StringTokenizer(line);
+
+        while (str.hasMoreTokens())
+        {
+          String inStr = str.nextToken();
+
+          //If line has header information add to the headers vector
+          if (inStr.indexOf("Name:") != -1)
+          {
+            key = str.nextToken();
+            headers.addElement(key);
+          }
+
+          //if line has // set SeqFlag to 1 so we know sequences are coming
+          if (inStr.indexOf("//") != -1)
+          {
+            seqFlag = true;
+          }
+
+          //Process lines as sequence lines if seqFlag is set
+          if ( (inStr.indexOf("//") == -1) && (seqFlag == true))
+          {
+            //seqeunce id is the first field
+            key = inStr;
+
+            StringBuffer tempseq;
+
+            //Get sequence from hash if it exists
+            if (seqhash.containsKey(key))
+            {
+              tempseq = (StringBuffer) seqhash.get(key);
+            }
+            else
+            {
+              tempseq = new StringBuffer();
+              seqhash.put(key, tempseq);
+            }
 
-    public void parse() {
-        int i = 0;
-        boolean seqFlag = false;
-        String key = new String();
-        Vector headers = new Vector();
-        Hashtable seqhash = new Hashtable();
-        String line;
-
-        try {
-            while ((line = nextLine()) != null) {
-                StringTokenizer str = new StringTokenizer(line);
-
-                while (str.hasMoreTokens()) {
-                    String inStr = str.nextToken();
-
-                    //If line has header information add to the headers vector
-                    if (inStr.indexOf("Name:") != -1) {
-                        key = str.nextToken();
-                        headers.addElement(key);
-                    }
-
-                    //if line has // set SeqFlag to 1 so we know sequences are coming
-                    if (inStr.indexOf("//") != -1) {
-                        seqFlag = true;
-                    }
-
-                    //Process lines as sequence lines if seqFlag is set
-                    if ((inStr.indexOf("//") == -1) && (seqFlag == true)) {
-                        //seqeunce id is the first field
-                        key = inStr;
-
-                        StringBuffer tempseq;
-
-                        //Get sequence from hash if it exists
-                        if (seqhash.containsKey(key)) {
-                            tempseq = (StringBuffer) seqhash.get(key);
-                        } else {
-                            tempseq = new StringBuffer();
-                            seqhash.put(key, tempseq);
-                        }
-
-                        //loop through the rest of the words
-                        while (str.hasMoreTokens()) {
-                            //append the word to the sequence
-                            tempseq.append(str.nextToken());
-                        }
-                    }
-                }
+            //loop through the rest of the words
+            while (str.hasMoreTokens())
+            {
+              //append the word to the sequence
+              tempseq.append(str.nextToken());
             }
-        } catch (IOException e) {
-            System.err.println("Exception parsing PileUpfile " + e);
-            e.printStackTrace();
+          }
         }
+      }
+    }
+    catch (IOException e)
+    {
+      System.err.println("Exception parsing PileUpfile " + e);
+      e.printStackTrace();
+    }
 
-        this.noSeqs = headers.size();
-
-        //Add sequences to the hash
-        for (i = 0; i < headers.size(); i++) {
-            if (seqhash.get(headers.elementAt(i)) != null) {
-                String head = headers.elementAt(i).toString();
-                String seq = seqhash.get(head).toString();
-
-                int start = 1;
-                int end = seq.length();
+    this.noSeqs = headers.size();
 
-                if (maxLength < head.length()) {
-                    maxLength = head.length();
-                }
+    //Add sequences to the hash
+    for (i = 0; i < headers.size(); i++)
+    {
+      if (seqhash.get(headers.elementAt(i)) != null)
+      {
+        String head = headers.elementAt(i).toString();
+        String seq = seqhash.get(head).toString();
 
-                if (head.indexOf("/") > 0) {
-                    StringTokenizer st = new StringTokenizer(head, "/");
+        int start = 1;
+        int end = seq.length();
 
-                    if (st.countTokens() == 2) {
-                        head = st.nextToken();
+        if (maxLength < head.length())
+        {
+          maxLength = head.length();
+        }
 
-                        String tmp = st.nextToken();
-                        st = new StringTokenizer(tmp, "-");
+        if (head.indexOf("/") > 0)
+        {
+          StringTokenizer st = new StringTokenizer(head, "/");
 
-                        if (st.countTokens() == 2) {
-                            start = Integer.valueOf(st.nextToken()).intValue();
-                            end = Integer.valueOf(st.nextToken()).intValue();
-                        }
-                    }
-                }
+          if (st.countTokens() == 2)
+          {
+            head = st.nextToken();
 
-                Sequence newSeq = new Sequence(head, seq, start, end);
+            String tmp = st.nextToken();
+            st = new StringTokenizer(tmp, "-");
 
-                seqs.addElement(newSeq);
-            } else {
-                System.err.println(
-                    "PileUpfile Parser: Can't find sequence for " +
-                    headers.elementAt(i));
+            if (st.countTokens() == 2)
+            {
+              start = Integer.valueOf(st.nextToken()).intValue();
+              end = Integer.valueOf(st.nextToken()).intValue();
             }
+          }
         }
-    }
 
-    public static int checkSum(String seq) {
-        //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
-        int check = 0;
-
-        String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
-        index += "--------------------------------------------------------------------------------------------------------------------------------";
-
-        for (int i = 0; i < seq.length(); i++) {
-            try {
-                if (i < seq.length()) {
-                    int pos = index.indexOf(seq.substring(i, i + 1));
-
-                    if (!index.substring(pos, pos + 1).equals("_")) {
-                        check += (((i % 57) + 1) * pos);
-                    }
-                }
-            } catch (Exception e) {
-                System.err.println("Exception during MSF Checksum calculation");
-                e.printStackTrace();
-            }
-        }
+        Sequence newSeq = new Sequence(head, seq, start, end);
 
-        return check % 10000;
+        seqs.addElement(newSeq);
+      }
+      else
+      {
+        System.err.println(
+            "PileUpfile Parser: Can't find sequence for " +
+            headers.elementAt(i));
+      }
+    }
+  }
+
+  public static int checkSum(String seq)
+  {
+    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
+    int check = 0;
+
+    String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
+    index += "--------------------------------------------------------------------------------------------------------------------------------";
+
+    for (int i = 0; i < seq.length(); i++)
+    {
+      try
+      {
+        if (i < seq.length())
+        {
+          int pos = index.indexOf(seq.substring(i, i + 1));
+
+          if (!index.substring(pos, pos + 1).equals("_"))
+          {
+            check += ( ( (i % 57) + 1) * pos);
+          }
+        }
+      }
+      catch (Exception e)
+      {
+        System.err.println("Exception during MSF Checksum calculation");
+        e.printStackTrace();
+      }
     }
 
-    public static String print(SequenceI[] s) {
-        StringBuffer out = new StringBuffer("PileUp\n\n");
+    return check % 10000;
+  }
 
-        int max = 0;
-        int maxid = 0;
+  public static String print(SequenceI[] s)
+  {
+    StringBuffer out = new StringBuffer("PileUp\n\n");
 
-        int i = 0;
-        String big = "";
+    int max = 0;
+    int maxid = 0;
 
-        while ((i < s.length) && (s[i] != null)) {
-            big += s[i].getSequence();
-            i++;
-        }
+    int i = 0;
+    String big = "";
 
-        i = 0;
+    while ( (i < s.length) && (s[i] != null))
+    {
+      big += s[i].getSequence();
+      i++;
+    }
 
-        int bigcheck = checkSum(big);
+    i = 0;
 
-        out.append("   MSF: " + s[0].getSequence().length() +
-            "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");
+    int bigcheck = checkSum(big);
 
-        while ((i < s.length) && (s[i] != null)) {
-            String seq = s[i].getSequence();
-            String name = s[i].getName() + "/" + s[i].getStart() + "-" +
-                s[i].getEnd();
-            int check = checkSum(s[i].getSequence());
-            out.append(" Name: " + name + " oo  Len:  " +
-                s[i].getSequence().length() + "  Check:  " + check +
-                "  Weight:  1.00\n");
+    out.append("   MSF: " + s[0].getSequence().length() +
+               "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");
 
-            if (seq.length() > max) {
-                max = seq.length();
-            }
+    while ( (i < s.length) && (s[i] != null))
+    {
+      String seq = s[i].getSequence();
+      String name = s[i].getName() + "/" + s[i].getStart() + "-" +
+          s[i].getEnd();
+      int check = checkSum(s[i].getSequence());
+      out.append(" Name: " + name + " oo  Len:  " +
+                 s[i].getSequence().length() + "  Check:  " + check +
+                 "  Weight:  1.00\n");
 
-            if (name.length() > maxid) {
-                maxid = name.length();
-            }
+      if (seq.length() > max)
+      {
+        max = seq.length();
+      }
 
-            i++;
-        }
+      if (name.length() > maxid)
+      {
+        maxid = name.length();
+      }
 
-        if (maxid < 10) {
-            maxid = 10;
-        }
+      i++;
+    }
 
-        maxid++;
-        out.append("\n\n//\n\n");
+    if (maxid < 10)
+    {
+      maxid = 10;
+    }
 
-        int len = 50;
+    maxid++;
+    out.append("\n\n//\n\n");
 
-        int nochunks = (max / len) + 1;
+    int len = 50;
 
-        if ((max % len) == 0) {
-            nochunks--;
-        }
+    int nochunks = (max / len) + 1;
 
-        for (i = 0; i < nochunks; i++) {
-            int j = 0;
-
-            while ((j < s.length) && (s[j] != null)) {
-                String name = s[j].getName();
-                out.append(new Format("%-" + maxid + "s").form(name + "/" +
-                        s[j].getStart() + "-" + s[j].getEnd()) + " ");
-
-                for (int k = 0; k < 5; k++) {
-                    int start = (i * 50) + (k * 10);
-                    int end = start + 10;
-
-                    if ((end < s[j].getSequence().length()) &&
-                            (start < s[j].getSequence().length())) {
-                        out.append(s[j].getSequence().substring(start, end));
-
-                        if (k < 4) {
-                            out.append(" ");
-                        } else {
-                            out.append("\n");
-                        }
-                    } else {
-                        if (start < s[j].getSequence().length()) {
-                            out.append(s[j].getSequence().substring(start));
-                            out.append("\n");
-                        } else {
-                            if (k == 0) {
-                                out.append("\n");
-                            }
-                        }
-                    }
-                }
-
-                j++;
-            }
+    if ( (max % len) == 0)
+    {
+      nochunks--;
+    }
 
-            out.append("\n");
+    for (i = 0; i < nochunks; i++)
+    {
+      int j = 0;
+
+      while ( (j < s.length) && (s[j] != null))
+      {
+        String name = s[j].getName();
+        out.append(new Format("%-" + maxid + "s").form(name + "/" +
+            s[j].getStart() + "-" + s[j].getEnd()) + " ");
+
+        for (int k = 0; k < 5; k++)
+        {
+          int start = (i * 50) + (k * 10);
+          int end = start + 10;
+
+          if ( (end < s[j].getSequence().length()) &&
+              (start < s[j].getSequence().length()))
+          {
+            out.append(s[j].getSequence().substring(start, end));
+
+            if (k < 4)
+            {
+              out.append(" ");
+            }
+            else
+            {
+              out.append("\n");
+            }
+          }
+          else
+          {
+            if (start < s[j].getSequence().length())
+            {
+              out.append(s[j].getSequence().substring(start));
+              out.append("\n");
+            }
+            else
+            {
+              if (k == 0)
+              {
+                out.append("\n");
+              }
+            }
+          }
         }
 
-        return out.toString();
-    }
+        j++;
+      }
 
-    public String print() {
-        return print(getSeqsAsArray());
+      out.append("\n");
     }
+
+    return out.toString();
+  }
+
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
 }
diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index cdd628b..89d84b0 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -29,14 +29,28 @@ import java.io.*;
 import java.util.*;
 
 
-public class SequenceFeatureFetcher implements Runnable {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceFeatureFetcher implements Runnable
+{
     AlignmentI align;
     AlignmentPanel ap;
     ArrayList unknownSequences;
     CutAndPasteTransfer output = new CutAndPasteTransfer();
     StringBuffer sbuffer = new StringBuffer();
 
-    public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap) {
+    /**
+     * Creates a new SequenceFeatureFetcher object.
+     *
+     * @param align DOCUMENT ME!
+     * @param ap DOCUMENT ME!
+     */
+    public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
+    {
         unknownSequences = new ArrayList();
         this.align = align;
         this.ap = ap;
@@ -45,28 +59,38 @@ public class SequenceFeatureFetcher implements Runnable {
         thread.start();
     }
 
-    public void run() {
-
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
+    {
         RandomAccessFile out = null;
 
-        try {
-            String cache = System.getProperty("user.home") + "/.jalview.uniprot.xml";
+        try
+        {
+            String cache = System.getProperty("user.home") +
+                "/.jalview.uniprot.xml";
 
             File test = new File(cache);
 
-            if (!test.exists()) {
+            if (!test.exists())
+            {
                 out = new RandomAccessFile(cache, "rw");
                 out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
                 out.writeBytes("<UNIPROT_CACHE>\n");
-            } else {
+            }
+            else
+            {
                 out = new RandomAccessFile(cache, "rw");
 
                 // open exisiting cache and remove </UNIPROT_CACHE> from the end
                 long lastLine = 0;
                 String data;
 
-                while ((data = out.readLine()) != null) {
-                    if (data.indexOf("</entry>") > -1) {
+                while ((data = out.readLine()) != null)
+                {
+                    if (data.indexOf("</entry>") > -1)
+                    {
                         lastLine = out.getFilePointer();
                     }
                 }
@@ -77,18 +101,21 @@ public class SequenceFeatureFetcher implements Runnable {
             int seqIndex = 0;
             Vector sequences = align.getSequences();
 
-            while (seqIndex < sequences.size()) {
+            while (seqIndex < sequences.size())
+            {
                 ArrayList ids = new ArrayList();
 
                 for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
-                        seqIndex++, i++) {
+                        seqIndex++, i++)
+                {
                     SequenceI sequence = (SequenceI) sequences.get(seqIndex);
                     ids.add(sequence.getName());
                 }
 
                 tryLocalCacheFirst(ids, align);
 
-                if (ids.size() > 0) {
+                if (ids.size() > 0)
+                {
                     StringBuffer remainingIds = new StringBuffer("uniprot:");
 
                     for (int i = 0; i < ids.size(); i++)
@@ -98,23 +125,28 @@ public class SequenceFeatureFetcher implements Runnable {
                     String[] result = ebi.fetchData(remainingIds.toString(),
                             "xml", null);
 
-                    if (result != null) {
+                    if (result != null)
+                    {
                         ReadUniprotFile(result, out, align);
                     }
                 }
             }
 
-            if (out != null) {
+            if (out != null)
+            {
                 out.writeBytes("</UNIPROT_CACHE>\n");
                 out.close();
             }
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             ex.printStackTrace();
         }
 
         findMissingIds(align);
 
-        if (sbuffer.length() > 0) {
+        if (sbuffer.length() > 0)
+        {
             output.setText(
                 "Your sequences have been matched to Uniprot. Some of the ids have been\n" +
                 "altered, most likely the start/end residue will have been updated.\n" +
@@ -123,7 +155,8 @@ public class SequenceFeatureFetcher implements Runnable {
             Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
         }
 
-        if (unknownSequences.size() > 0) {
+        if (unknownSequences.size() > 0)
+        {
             //ignore for now!!!!!!!!!!
             //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
         }
@@ -131,7 +164,15 @@ public class SequenceFeatureFetcher implements Runnable {
         jalview.gui.PaintRefresher.Refresh(null, align);
     }
 
-    void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param result DOCUMENT ME!
+     * @param out DOCUMENT ME!
+     * @param align DOCUMENT ME!
+     */
+    void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align)
+    {
         SequenceI sequence = null;
         Vector features = null;
         String type;
@@ -141,42 +182,54 @@ public class SequenceFeatureFetcher implements Runnable {
         String end;
         String pdb = null;
 
-        for (int r = 0; r < result.length; r++) {
-            if ((sequence == null) && (result[r].indexOf("<name>") > -1)) {
+        for (int r = 0; r < result.length; r++)
+        {
+            if ((sequence == null) && (result[r].indexOf("<name>") > -1))
+            {
                 long filePointer = 0;
 
-                if (out != null) {
-                    try {
+                if (out != null)
+                {
+                    try
+                    {
                         filePointer = out.getFilePointer();
                         out.writeBytes("<entry>\n");
-                    } catch (Exception ex) {
+                    }
+                    catch (Exception ex)
+                    {
                     }
                 }
 
                 String seqName = parseElement(result[r], "<name>", out);
                 sequence = align.findName(seqName);
 
-                if (sequence == null) {
+                if (sequence == null)
+                {
                     sequence = align.findName(seqName.substring(0,
                                 seqName.indexOf('_')));
 
-                    if (sequence != null) {
+                    if (sequence != null)
+                    {
                         sbuffer.append("changing " + sequence.getName() +
                             " to " + seqName + "\n");
                         sequence.setName(seqName);
                     }
                 }
 
-                if (sequence == null) {
+                if (sequence == null)
+                {
                     sbuffer.append("UNIPROT updated suggestion is " +
                         result[r] + "\n");
                     sequence = align.findName(result[r]);
 
                     // this entry has been suggested by ebi.
                     // doesn't match id in alignment file
-                    try {
+                    try
+                    {
                         out.setLength(filePointer);
-                    } catch (Exception ex) {
+                    }
+                    catch (Exception ex)
+                    {
                     }
 
                     // now skip to next entry
@@ -193,29 +246,36 @@ public class SequenceFeatureFetcher implements Runnable {
                 pdb = "";
             }
 
-            if (sequence == null) {
+            if (sequence == null)
+            {
                 continue;
             }
 
-            if (result[r].indexOf("<property type=\"pdb accession\"") > -1) {
+            if (result[r].indexOf("<property type=\"pdb accession\"") > -1)
+            {
                 pdb = parseValue(result[r], "value=", out);
                 sequence.setPDBId(pdb);
             }
 
-            if (result[r].indexOf("feature type") > -1) {
+            if (result[r].indexOf("feature type") > -1)
+            {
                 type = parseValue(result[r], "type=", out);
                 description = parseValue(result[r], "description=", null);
                 status = parseValue(result[r], "status=", null);
 
-                while (result[r].indexOf("position") == -1) {
+                while (result[r].indexOf("position") == -1)
+                {
                     r++; //<location>
                 }
 
                 // r++;
-                if (result[r].indexOf("begin") > -1) {
+                if (result[r].indexOf("begin") > -1)
+                {
                     start = parseValue(result[r], "position=", out);
                     end = parseValue(result[++r], "position=", out);
-                } else {
+                }
+                else
+                {
                     start = parseValue(result[r], "position=", out);
                     end = parseValue(result[r], "position=", null);
                 }
@@ -223,10 +283,14 @@ public class SequenceFeatureFetcher implements Runnable {
                 int sstart = Integer.parseInt(start);
                 int eend = Integer.parseInt(end);
 
-                if (out != null) {
-                    try {
+                if (out != null)
+                {
+                    try
+                    {
                         out.writeBytes("</feature>\n");
-                    } catch (Exception ex) {
+                    }
+                    catch (Exception ex)
+                    {
                     }
                 }
 
@@ -235,45 +299,62 @@ public class SequenceFeatureFetcher implements Runnable {
                 features.add(sf);
             }
 
-            if (result[r].indexOf("<sequence") > -1) {
+            if (result[r].indexOf("<sequence") > -1)
+            {
                 StringBuffer seqString = new StringBuffer();
 
-                if (out != null) {
-                    try {
+                if (out != null)
+                {
+                    try
+                    {
                         out.writeBytes(result[r] + "\n");
-                    } catch (Exception ex) {
+                    }
+                    catch (Exception ex)
+                    {
                     }
                 }
 
-                while (result[++r].indexOf("</sequence>") == -1) {
+                while (result[++r].indexOf("</sequence>") == -1)
+                {
                     seqString.append(result[r]);
 
-                    if (out != null) {
-                        try {
+                    if (out != null)
+                    {
+                        try
+                        {
                             out.writeBytes(result[r] + "\n");
-                        } catch (Exception ex) {
+                        }
+                        catch (Exception ex)
+                        {
                         }
                     }
                 }
 
-                if (out != null) {
-                    try {
+                if (out != null)
+                {
+                    try
+                    {
                         out.writeBytes(result[r] + "\n");
-                    } catch (Exception ex) {
+                    }
+                    catch (Exception ex)
+                    {
                     }
                 }
 
                 StringBuffer nonGapped = new StringBuffer();
 
-                for (int i = 0; i < sequence.getSequence().length(); i++) {
-                    if (!jalview.util.Comparison.isGap(sequence.getCharAt(i))) {
+                for (int i = 0; i < sequence.getSequence().length(); i++)
+                {
+                    if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
+                    {
                         nonGapped.append(sequence.getCharAt(i));
                     }
                 }
 
                 int absStart = seqString.toString().indexOf(nonGapped.toString());
 
-                if (absStart == -1) {
+                if (absStart == -1)
+                {
                     unknownSequences.add(sequence.getName());
                     features = null;
                     sbuffer.append(sequence.getName() +
@@ -286,7 +367,8 @@ public class SequenceFeatureFetcher implements Runnable {
                 absStart += 1;
 
                 if ((absStart != sequence.getStart()) ||
-                        (absEnd != sequence.getEnd())) {
+                        (absEnd != sequence.getEnd()))
+                {
                     sbuffer.append("Updated: " + sequence.getName() + " " +
                         sequence.getStart() + "/" + sequence.getEnd() +
                         "  to  " + absStart + "/" + absEnd + "\n");
@@ -296,52 +378,78 @@ public class SequenceFeatureFetcher implements Runnable {
                 sequence.setEnd(absEnd);
             }
 
-            if (result[r].indexOf("</entry>") > -1) {
-                if (features != null) {
+            if (result[r].indexOf("</entry>") > -1)
+            {
+                if (features != null)
+                {
                     sequence.setSequenceFeatures(features);
                 }
 
                 features = null;
                 sequence = null;
 
-                if (out != null) {
-                    try {
+                if (out != null)
+                {
+                    try
+                    {
                         out.writeBytes("</entry>\n");
-                    } catch (Exception ex) {
+                    }
+                    catch (Exception ex)
+                    {
                     }
                 }
             }
         }
     }
 
-    void findMissingIds(AlignmentI align) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param align DOCUMENT ME!
+     */
+    void findMissingIds(AlignmentI align)
+    {
         String data;
         ArrayList cachedIds = new ArrayList();
 
-        try {
+        try
+        {
             BufferedReader in = new BufferedReader(new FileReader(
                         jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
 
-            while ((data = in.readLine()) != null) {
-                if (data.indexOf("name") > -1) {
+            while ((data = in.readLine()) != null)
+            {
+                if (data.indexOf("name") > -1)
+                {
                     String name = parseElement(data, "<name>", null);
                     cachedIds.add(name);
                 }
             }
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             ex.printStackTrace();
         }
 
         for (int i = 0; i < align.getHeight(); i++)
-            if (!cachedIds.contains(align.getSequenceAt(i).getName())) {
+            if (!cachedIds.contains(align.getSequenceAt(i).getName()))
+            {
                 unknownSequences.add(align.getSequenceAt(i).getName());
             }
     }
 
-    void tryLocalCacheFirst(ArrayList ids, AlignmentI align) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ids DOCUMENT ME!
+     * @param align DOCUMENT ME!
+     */
+    void tryLocalCacheFirst(ArrayList ids, AlignmentI align)
+    {
         ArrayList cacheData = new ArrayList();
 
-        try {
+        try
+        {
             BufferedReader in = new BufferedReader(new FileReader(
                         jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
 
@@ -350,15 +458,19 @@ public class SequenceFeatureFetcher implements Runnable {
             // make sure we remove the ids from the list to retrieve from EBI
             String data;
 
-            while ((data = in.readLine()) != null) {
-                if (data.indexOf("name") > -1) {
+            while ((data = in.readLine()) != null)
+            {
+                if (data.indexOf("name") > -1)
+                {
                     String name = parseElement(data, "<name>", null);
 
-                    if (ids.contains(name)) {
+                    if (ids.contains(name))
+                    {
                         cacheData.add("<entry>");
                         cacheData.add(data);
 
-                        while (data.indexOf("</entry>") == -1) {
+                        while (data.indexOf("</entry>") == -1)
+                        {
                             data = in.readLine();
                             cacheData.add(data);
                         }
@@ -369,40 +481,72 @@ public class SequenceFeatureFetcher implements Runnable {
                     }
                 }
             }
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             ex.printStackTrace();
         }
 
         String[] localData = new String[cacheData.size()];
         cacheData.toArray(localData);
 
-        if ((localData != null) && (localData.length > 0)) {
+        if ((localData != null) && (localData.length > 0))
+        {
             ReadUniprotFile(localData, null, align);
         }
     }
 
-    String parseValue(String line, String tag, RandomAccessFile out) {
-        if (out != null) {
-            try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param line DOCUMENT ME!
+     * @param tag DOCUMENT ME!
+     * @param out DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    String parseValue(String line, String tag, RandomAccessFile out)
+    {
+        if (out != null)
+        {
+            try
+            {
                 out.writeBytes(line + "\n");
-            } catch (Exception ex) {
+            }
+            catch (Exception ex)
+            {
             }
         }
 
         int index = line.indexOf(tag) + tag.length() + 1;
 
-        if (index == tag.length()) {
+        if (index == tag.length())
+        {
             return "";
         }
 
         return line.substring(index, line.indexOf("\"", index + 1));
     }
 
-    String parseElement(String line, String tag, RandomAccessFile out) {
-        if (out != null) {
-            try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param line DOCUMENT ME!
+     * @param tag DOCUMENT ME!
+     * @param out DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    String parseElement(String line, String tag, RandomAccessFile out)
+    {
+        if (out != null)
+        {
+            try
+            {
                 out.writeBytes(line + "\n");
-            } catch (Exception ex) {
+            }
+            catch (Exception ex)
+            {
             }
         }
 
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 29a0900..33d6d92 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -33,23 +33,40 @@ import javax.swing.*;
 import javax.xml.namespace.QName;
 
 
-public class WSWUBlastClient {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class WSWUBlastClient
+{
     CutAndPasteTransfer output = new CutAndPasteTransfer();
     int jobsRunning = 0;
 
-    public WSWUBlastClient(AlignmentI al, ArrayList ids) {
+    /**
+     * Creates a new WSWUBlastClient object.
+     *
+     * @param al DOCUMENT ME!
+     * @param ids DOCUMENT ME!
+     */
+    public WSWUBlastClient(AlignmentI al, ArrayList ids)
+    {
         output.setText(
             "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +
             "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");
         Desktop.addInternalFrame(output,
             "BLASTing for unidentified sequences ", 800, 300);
 
-        for (int i = 0; i < ids.size(); i++) {
+        for (int i = 0; i < ids.size(); i++)
+        {
             SequenceI sequence = al.findName(ids.get(i).toString());
             StringBuffer nonGapped = new StringBuffer();
 
-            for (int n = 0; n < sequence.getSequence().length(); n++) {
-                if (!jalview.util.Comparison.isGap(sequence.getCharAt(n))) {
+            for (int n = 0; n < sequence.getSequence().length(); n++)
+            {
+                if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))
+                {
                     nonGapped.append(sequence.getCharAt(n));
                 }
             }
@@ -64,29 +81,41 @@ public class WSWUBlastClient {
         thread.start();
     }
 
-    void parseResult(String id1, String res) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id1 DOCUMENT ME!
+     * @param res DOCUMENT ME!
+     */
+    void parseResult(String id1, String res)
+    {
         StringTokenizer st = new StringTokenizer(res, "\n");
         String data;
         String id2;
         int maxFound = 90;
         StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");
 
-        while (st.hasMoreTokens()) {
+        while (st.hasMoreTokens())
+        {
             data = st.nextToken();
 
-            if (data.indexOf("database=\"uniprot\" id=") > -1) {
+            if (data.indexOf("database=\"uniprot\" id=") > -1)
+            {
                 int index = data.indexOf("database=\"uniprot\" id=") + 23;
                 id2 = data.substring(index, data.indexOf("\"", index));
 
-                while (data.indexOf("</alignment>") == -1) {
+                while (data.indexOf("</alignment>") == -1)
+                {
                     data = st.nextToken();
 
-                    if (data.indexOf("<identity>") > -1) {
+                    if (data.indexOf("<identity>") > -1)
+                    {
                         int value = Integer.parseInt(data.substring(data.indexOf(
                                         "<identity>") + 10,
                                     data.indexOf("</identity>")));
 
-                        if (value >= maxFound) {
+                        if (value >= maxFound)
+                        {
                             maxFound = value;
                             buffer.append(" " + id2 + " " + value + "%; ");
                         }
@@ -98,65 +127,81 @@ public class WSWUBlastClient {
         output.setText(output.getText() + buffer.toString());
     }
 
-    class ImageTwirler extends Thread {
+    class ImageTwirler extends Thread
+    {
         ImageIcon[] imageIcon;
         int imageIndex = 0;
 
-        public ImageTwirler() {
+        public ImageTwirler()
+        {
             imageIcon = new ImageIcon[9];
 
-            for (int i = 0; i < 9; i++) {
+            for (int i = 0; i < 9; i++)
+            {
                 java.net.URL url = getClass().getResource("/images/dna" +
                         (i + 1) + ".gif");
 
-                if (url != null) {
+                if (url != null)
+                {
                     imageIcon[i] = new ImageIcon(url);
                 }
             }
         }
 
-        public void run() {
-            while (jobsRunning > 0) {
-                try {
+        public void run()
+        {
+            while (jobsRunning > 0)
+            {
+                try
+                {
                     Thread.sleep(100);
                     imageIndex++;
                     imageIndex %= 9;
                     output.setFrameIcon(imageIcon[imageIndex]);
                     output.setTitle("BLASTing for unidentified sequences - " +
                         jobsRunning + " jobs running.");
-                } catch (Exception ex) {
+                }
+                catch (Exception ex)
+                {
                 }
             }
         }
     }
 
-    class BlastThread extends Thread {
+    class BlastThread extends Thread
+    {
         String sequence;
         String seqid;
         String jobid;
         boolean jobComplete = false;
 
-        BlastThread(String id, String sequence) {
+        BlastThread(String id, String sequence)
+        {
             this.sequence = sequence;
             seqid = id;
         }
 
-        public void run() {
+        public void run()
+        {
             StartJob();
 
-            while (!jobComplete) {
-                try {
+            while (!jobComplete)
+            {
+                try
+                {
                     Call call = (Call) new Service().createCall();
                     call.setTargetEndpointAddress(new java.net.URL(
                             "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
                     call.setOperationName(new QName("WSWUBlast", "polljob"));
 
-                    String result = (String) call.invoke(new Object[] {
+                    String result = (String) call.invoke(new Object[]
+                            {
                                 jobid, "xml"
                             });
 
                     if ((result.indexOf("JOB PENDING") == -1) &&
-                            (result.indexOf("JOB RUNNING") == -1)) {
+                            (result.indexOf("JOB RUNNING") == -1))
+                    {
                         parseResult(seqid, result);
                         jobComplete = true;
                         jobsRunning--;
@@ -165,12 +210,15 @@ public class WSWUBlastClient {
                     Thread.sleep(5000);
 
                     // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
-                } catch (Exception ex) {
+                }
+                catch (Exception ex)
+                {
                 }
             }
         }
 
-        void StartJob() {
+        void StartJob()
+        {
             HashMap params = new HashMap();
             params.put("database", "uniprot");
             params.put("sensitivity", "low");
@@ -183,20 +231,24 @@ public class WSWUBlastClient {
 
             byte[] seqbytes = sequence.getBytes();
 
-            try {
+            try
+            {
                 Call call = (Call) new Service().createCall();
                 call.setTargetEndpointAddress(new java.net.URL(
                         "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
                 call.setOperationName(new QName("WSWUBlast", "doWUBlast"));
 
-                String result = (String) call.invoke(new Object[] {
+                String result = (String) call.invoke(new Object[]
+                        {
                             params, seqbytes
                         });
                 jobid = result;
                 System.out.println(
                     "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +
                     jobid + "'");
-            } catch (Exception exp) {
+            }
+            catch (Exception exp)
+            {
                 System.err.println("WSWUBlastClient error:\n" + exp.toString());
                 exp.printStackTrace();
             }
diff --git a/src/jalview/jbappletgui/GAlignFrame.java b/src/jalview/jbappletgui/GAlignFrame.java
index a401b6e..7775b65 100755
--- a/src/jalview/jbappletgui/GAlignFrame.java
+++ b/src/jalview/jbappletgui/GAlignFrame.java
@@ -229,20 +229,20 @@ public class GAlignFrame extends Frame {
                     pairwiseAlignmentMenuItem_actionPerformed(e);
                 }
             });
-        PCAMenuItem.setLabel("Principal Component Analysis...");
+        PCAMenuItem.setLabel("Principal Component Analysis");
         PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {
                 public void actionPerformed(ActionEvent e) {
                     PCAMenuItem_actionPerformed(e);
                 }
             });
         averageDistanceTreeMenuItem.setLabel(
-            "Average Distance Using % Identity...");
+            "Average Distance Using % Identity");
         averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
                 public void actionPerformed(ActionEvent e) {
                     averageDistanceTreeMenuItem_actionPerformed(e);
                 }
             });
-        neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");
+        neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
         neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
                 public void actionPerformed(ActionEvent e) {
                     neighbourTreeMenuItem_actionPerformed(e);
@@ -321,13 +321,13 @@ public class GAlignFrame extends Frame {
                 }
             });
         avDistanceTreeBlosumMenuItem.setLabel(
-            "Average Distance Using BLOSUM62...");
+            "Average Distance Using BLOSUM62");
         avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
                 public void actionPerformed(ActionEvent e) {
                     avTreeBlosumMenuItem_actionPerformed(e);
                 }
             });
-        njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62...");
+        njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
         njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
                 public void actionPerformed(ActionEvent e) {
                     njTreeBlosumMenuItem_actionPerformed(e);
@@ -347,7 +347,7 @@ public class GAlignFrame extends Frame {
                     colourTextMenuItem_actionPerformed(null);
                 }
             });
-        overviewMenuItem.setLabel("Overview Window...");
+        overviewMenuItem.setLabel("Overview Window");
         overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
                 public void actionPerformed(ActionEvent e) {
                     overviewMenuItem_actionPerformed(e);
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6bf71cf..6c235a4 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,1030 +1,1263 @@
 /*
-* 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
-*/
+ * 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.jbgui;
 
-import jalview.gui.Preferences;
-
-import jalview.schemes.ColourSchemeProperty;
-
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
-import javax.swing.event.AncestorEvent;
-import javax.swing.event.AncestorListener;
-
-
-public class GAlignFrame extends JInternalFrame {
-    protected JMenuBar alignFrameMenuBar = new JMenuBar();
-    protected JMenu fileMenu = new JMenu();
-    protected JMenuItem closeMenuItem = new JMenuItem();
-    protected JMenu editMenu = new JMenu();
-    protected JMenu viewMenu = new JMenu();
-    protected JMenu colourMenu = new JMenu();
-    protected JMenu calculateMenu = new JMenu();
-    protected JMenu webService = new JMenu();
-    protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
-    protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
-    protected JMenuItem invertSequenceMenuItem = new JMenuItem();
-    protected JMenuItem remove2LeftMenuItem = new JMenuItem();
-    protected JMenuItem remove2RightMenuItem = new JMenuItem();
-    protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
-    protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-    public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
-    public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
-    protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
-    protected JMenuItem sortIDMenuItem = new JMenuItem();
-    protected JMenuItem sortGroupMenuItem = new JMenuItem();
-    protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
-    protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
-    protected JMenuItem PCAMenuItem = new JMenuItem();
-    protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
-    protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
-    protected JMenuItem clustalAlignMenuItem = new JMenuItem();
-    BorderLayout borderLayout1 = new BorderLayout();
-    public JLabel statusBar = new JLabel();
-    protected JMenuItem saveAlignmentMenu = new JMenuItem();
-    protected JMenu outputTextboxMenu = new JMenu();
-    protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-    protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-    JMenuItem njTreeBlosumMenuItem = new JMenuItem();
-    JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-    public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-    public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
-    JMenuItem htmlMenuItem = new JMenuItem();
-    JMenuItem overviewMenuItem = new JMenuItem();
-    protected JMenuItem undoMenuItem = new JMenuItem();
-    protected JMenuItem redoMenuItem = new JMenuItem();
-    public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-    JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-    public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-    JMenuItem printMenuItem = new JMenuItem();
-    public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
-    JMenuItem findMenuItem = new JMenuItem();
-    JMenu searchMenu = new JMenu();
-    public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-    public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
-    protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-    JMenuItem deleteGroups = new JMenuItem();
-    JMenuItem delete = new JMenuItem();
-    JMenuItem copy = new JMenuItem();
-    JMenuItem cut = new JMenuItem();
-    JMenu jMenu1 = new JMenu();
-    JMenuItem pasteNew = new JMenuItem();
-    JMenuItem pasteThis = new JMenuItem();
-    public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
-    JMenuItem createPNG = new JMenuItem();
-    protected JMenuItem font = new JMenuItem();
-    public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
-    JMenuItem epsFile = new JMenuItem();
-    JMenuItem LoadtreeMenuItem = new JMenuItem();
-    JMenuItem jnet = new JMenuItem();
-    public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
-    public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
-    public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
-    JMenuItem modifyPID = new JMenuItem();
-    JMenuItem modifyConservation = new JMenuItem();
-    protected JMenu sortByTreeMenu = new JMenu();
-    protected JMenu sort = new JMenu();
-    JMenu calculate = new JMenu();
-    JMenuItem msaAlignMenuItem = new JMenuItem();
-    JMenu jMenu2 = new JMenu();
-    JMenuItem padGapsMenuitem = new JMenuItem();
-    JMenuItem ClustalRealign = new JMenuItem();
-
-    public GAlignFrame() {
-        ButtonGroup colours = new ButtonGroup();
-        colours.add(noColourmenuItem);
-        colours.add(clustalColour);
-        colours.add(zappoColour);
-        colours.add(taylorColour);
-        colours.add(hydrophobicityColour);
-        colours.add(helixColour);
-        colours.add(strandColour);
-        colours.add(turnColour);
-        colours.add(buriedColour);
-        colours.add(userDefinedColour);
-        colours.add(PIDColour);
-        colours.add(BLOSUM62Colour);
-        colours.add(nucleotideColour);
-
-        noColourmenuItem.setSelected(true);
-
-        String defaultColour = Preferences.defaultColour;
-
-        if (defaultColour != null) {
-            int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
-
-            switch (index) {
-            case ColourSchemeProperty.CLUSTAL:
-                clustalColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.BLOSUM:
-                BLOSUM62Colour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.PID:
-                PIDColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.ZAPPO:
-                zappoColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.HYDROPHOBIC:
-                hydrophobicityColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.HELIX:
-                helixColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.STRAND:
-                strandColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.TURN:
-                turnColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.BURIED:
-                buriedColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.NUCLEOTIDE:
-                nucleotideColour.setSelected(true);
-
-                break;
-
-            case ColourSchemeProperty.USER_DEFINED:
-                userDefinedColour.setSelected(true);
-
-                break;
-            }
-        }
-
-        try {
-            jbInit();
-            setJMenuBar(alignFrameMenuBar);
-
-            JMenuItem item;
-
-            // dynamically fill save as menu with available formats
-            for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
-                item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(
-                            i));
-                item.addActionListener(new java.awt.event.ActionListener() {
-                        public void actionPerformed(ActionEvent e) {
-                            outputText_actionPerformed(e);
-                        }
-                    });
-
-                outputTextboxMenu.add(item);
-            }
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-
-    }
-
-    private void jbInit() throws Exception {
-        fileMenu.setMnemonic('F');
-        fileMenu.setText("File");
-        saveAlignmentMenu.setMnemonic('L');
-        saveAlignmentMenu.setText("Save As");
-        saveAlignmentMenu.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    saveAlignmentMenu_actionPerformed(e);
-                }
-            });
-        closeMenuItem.setMnemonic('C');
-        closeMenuItem.setText("Close");
-        closeMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    closeMenuItem_actionPerformed(e);
-                }
-            });
-        editMenu.setText("Edit");
-        viewMenu.setText("View");
-        colourMenu.setText("Colour");
-        calculateMenu.setText("Calculate");
-        webService.setText("Web Service");
-        selectAllSequenceMenuItem.setText("Select all");
-        selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-                java.awt.event.KeyEvent.VK_A,
-                Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-        selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    selectAllSequenceMenuItem_actionPerformed(e);
-                }
-            });
-        deselectAllSequenceMenuItem.setText("Deselect All");
-        deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-                java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
-        deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    deselectAllSequenceMenuItem_actionPerformed(e);
-                }
-            });
-        invertSequenceMenuItem.setText("Invert Selection");
-        invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    invertSequenceMenuItem_actionPerformed(e);
-                }
-            });
-        remove2LeftMenuItem.setText("Remove Left");
-        remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    remove2LeftMenuItem_actionPerformed(e);
-                }
-            });
-        remove2RightMenuItem.setText("Remove Right");
-        remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    remove2RightMenuItem_actionPerformed(e);
-                }
-            });
-        removeGappedColumnMenuItem.setText("Remove Empty Columns");
-        removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    removeGappedColumnMenuItem_actionPerformed(e);
-                }
-            });
-        removeAllGapsMenuItem.setText("Remove All Gaps");
-        removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    removeAllGapsMenuItem_actionPerformed(e);
-                }
-            });
-        viewBoxesMenuItem.setText("Boxes");
-        viewBoxesMenuItem.setState(true);
-        viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    viewBoxesMenuItem_actionPerformed(e);
-                }
-            });
-        viewTextMenuItem.setText("Text");
-        viewTextMenuItem.setState(true);
-        viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    viewTextMenuItem_actionPerformed(e);
-                }
-            });
-        sortPairwiseMenuItem.setText("by Pairwise Identity");
-        sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    sortPairwiseMenuItem_actionPerformed(e);
-                }
-            });
-        sortIDMenuItem.setText("by ID");
-        sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    sortIDMenuItem_actionPerformed(e);
-                }
-            });
-        sortGroupMenuItem.setText("by Group");
-        sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    sortGroupMenuItem_actionPerformed(e);
-                }
-            });
-        removeRedundancyMenuItem.setText("Remove Redundancy...");
-        removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    removeRedundancyMenuItem_actionPerformed(e);
-                }
-            });
-        pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
-        pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    pairwiseAlignmentMenuItem_actionPerformed(e);
-                }
-            });
-        PCAMenuItem.setText("Principal Component Analysis...");
-        PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    PCAMenuItem_actionPerformed(e);
-                }
-            });
-        averageDistanceTreeMenuItem.setText(
-            "Average Distance Using % Identity...");
-        averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    averageDistanceTreeMenuItem_actionPerformed(e);
-                }
-            });
-        neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
-        neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    neighbourTreeMenuItem_actionPerformed(e);
-                }
-            });
-        clustalAlignMenuItem.setText("Clustal Alignment...");
-        clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    clustalAlignMenuItem_actionPerformed(e);
-                }
-            });
-        this.getContentPane().setLayout(borderLayout1);
-        alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
-        alignFrameMenuBar.addAncestorListener(new AncestorListener() {
-                public void ancestorAdded(AncestorEvent event) {
-                    alignFrameMenuBar_ancestorAdded(event);
-                }
-
-                public void ancestorRemoved(AncestorEvent event) {
-                }
-
-                public void ancestorMoved(AncestorEvent event) {
-                }
-            });
-        statusBar.setBackground(Color.white);
-        statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
-        statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
-        statusBar.setText("Status bar");
-        outputTextboxMenu.setMnemonic('T');
-        outputTextboxMenu.setText("Output to Textbox");
-        clustalColour.setText("Clustalx");
-
-        clustalColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    clustalColour_actionPerformed(e);
-                }
-            });
-        zappoColour.setText("Zappo");
-        zappoColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    zappoColour_actionPerformed(e);
-                }
-            });
-        taylorColour.setText("Taylor");
-        taylorColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    taylorColour_actionPerformed(e);
-                }
-            });
-        hydrophobicityColour.setText("Hydrophobicity");
-        hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    hydrophobicityColour_actionPerformed(e);
-                }
-            });
-        helixColour.setText("Helix Propensity");
-        helixColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    helixColour_actionPerformed(e);
-                }
-            });
-        strandColour.setText("Strand Propensity");
-        strandColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    strandColour_actionPerformed(e);
-                }
-            });
-        turnColour.setText("Turn Propensity");
-        turnColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    turnColour_actionPerformed(e);
-                }
-            });
-        buriedColour.setText("Buried Index");
-        buriedColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    buriedColour_actionPerformed(e);
-                }
-            });
-        userDefinedColour.setText("User Defined...");
-        userDefinedColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    userDefinedColour_actionPerformed(e);
-                }
-            });
-        PIDColour.setText("Percentage Identity");
-        PIDColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    PIDColour_actionPerformed(e);
-                }
-            });
-        BLOSUM62Colour.setText("BLOSUM62 Score");
-        BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    BLOSUM62Colour_actionPerformed(e);
-                }
-            });
-        avDistanceTreeBlosumMenuItem.setText(
-            "Average Distance Using BLOSUM62...");
-        avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    avTreeBlosumMenuItem_actionPerformed(e);
-                }
-            });
-        njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
-        njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    njTreeBlosumMenuItem_actionPerformed(e);
-                }
-            });
-        annotationPanelMenuItem.setActionCommand("");
-        annotationPanelMenuItem.setText("Show Annotations");
-        annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);
-        annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    annotationPanelMenuItem_actionPerformed(e);
-                }
-            });
-        colourTextMenuItem.setText("Colour Text");
-        colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    colourTextMenuItem_actionPerformed(e);
-                }
-            });
-        htmlMenuItem.setText("HTML");
-        htmlMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    htmlMenuItem_actionPerformed(e);
-                }
-            });
-        overviewMenuItem.setText("Overview Window...");
-        overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    overviewMenuItem_actionPerformed(e);
-                }
-            });
-        undoMenuItem.setEnabled(false);
-        undoMenuItem.setMnemonic('Z');
-        undoMenuItem.setText("Undo");
-        undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-                java.awt.event.KeyEvent.VK_Z,
-                Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-        undoMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    undoMenuItem_actionPerformed(e);
-                }
-            });
-        redoMenuItem.setEnabled(false);
-        redoMenuItem.setMnemonic('0');
-        redoMenuItem.setText("Redo");
-        redoMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    redoMenuItem_actionPerformed(e);
-                }
-            });
-        conservationMenuItem.setText("By Conservation");
-        conservationMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    conservationMenuItem_actionPerformed(e);
-                }
-            });
-        noColourmenuItem.setText("None");
-        noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    noColourmenuItem_actionPerformed(e);
-                }
-            });
-        wrapMenuItem.setText("Wrap");
-        wrapMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    wrapMenuItem_actionPerformed(e);
-                }
-            });
-        printMenuItem.setText("Print");
-        printMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    printMenuItem_actionPerformed(e);
-                }
-            });
-        renderGapsMenuItem.setText("Show Gaps");
-        renderGapsMenuItem.setState(true);
-        renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    renderGapsMenuItem_actionPerformed(e);
-                }
-            });
-        findMenuItem.setText("Find...");
-        findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-                java.awt.event.KeyEvent.VK_F,
-                Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-        findMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    findMenuItem_actionPerformed(e);
-                }
-            });
-        searchMenu.setText("Search");
-
-        abovePIDThreshold.setText("Above Identity Threshold");
-        abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    abovePIDThreshold_actionPerformed(e);
-                }
-            });
-        sequenceFeatures.setText("Sequence Features");
-        sequenceFeatures.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent actionEvent) {
-                    sequenceFeatures_actionPerformed(actionEvent);
-                }
-            });
-        nucleotideColour.setText("Nucleotide");
-        nucleotideColour.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    nucleotideColour_actionPerformed(e);
-                }
-            });
-        deleteGroups.setText("Undefine groups");
-        deleteGroups.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    deleteGroups_actionPerformed(e);
-                }
-            });
-        copy.setText("Copy");
-        copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-                java.awt.event.KeyEvent.VK_C,
-                Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-        copy.setMnemonic(KeyEvent.VK_C);
-
-        copy.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    copy_actionPerformed(e);
-                }
-            });
-        cut.setText("Cut");
-        cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-                java.awt.event.KeyEvent.VK_X,
-                Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-        cut.setMnemonic(KeyEvent.VK_X);
-        cut.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    cut_actionPerformed(e);
-                }
-            });
-        delete.setText("Delete");
-        delete.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    delete_actionPerformed(e);
-                }
-            });
-        jMenu1.setMnemonic('V');
-        jMenu1.setText("Paste");
-        pasteNew.setText("To New Alignment");
-        pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-                java.awt.event.KeyEvent.VK_V,
-                Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-        pasteNew.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    pasteNew_actionPerformed(e);
-                }
-            });
-        pasteThis.setText("Add To This Alignment");
-        pasteThis.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    pasteThis_actionPerformed(e);
-                }
-            });
-        applyToAllGroups.setText("Apply Colour To All Groups");
-        applyToAllGroups.setState(true);
-        applyToAllGroups.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    applyToAllGroups_actionPerformed(e);
-                }
-            });
-        createPNG.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    createPNG_actionPerformed(e);
-                }
-            });
-        createPNG.setActionCommand("Save As PNG Image");
-        createPNG.setText("PNG");
-        font.setText("Font...");
-        font.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    font_actionPerformed(e);
-                }
-            });
-        fullSeqId.setText("Show Full Sequence ID");
-        fullSeqId.setState(true);
-        fullSeqId.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    fullSeqId_actionPerformed(e);
-                }
-            });
-        epsFile.setText("EPS");
-        epsFile.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    epsFile_actionPerformed(e);
-                }
-            });
-        LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-        LoadtreeMenuItem.setText("Load Assocated Tree");
-        LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    LoadtreeMenuItem_actionPerformed(e);
-                }
-            });
-        jnet.setText("JNet...");
-        jnet.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    jpred_actionPerformed(e);
-                }
-            });
-        scaleAbove.setVisible(false);
-        scaleAbove.setText("Scale Above");
-        scaleAbove.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    scaleAbove_actionPerformed(e);
-                }
-            });
-        scaleLeft.setVisible(false);
-        scaleLeft.setSelected(true);
-        scaleLeft.setText("Scale Left");
-        scaleLeft.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    scaleLeft_actionPerformed(e);
-                }
-            });
-        scaleRight.setVisible(false);
-        scaleRight.setSelected(true);
-        scaleRight.setText("Scale Right");
-        scaleRight.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    scaleRight_actionPerformed(e);
-                }
-            });
-        modifyPID.setText("Modify Identity Threshold...");
-        modifyPID.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    modifyPID_actionPerformed(e);
-                }
-            });
-        modifyConservation.setText("Modify Conservation Threshold...");
-        modifyConservation.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    modifyConservation_actionPerformed(e);
-                }
-            });
-        sortByTreeMenu.setText("By Tree Order");
-        sort.setText("Sort");
-        calculate.setText("Calculate Tree");
-        msaAlignMenuItem.setText("Muscle Alignment...");
-        msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    msaAlignMenuItem_actionPerformed(e);
-                }
-            });
-        jMenu2.setText("Export");
-        padGapsMenuitem.setText("Pad Gaps");
-        padGapsMenuitem.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    padGapsMenuitem_actionPerformed(e);
-                }
-            });
-        ClustalRealign.setText("Clustal Realign...");
-        ClustalRealign.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    ClustalRealign_actionPerformed(e);
-                }
-            });
-        alignFrameMenuBar.add(fileMenu);
-        alignFrameMenuBar.add(editMenu);
-        alignFrameMenuBar.add(searchMenu);
-        alignFrameMenuBar.add(viewMenu);
-        alignFrameMenuBar.add(colourMenu);
-        alignFrameMenuBar.add(calculateMenu);
-        fileMenu.add(saveAlignmentMenu);
-        fileMenu.add(jMenu2);
-        fileMenu.add(outputTextboxMenu);
-        fileMenu.add(printMenuItem);
-        fileMenu.addSeparator();
-        fileMenu.add(LoadtreeMenuItem);
-        fileMenu.addSeparator();
-        fileMenu.add(closeMenuItem);
-        editMenu.add(undoMenuItem);
-        editMenu.add(redoMenuItem);
-        editMenu.add(cut);
-        editMenu.add(copy);
-        editMenu.add(jMenu1);
-        editMenu.add(delete);
-        editMenu.addSeparator();
-        editMenu.add(selectAllSequenceMenuItem);
-        editMenu.add(deselectAllSequenceMenuItem);
-        editMenu.add(invertSequenceMenuItem);
-        editMenu.add(deleteGroups);
-        editMenu.addSeparator();
-        editMenu.add(remove2LeftMenuItem);
-        editMenu.add(remove2RightMenuItem);
-        editMenu.add(removeGappedColumnMenuItem);
-        editMenu.add(removeAllGapsMenuItem);
-        editMenu.add(removeRedundancyMenuItem);
-        editMenu.addSeparator();
-        editMenu.add(padGapsMenuitem);
-        searchMenu.add(findMenuItem);
-        viewMenu.add(font);
-        viewMenu.addSeparator();
-        viewMenu.add(wrapMenuItem);
-        viewMenu.add(fullSeqId);
-        viewMenu.add(scaleAbove);
-        viewMenu.add(scaleLeft);
-        viewMenu.add(scaleRight);
-        viewMenu.add(viewBoxesMenuItem);
-        viewMenu.add(viewTextMenuItem);
-        viewMenu.add(colourTextMenuItem);
-        viewMenu.add(renderGapsMenuItem);
-        viewMenu.add(annotationPanelMenuItem);
-        viewMenu.add(sequenceFeatures);
-        viewMenu.addSeparator();
-        viewMenu.add(overviewMenuItem);
-        colourMenu.add(applyToAllGroups);
-        colourMenu.addSeparator();
-        colourMenu.add(noColourmenuItem);
-        colourMenu.add(clustalColour);
-        colourMenu.add(BLOSUM62Colour);
-        colourMenu.add(PIDColour);
-        colourMenu.add(zappoColour);
-        colourMenu.add(taylorColour);
-        colourMenu.add(hydrophobicityColour);
-        colourMenu.add(helixColour);
-        colourMenu.add(strandColour);
-        colourMenu.add(turnColour);
-        colourMenu.add(buriedColour);
-        colourMenu.add(nucleotideColour);
-        colourMenu.add(userDefinedColour);
-        colourMenu.addSeparator();
-        colourMenu.add(conservationMenuItem);
-        colourMenu.add(modifyConservation);
-        colourMenu.add(abovePIDThreshold);
-        colourMenu.add(modifyPID);
-        calculateMenu.add(sort);
-        calculateMenu.add(calculate);
-        calculateMenu.addSeparator();
-        calculateMenu.add(pairwiseAlignmentMenuItem);
-        calculateMenu.add(PCAMenuItem);
-        calculateMenu.addSeparator();
-        calculateMenu.add(webService);
-        webService.add(clustalAlignMenuItem);
-        webService.add(msaAlignMenuItem);
-        webService.add(jnet);
-        webService.add(ClustalRealign);
-        this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-        jMenu1.add(pasteNew);
-        jMenu1.add(pasteThis);
-        sort.add(sortIDMenuItem);
-        sort.add(sortGroupMenuItem);
-        sort.add(sortPairwiseMenuItem);
-        calculate.add(averageDistanceTreeMenuItem);
-        calculate.add(neighbourTreeMenuItem);
-        calculate.add(avDistanceTreeBlosumMenuItem);
-        calculate.add(njTreeBlosumMenuItem);
-        jMenu2.add(htmlMenuItem);
-        jMenu2.add(epsFile);
-        jMenu2.add(createPNG);
-    }
-
-    protected void outputText_actionPerformed(ActionEvent e) {
-    }
-
-    protected void htmlMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void closeMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void redoMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void undoMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void wrapMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void viewTextMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void colourTextMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void overviewMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void sortIDMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {
-    }
+import javax.swing.event.*;
+
+import jalview.gui.*;
+import jalview.schemes.*;
+
+public class GAlignFrame
+    extends JInternalFrame
+{
+  protected JMenuBar alignFrameMenuBar = new JMenuBar();
+  protected JMenu fileMenu = new JMenu();
+  protected JMenuItem closeMenuItem = new JMenuItem();
+  protected JMenu editMenu = new JMenu();
+  protected JMenu viewMenu = new JMenu();
+  protected JMenu colourMenu = new JMenu();
+  protected JMenu calculateMenu = new JMenu();
+  protected JMenu webService = new JMenu();
+  protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
+  protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
+  protected JMenuItem invertSequenceMenuItem = new JMenuItem();
+  protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+  protected JMenuItem remove2RightMenuItem = new JMenuItem();
+  protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+  protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+  protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
+  protected JMenuItem sortIDMenuItem = new JMenuItem();
+  protected JMenuItem sortGroupMenuItem = new JMenuItem();
+  protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
+  protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
+  protected JMenuItem PCAMenuItem = new JMenuItem();
+  protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
+  protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
+  protected JMenuItem clustalAlignMenuItem = new JMenuItem();
+  BorderLayout borderLayout1 = new BorderLayout();
+  public JLabel statusBar = new JLabel();
+  protected JMenuItem saveAlignmentMenu = new JMenuItem();
+  protected JMenu outputTextboxMenu = new JMenu();
+  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem hydrophobicityColour = new
+      JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+  JMenuItem njTreeBlosumMenuItem = new JMenuItem();
+  JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+  JMenuItem htmlMenuItem = new JMenuItem();
+  JMenuItem overviewMenuItem = new JMenuItem();
+  protected JMenuItem undoMenuItem = new JMenuItem();
+  protected JMenuItem redoMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+  JMenuItem printMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+  JMenuItem findMenuItem = new JMenuItem();
+  JMenu searchMenu = new JMenu();
+  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+  JMenuItem deleteGroups = new JMenuItem();
+  JMenuItem delete = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem cut = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+  JMenuItem pasteNew = new JMenuItem();
+  JMenuItem pasteThis = new JMenuItem();
+  public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+  JMenuItem createPNG = new JMenuItem();
+  protected JMenuItem font = new JMenuItem();
+  public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+  JMenuItem epsFile = new JMenuItem();
+  JMenuItem LoadtreeMenuItem = new JMenuItem();
+  JMenuItem jnet = new JMenuItem();
+  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+  JMenuItem modifyPID = new JMenuItem();
+  JMenuItem modifyConservation = new JMenuItem();
+  protected JMenu sortByTreeMenu = new JMenu();
+  protected JMenu sort = new JMenu();
+  JMenu calculate = new JMenu();
+  JMenuItem msaAlignMenuItem = new JMenuItem();
+  JMenu jMenu2 = new JMenu();
+  JMenuItem padGapsMenuitem = new JMenuItem();
+  JMenuItem ClustalRealign = new JMenuItem();
+
+  public GAlignFrame()
+  {
+    ButtonGroup colours = new ButtonGroup();
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+    colours.add(nucleotideColour);
+
+    noColourmenuItem.setSelected(true);
+
+    String defaultColour = Preferences.defaultColour;
+
+    if (defaultColour != null)
+    {
+      int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+
+      switch (index)
+      {
+        case ColourSchemeProperty.CLUSTAL:
+          clustalColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.BLOSUM:
+          BLOSUM62Colour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.PID:
+          PIDColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.ZAPPO:
+          zappoColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.HYDROPHOBIC:
+          hydrophobicityColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.HELIX:
+          helixColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.STRAND:
+          strandColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.TURN:
+          turnColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.BURIED:
+          buriedColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.NUCLEOTIDE:
+          nucleotideColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.USER_DEFINED:
+          userDefinedColour.setSelected(true);
+
+          break;
+      }
+    }
+
+    try
+    {
+      jbInit();
+      setJMenuBar(alignFrameMenuBar);
+
+      JMenuItem item;
+
+      // dynamically fill save as menu with available formats
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+      {
+        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
+                             elementAt(
+                                 i));
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            outputText_actionPerformed(e);
+          }
+        });
+
+        outputTextboxMenu.add(item);
+      }
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    fileMenu.setMnemonic('F');
+    fileMenu.setText("File");
+    saveAlignmentMenu.setMnemonic('L');
+    saveAlignmentMenu.setText("Save As");
+    saveAlignmentMenu.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveAlignmentMenu_actionPerformed(e);
+      }
+    });
+    closeMenuItem.setMnemonic('C');
+    closeMenuItem.setText("Close");
+    closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        closeMenuItem_actionPerformed(e);
+      }
+    });
+    editMenu.setText("Edit");
+    viewMenu.setText("View");
+    colourMenu.setText("Colour");
+    calculateMenu.setText("Calculate");
+    webService.setText("Web Service");
+    selectAllSequenceMenuItem.setText("Select all");
+    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_A,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        selectAllSequenceMenuItem_actionPerformed(e);
+      }
+    });
+    deselectAllSequenceMenuItem.setText("Deselect All");
+    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                               getKeyStroke(
+        java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        deselectAllSequenceMenuItem_actionPerformed(e);
+      }
+    });
+    invertSequenceMenuItem.setText("Invert Selection");
+    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertSequenceMenuItem_actionPerformed(e);
+      }
+    });
+    remove2LeftMenuItem.setText("Remove Left");
+    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        remove2LeftMenuItem_actionPerformed(e);
+      }
+    });
+    remove2RightMenuItem.setText("Remove Right");
+    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        remove2RightMenuItem_actionPerformed(e);
+      }
+    });
+    removeGappedColumnMenuItem.setText("Remove Empty Columns");
+    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+                                                 ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        removeGappedColumnMenuItem_actionPerformed(e);
+      }
+    });
+    removeAllGapsMenuItem.setText("Remove All Gaps");
+    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        removeAllGapsMenuItem_actionPerformed(e);
+      }
+    });
+    viewBoxesMenuItem.setText("Boxes");
+    viewBoxesMenuItem.setState(true);
+    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        viewBoxesMenuItem_actionPerformed(e);
+      }
+    });
+    viewTextMenuItem.setText("Text");
+    viewTextMenuItem.setState(true);
+    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        viewTextMenuItem_actionPerformed(e);
+      }
+    });
+    sortPairwiseMenuItem.setText("by Pairwise Identity");
+    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortPairwiseMenuItem_actionPerformed(e);
+      }
+    });
+    sortIDMenuItem.setText("by ID");
+    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortIDMenuItem_actionPerformed(e);
+      }
+    });
+    sortGroupMenuItem.setText("by Group");
+    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortGroupMenuItem_actionPerformed(e);
+      }
+    });
+    removeRedundancyMenuItem.setText("Remove Redundancy...");
+    removeRedundancyMenuItem.addActionListener(new java.awt.event.
+                                               ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        removeRedundancyMenuItem_actionPerformed(e);
+      }
+    });
+    pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
+    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pairwiseAlignmentMenuItem_actionPerformed(e);
+      }
+    });
+    PCAMenuItem.setText("Principal Component Analysis");
+    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PCAMenuItem_actionPerformed(e);
+      }
+    });
+    averageDistanceTreeMenuItem.setText(
+        "Average Distance Using % Identity");
+    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        averageDistanceTreeMenuItem_actionPerformed(e);
+      }
+    });
+    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
+    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        neighbourTreeMenuItem_actionPerformed(e);
+      }
+    });
+    clustalAlignMenuItem.setText("Clustal Alignment");
+    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clustalAlignMenuItem_actionPerformed(e);
+      }
+    });
+    this.getContentPane().setLayout(borderLayout1);
+    alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    alignFrameMenuBar.addAncestorListener(new AncestorListener()
+    {
+      public void ancestorAdded(AncestorEvent event)
+      {
+        alignFrameMenuBar_ancestorAdded(event);
+      }
+
+      public void ancestorRemoved(AncestorEvent event)
+      {
+      }
+
+      public void ancestorMoved(AncestorEvent event)
+      {
+      }
+    });
+    statusBar.setBackground(Color.white);
+    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
+    statusBar.setText("Status bar");
+    outputTextboxMenu.setMnemonic('T');
+    outputTextboxMenu.setText("Output to Textbox");
+    clustalColour.setText("Clustalx");
+
+    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clustalColour_actionPerformed(e);
+      }
+    });
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zappoColour_actionPerformed(e);
+      }
+    });
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        taylorColour_actionPerformed(e);
+      }
+    });
+    hydrophobicityColour.setText("Hydrophobicity");
+    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hydrophobicityColour_actionPerformed(e);
+      }
+    });
+    helixColour.setText("Helix Propensity");
+    helixColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        helixColour_actionPerformed(e);
+      }
+    });
+    strandColour.setText("Strand Propensity");
+    strandColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        strandColour_actionPerformed(e);
+      }
+    });
+    turnColour.setText("Turn Propensity");
+    turnColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        turnColour_actionPerformed(e);
+      }
+    });
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        buriedColour_actionPerformed(e);
+      }
+    });
+    userDefinedColour.setText("User Defined...");
+    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        userDefinedColour_actionPerformed(e);
+      }
+    });
+    PIDColour.setText("Percentage Identity");
+    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PIDColour_actionPerformed(e);
+      }
+    });
+    BLOSUM62Colour.setText("BLOSUM62 Score");
+    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        BLOSUM62Colour_actionPerformed(e);
+      }
+    });
+    avDistanceTreeBlosumMenuItem.setText(
+        "Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
+        ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        avTreeBlosumMenuItem_actionPerformed(e);
+      }
+    });
+    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
+    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        njTreeBlosumMenuItem_actionPerformed(e);
+      }
+    });
+    annotationPanelMenuItem.setActionCommand("");
+    annotationPanelMenuItem.setText("Show Annotations");
+    annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);
+    annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationPanelMenuItem_actionPerformed(e);
+      }
+    });
+    colourTextMenuItem.setText("Colour Text");
+    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        colourTextMenuItem_actionPerformed(e);
+      }
+    });
+    htmlMenuItem.setText("HTML");
+    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        htmlMenuItem_actionPerformed(e);
+      }
+    });
+    overviewMenuItem.setText("Overview Window");
+    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        overviewMenuItem_actionPerformed(e);
+      }
+    });
+    undoMenuItem.setEnabled(false);
+    undoMenuItem.setMnemonic('Z');
+    undoMenuItem.setText("Undo");
+    undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_Z,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        undoMenuItem_actionPerformed(e);
+      }
+    });
+    redoMenuItem.setEnabled(false);
+    redoMenuItem.setMnemonic('0');
+    redoMenuItem.setText("Redo");
+    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        redoMenuItem_actionPerformed(e);
+      }
+    });
+    conservationMenuItem.setText("By Conservation");
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed(e);
+      }
+    });
+    noColourmenuItem.setText("None");
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed(e);
+      }
+    });
+    wrapMenuItem.setText("Wrap");
+    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        wrapMenuItem_actionPerformed(e);
+      }
+    });
+    printMenuItem.setText("Print");
+    printMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        printMenuItem_actionPerformed(e);
+      }
+    });
+    renderGapsMenuItem.setText("Show Gaps");
+    renderGapsMenuItem.setState(true);
+    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        renderGapsMenuItem_actionPerformed(e);
+      }
+    });
+    findMenuItem.setText("Find...");
+    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_F,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    findMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        findMenuItem_actionPerformed(e);
+      }
+    });
+    searchMenu.setText("Search");
+
+    abovePIDThreshold.setText("Above Identity Threshold");
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDThreshold_actionPerformed(e);
+      }
+    });
+    sequenceFeatures.setText("Sequence Features");
+    sequenceFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        sequenceFeatures_actionPerformed(actionEvent);
+      }
+    });
+    nucleotideColour.setText("Nucleotide");
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideColour_actionPerformed(e);
+      }
+    });
+    deleteGroups.setText("Undefine groups");
+    deleteGroups.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        deleteGroups_actionPerformed(e);
+      }
+    });
+    copy.setText("Copy");
+    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_C,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    copy.setMnemonic(KeyEvent.VK_C);
+
+    copy.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed(e);
+      }
+    });
+    cut.setText("Cut");
+    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_X,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    cut.setMnemonic(KeyEvent.VK_X);
+    cut.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed(e);
+      }
+    });
+    delete.setText("Delete");
+    delete.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        delete_actionPerformed(e);
+      }
+    });
+    jMenu1.setMnemonic('V');
+    jMenu1.setText("Paste");
+    pasteNew.setText("To New Alignment");
+    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    pasteNew.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteNew_actionPerformed(e);
+      }
+    });
+    pasteThis.setText("Add To This Alignment");
+    pasteThis.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteThis_actionPerformed(e);
+      }
+    });
+    applyToAllGroups.setText("Apply Colour To All Groups");
+    applyToAllGroups.setState(true);
+    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        applyToAllGroups_actionPerformed(e);
+      }
+    });
+    createPNG.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createPNG(null);
+      }
+    });
+    createPNG.setActionCommand("Save As PNG Image");
+    createPNG.setText("PNG");
+    font.setText("Font...");
+    font.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        font_actionPerformed(e);
+      }
+    });
+    fullSeqId.setText("Show Full Sequence ID");
+    fullSeqId.setState(true);
+    fullSeqId.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fullSeqId_actionPerformed(e);
+      }
+    });
+    epsFile.setText("EPS");
+    epsFile.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createEPS(null);
+      }
+    });
+    LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
+    LoadtreeMenuItem.setText("Load Assocated Tree");
+    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        LoadtreeMenuItem_actionPerformed(e);
+      }
+    });
+    jnet.setText("JNet");
+    jnet.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        jpred_actionPerformed(e);
+      }
+    });
+    scaleAbove.setVisible(false);
+    scaleAbove.setText("Scale Above");
+    scaleAbove.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleAbove_actionPerformed(e);
+      }
+    });
+    scaleLeft.setVisible(false);
+    scaleLeft.setSelected(true);
+    scaleLeft.setText("Scale Left");
+    scaleLeft.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleLeft_actionPerformed(e);
+      }
+    });
+    scaleRight.setVisible(false);
+    scaleRight.setSelected(true);
+    scaleRight.setText("Scale Right");
+    scaleRight.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleRight_actionPerformed(e);
+      }
+    });
+    modifyPID.setText("Modify Identity Threshold...");
+    modifyPID.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyPID_actionPerformed(e);
+      }
+    });
+    modifyConservation.setText("Modify Conservation Threshold...");
+    modifyConservation.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed(e);
+      }
+    });
+    sortByTreeMenu.setText("By Tree Order");
+    sort.setText("Sort");
+    calculate.setText("Calculate Tree");
+    msaAlignMenuItem.setText("Muscle Alignment");
+    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        msaAlignMenuItem_actionPerformed(e);
+      }
+    });
+    jMenu2.setText("Export");
+    padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        padGapsMenuitem_actionPerformed(e);
+      }
+    });
+    ClustalRealign.setText("Clustal Realign");
+    ClustalRealign.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ClustalRealign_actionPerformed(e);
+      }
+    });
+    alignFrameMenuBar.add(fileMenu);
+    alignFrameMenuBar.add(editMenu);
+    alignFrameMenuBar.add(searchMenu);
+    alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(colourMenu);
+    alignFrameMenuBar.add(calculateMenu);
+    fileMenu.add(saveAlignmentMenu);
+    fileMenu.add(jMenu2);
+    fileMenu.add(outputTextboxMenu);
+    fileMenu.add(printMenuItem);
+    fileMenu.addSeparator();
+    fileMenu.add(LoadtreeMenuItem);
+    fileMenu.addSeparator();
+    fileMenu.add(closeMenuItem);
+    editMenu.add(undoMenuItem);
+    editMenu.add(redoMenuItem);
+    editMenu.add(cut);
+    editMenu.add(copy);
+    editMenu.add(jMenu1);
+    editMenu.add(delete);
+    editMenu.addSeparator();
+    editMenu.add(selectAllSequenceMenuItem);
+    editMenu.add(deselectAllSequenceMenuItem);
+    editMenu.add(invertSequenceMenuItem);
+    editMenu.add(deleteGroups);
+    editMenu.addSeparator();
+    editMenu.add(remove2LeftMenuItem);
+    editMenu.add(remove2RightMenuItem);
+    editMenu.add(removeGappedColumnMenuItem);
+    editMenu.add(removeAllGapsMenuItem);
+    editMenu.add(removeRedundancyMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(padGapsMenuitem);
+    searchMenu.add(findMenuItem);
+    viewMenu.add(font);
+    viewMenu.addSeparator();
+    viewMenu.add(wrapMenuItem);
+    viewMenu.add(fullSeqId);
+    viewMenu.add(scaleAbove);
+    viewMenu.add(scaleLeft);
+    viewMenu.add(scaleRight);
+    viewMenu.add(viewBoxesMenuItem);
+    viewMenu.add(viewTextMenuItem);
+    viewMenu.add(colourTextMenuItem);
+    viewMenu.add(renderGapsMenuItem);
+    viewMenu.add(annotationPanelMenuItem);
+    viewMenu.add(sequenceFeatures);
+    viewMenu.addSeparator();
+    viewMenu.add(overviewMenuItem);
+    colourMenu.add(applyToAllGroups);
+    colourMenu.addSeparator();
+    colourMenu.add(noColourmenuItem);
+    colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
+    colourMenu.add(zappoColour);
+    colourMenu.add(taylorColour);
+    colourMenu.add(hydrophobicityColour);
+    colourMenu.add(helixColour);
+    colourMenu.add(strandColour);
+    colourMenu.add(turnColour);
+    colourMenu.add(buriedColour);
+    colourMenu.add(nucleotideColour);
+    colourMenu.add(userDefinedColour);
+    colourMenu.addSeparator();
+    colourMenu.add(conservationMenuItem);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDThreshold);
+    colourMenu.add(modifyPID);
+    calculateMenu.add(sort);
+    calculateMenu.add(calculate);
+    calculateMenu.addSeparator();
+    calculateMenu.add(pairwiseAlignmentMenuItem);
+    calculateMenu.add(PCAMenuItem);
+    calculateMenu.addSeparator();
+    calculateMenu.add(webService);
+    webService.add(clustalAlignMenuItem);
+    webService.add(msaAlignMenuItem);
+    webService.add(jnet);
+    webService.add(ClustalRealign);
+    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
+    jMenu1.add(pasteNew);
+    jMenu1.add(pasteThis);
+    sort.add(sortIDMenuItem);
+    sort.add(sortGroupMenuItem);
+    sort.add(sortPairwiseMenuItem);
+    calculate.add(averageDistanceTreeMenuItem);
+    calculate.add(neighbourTreeMenuItem);
+    calculate.add(avDistanceTreeBlosumMenuItem);
+    calculate.add(njTreeBlosumMenuItem);
+    jMenu2.add(htmlMenuItem);
+    jMenu2.add(epsFile);
+    jMenu2.add(createPNG);
+  }
+
+  protected void outputText_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void closeMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void overviewMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void PCAMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void PCAMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void clustalColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void zappoColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void taylorColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void clustalColour_actionPerformed(ActionEvent e) {
-    }
+  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void zappoColour_actionPerformed(ActionEvent e) {
-    }
+  protected void helixColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void taylorColour_actionPerformed(ActionEvent e) {
-    }
+  protected void strandColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void hydrophobicityColour_actionPerformed(ActionEvent e) {
-    }
+  protected void turnColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void helixColour_actionPerformed(ActionEvent e) {
-    }
+  protected void buriedColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void strandColour_actionPerformed(ActionEvent e) {
-    }
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void turnColour_actionPerformed(ActionEvent e) {
-    }
+  protected void PIDColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void buriedColour_actionPerformed(ActionEvent e) {
-    }
+  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void userDefinedColour_actionPerformed(ActionEvent e) {
-    }
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void PIDColour_actionPerformed(ActionEvent e) {
-    }
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {
-    }
+  protected void printMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void noColourmenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void conservationMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void printMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {
-    }
-
-    protected void findMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void findMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
-    }
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+  {
+  }
 
-    public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {
-    }
+  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  {
+  }
 
-    protected void nucleotideColour_actionPerformed(ActionEvent e) {
-    }
+  protected void nucleotideColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void deleteGroups_actionPerformed(ActionEvent e) {
-    }
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void copy_actionPerformed(ActionEvent e) {
-    }
+  protected void copy_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void cut_actionPerformed(ActionEvent e) {
-    }
+  protected void cut_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void delete_actionPerformed(ActionEvent e) {
-    }
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void pasteNew_actionPerformed(ActionEvent e) {
-    }
+  protected void pasteNew_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void pasteThis_actionPerformed(ActionEvent e) {
-    }
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void applyToAllGroups_actionPerformed(ActionEvent e) {
-    }
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void createPNG_actionPerformed(ActionEvent e) {
-    }
+  public void createPNG(java.io.File f)
+  {
+  }
 
-    protected void font_actionPerformed(ActionEvent e) {
-    }
+  protected void font_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void fullSeqId_actionPerformed(ActionEvent e) {
-    }
+  protected void fullSeqId_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void epsFile_actionPerformed(ActionEvent e) {
-    }
+  public void createEPS(java.io.File f)
+  {
+  }
 
-    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void jpred_actionPerformed(ActionEvent e) {
-    }
+  protected void jpred_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void scaleAbove_actionPerformed(ActionEvent e) {
-    }
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void scaleLeft_actionPerformed(ActionEvent e) {
-    }
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void scaleRight_actionPerformed(ActionEvent e) {
-    }
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void modifyPID_actionPerformed(ActionEvent e) {
-    }
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void modifyConservation_actionPerformed(ActionEvent e) {
-    }
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void preferences_actionPerformed(ActionEvent e) {
-    }
+  protected void preferences_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
-    }
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) {
-    }
+  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
+  {
+  }
 
-    protected void saveAlignmentMenu_actionPerformed(ActionEvent e) {
-    }
+  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void padGapsMenuitem_actionPerformed(ActionEvent e) {
-    }
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void ClustalRealign_actionPerformed(ActionEvent e) {
-    }
+  protected void ClustalRealign_actionPerformed(ActionEvent e)
+  {
+  }
 }
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index fc8b8dd..3bc577a 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -1,102 +1,122 @@
-/*
-* 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
-*/
+/*
+ * 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.jbgui;
 
 import java.awt.*;
-
 import javax.swing.*;
 import javax.swing.border.*;
+import java.awt.event.MouseWheelListener;
+import java.awt.event.MouseWheelEvent;
 
+public class GAlignmentPanel
+    extends JPanel
+{
+  protected JPanel sequenceHolderPanel = new JPanel();
+  protected JScrollBar vscroll = new JScrollBar();
+  protected JScrollBar hscroll = new JScrollBar();
+  protected JPanel seqPanelHolder = new JPanel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout borderLayout3 = new BorderLayout();
+  protected JPanel scalePanelHolder = new JPanel();
+  protected JPanel idPanelHolder = new JPanel();
+  BorderLayout borderLayout5 = new BorderLayout();
+  protected JPanel idSpaceFillerPanel1 = new JPanel();
+  public JPanel annotationSpaceFillerHolder = new JPanel();
+  BorderLayout borderLayout6 = new BorderLayout();
+  ButtonGroup buttonGroup1 = new ButtonGroup();
+  BorderLayout borderLayout7 = new BorderLayout();
+  JPanel hscrollHolder = new JPanel();
+  BorderLayout borderLayout10 = new BorderLayout();
+  protected JPanel hscrollFillerPanel = new JPanel();
+  BorderLayout borderLayout11 = new BorderLayout();
+  public JScrollPane annotationScroller = new JScrollPane();
+  Border border1;
+  BorderLayout borderLayout4 = new BorderLayout();
 
-public class GAlignmentPanel extends JPanel {
-    protected JPanel sequenceHolderPanel = new JPanel();
-    protected JScrollBar vscroll = new JScrollBar();
-    protected JScrollBar hscroll = new JScrollBar();
-    protected JPanel seqPanelHolder = new JPanel();
-    BorderLayout borderLayout1 = new BorderLayout();
-    BorderLayout borderLayout3 = new BorderLayout();
-    protected JPanel scalePanelHolder = new JPanel();
-    protected JPanel idPanelHolder = new JPanel();
-    BorderLayout borderLayout5 = new BorderLayout();
-    protected JPanel idSpaceFillerPanel1 = new JPanel();
-    public JPanel annotationSpaceFillerHolder = new JPanel();
-    BorderLayout borderLayout6 = new BorderLayout();
-    ButtonGroup buttonGroup1 = new ButtonGroup();
-    BorderLayout borderLayout7 = new BorderLayout();
-    JPanel hscrollHolder = new JPanel();
-    BorderLayout borderLayout10 = new BorderLayout();
-    protected JPanel hscrollFillerPanel = new JPanel();
-    BorderLayout borderLayout11 = new BorderLayout();
-    public JScrollPane annotationScroller = new JScrollPane();
-    Border border1;
-    BorderLayout borderLayout4 = new BorderLayout();
-
-    public GAlignmentPanel() {
-        try {
-            jbInit();
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
+  public GAlignmentPanel()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
     }
+  }
 
-    private void jbInit() throws Exception {
-        border1 = BorderFactory.createLineBorder(Color.gray, 1);
-        idPanelHolder.setBorder(null);
-        idPanelHolder.setPreferredSize(new Dimension(70, 10));
-        this.setLayout(borderLayout7);
-        sequenceHolderPanel.setMaximumSize(new Dimension(2147483647, 2147483647));
-        sequenceHolderPanel.setMinimumSize(new Dimension(150, 150));
-        sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
-        sequenceHolderPanel.setLayout(borderLayout3);
-        seqPanelHolder.setLayout(borderLayout1);
-        scalePanelHolder.setBackground(Color.white);
-        scalePanelHolder.setMinimumSize(new Dimension(10, 80));
-        scalePanelHolder.setPreferredSize(new Dimension(10, 30));
-        scalePanelHolder.setLayout(borderLayout6);
-        idPanelHolder.setLayout(borderLayout5);
-        idSpaceFillerPanel1.setBackground(Color.white);
-        idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
-        idSpaceFillerPanel1.setLayout(borderLayout11);
-        annotationSpaceFillerHolder.setBackground(Color.white);
-        annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
-        annotationSpaceFillerHolder.setLayout(borderLayout4);
-        hscroll.setOrientation(JScrollBar.HORIZONTAL);
-        hscrollHolder.setLayout(borderLayout10);
-        hscrollFillerPanel.setBackground(Color.white);
-        hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
-        hscrollHolder.setBackground(Color.white);
-        annotationScroller.setBorder(null);
-        annotationScroller.setPreferredSize(new Dimension(10, 80));
-        this.setPreferredSize(new Dimension(220, 166));
-        this.setRequestFocusEnabled(true);
-        sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
-        sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
-        seqPanelHolder.add(vscroll, BorderLayout.EAST);
-        sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
+  private void jbInit()
+      throws Exception
+  {
+    border1 = BorderFactory.createLineBorder(Color.gray, 1);
+    idPanelHolder.setBorder(null);
+    idPanelHolder.setPreferredSize(new Dimension(70, 10));
+    this.setLayout(borderLayout7);
+    sequenceHolderPanel.setMaximumSize(new Dimension(2147483647, 2147483647));
+    sequenceHolderPanel.setMinimumSize(new Dimension(150, 150));
+    sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+    sequenceHolderPanel.setLayout(borderLayout3);
+    seqPanelHolder.setLayout(borderLayout1);
+    scalePanelHolder.setBackground(Color.white);
+    scalePanelHolder.setMinimumSize(new Dimension(10, 80));
+    scalePanelHolder.setPreferredSize(new Dimension(10, 30));
+    scalePanelHolder.setLayout(borderLayout6);
+    idPanelHolder.setLayout(borderLayout5);
+    idSpaceFillerPanel1.setBackground(Color.white);
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+    idSpaceFillerPanel1.setLayout(borderLayout11);
+    annotationSpaceFillerHolder.setBackground(Color.white);
+    annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+    annotationSpaceFillerHolder.setLayout(borderLayout4);
+    hscroll.setOrientation(JScrollBar.HORIZONTAL);
+    hscrollHolder.setLayout(borderLayout10);
+    hscrollFillerPanel.setBackground(Color.white);
+    hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+    hscrollHolder.setBackground(Color.white);
+    annotationScroller.setBorder(null);
+    annotationScroller.setPreferredSize(new Dimension(10, 80));
+    this.setPreferredSize(new Dimension(220, 166));
+    this.setRequestFocusEnabled(true);
+    this.addMouseWheelListener(new MouseWheelListener()
+    {
+      public void mouseWheelMoved(MouseWheelEvent e)
+      {
+        this_mouseWheelMoved(e);
+      }
+    });
+    sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+    sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
+    seqPanelHolder.add(vscroll, BorderLayout.EAST);
+    sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
 
-        //  jPanel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
-        this.add(idPanelHolder, BorderLayout.WEST);
-        idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
-        idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
-        this.add(hscrollHolder, BorderLayout.SOUTH);
-        hscrollHolder.add(hscroll, BorderLayout.CENTER);
-        hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
-        this.add(sequenceHolderPanel, BorderLayout.CENTER);
-    }
+    //  jPanel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
+    this.add(idPanelHolder, BorderLayout.WEST);
+    idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
+    idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
+    this.add(hscrollHolder, BorderLayout.SOUTH);
+    hscrollHolder.add(hscroll, BorderLayout.CENTER);
+    hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
+    this.add(sequenceHolderPanel, BorderLayout.CENTER);
+  }
+
+  public void this_mouseWheelMoved(MouseWheelEvent e)
+  {
+
+  }
 }
diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index e469571..0c42724 100755
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -28,7 +28,14 @@ import java.beans.VetoableChangeListener;
 import javax.swing.*;
 
 
-public class GCutAndPasteTransfer extends JInternalFrame {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GCutAndPasteTransfer extends JInternalFrame
+{
     protected JTextArea textarea = new JTextArea();
     protected JScrollPane scrollPane = new JScrollPane();
     BorderLayout borderLayout1 = new BorderLayout();
@@ -41,57 +48,85 @@ public class GCutAndPasteTransfer extends JInternalFrame {
     JButton ok = new JButton();
     JButton cancel = new JButton();
 
-    public GCutAndPasteTransfer() {
-        try {
+    /**
+     * Creates a new GCutAndPasteTransfer object.
+     */
+    public GCutAndPasteTransfer()
+    {
+        try
+        {
             setJMenuBar(editMenubar);
             jbInit();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             e.printStackTrace();
         }
     }
 
-    private void jbInit() throws Exception {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
         scrollPane.setBorder(null);
         ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
         ok.setText("Accept");
-        ok.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        ok.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     ok_actionPerformed(e);
                 }
             });
         cancel.setText("Cancel");
-        cancel.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        cancel.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     cancel_actionPerformed(e);
                 }
             });
         textarea.setBorder(null);
-        textarea.addVetoableChangeListener(new VetoableChangeListener() {
-                public void vetoableChange(PropertyChangeEvent evt) {
-                    try {
+        textarea.addVetoableChangeListener(new VetoableChangeListener()
+            {
+                public void vetoableChange(PropertyChangeEvent evt)
+                {
+                    try
+                    {
                         textarea_vetoableChange(evt);
-                    } catch (java.beans.PropertyVetoException exception0) {
+                    }
+                    catch (java.beans.PropertyVetoException exception0)
+                    {
                         exception0.printStackTrace();
                     }
                 }
             });
         editMenubar.add(editMenu);
         textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
-        textarea.addMouseListener(new java.awt.event.MouseAdapter() {
-                public void mousePressed(MouseEvent e) {
+        textarea.addMouseListener(new java.awt.event.MouseAdapter()
+            {
+                public void mousePressed(MouseEvent e)
+                {
                     textarea_mousePressed(e);
                 }
             });
         editMenu.setText("Edit");
         pasteMenu.setText("Paste");
-        pasteMenu.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        pasteMenu.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     pasteMenu_actionPerformed(e);
                 }
             });
         copyItem.setText("Copy");
-        copyItem.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        copyItem.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     copyItem_actionPerformed(e);
                 }
             });
@@ -105,25 +140,64 @@ public class GCutAndPasteTransfer extends JInternalFrame {
         inputButtonPanel.add(cancel);
     }
 
-    void textarea_mousePressed(MouseEvent e) {
-        if (textarea.getText().equals("Paste your alignment file here")) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    void textarea_mousePressed(MouseEvent e)
+    {
+        if (textarea.getText().equals("Paste your alignment file here"))
+        {
             textarea.setText("");
         }
     }
 
-    public void copyItem_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void copyItem_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void pasteMenu_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pasteMenu_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void ok_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ok_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void cancel_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void cancel_actionPerformed(ActionEvent e)
+    {
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     *
+     * @throws PropertyVetoException DOCUMENT ME!
+     */
     public void textarea_vetoableChange(PropertyChangeEvent evt)
-        throws PropertyVetoException {
+        throws PropertyVetoException
+    {
     }
 }
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 162f7e1..65ef8dc 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -24,7 +24,14 @@ import java.awt.event.*;
 import javax.swing.*;
 
 
-public class GDesktop extends JFrame {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GDesktop extends JFrame
+{
     protected static JMenu windowMenu = new JMenu();
     JMenuBar DesktopMenubar = new JMenuBar();
     JMenu FileMenu = new JMenu();
@@ -42,79 +49,110 @@ public class GDesktop extends JFrame {
     JMenuItem loadState = new JMenuItem();
     JMenu jMenu1 = new JMenu();
 
-    public GDesktop() {
-        try {
+    /**
+     * Creates a new GDesktop object.
+     */
+    public GDesktop()
+    {
+        try
+        {
             jbInit();
             this.setJMenuBar(DesktopMenubar);
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             e.printStackTrace();
         }
     }
 
-    private void jbInit() throws Exception {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
         FileMenu.setMnemonic('F');
         FileMenu.setText("File");
         HelpMenu.setText("Help");
         inputLocalFileMenuItem.setMnemonic('L');
         inputLocalFileMenuItem.setText("from File");
-        inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     inputLocalFileMenuItem_actionPerformed(e);
                 }
             });
         inputURLMenuItem.setMnemonic('U');
         inputURLMenuItem.setText("from URL");
-        inputURLMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     inputURLMenuItem_actionPerformed(e);
                 }
             });
         inputTextboxMenuItem.setMnemonic('C');
         inputTextboxMenuItem.setText("from Textbox");
-        inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     inputTextboxMenuItem_actionPerformed(e);
                 }
             });
         quit.setMnemonic('Q');
         quit.setText("Quit");
-        quit.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        quit.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     quit();
                 }
             });
         aboutMenuItem.setText("About");
-        aboutMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        aboutMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     aboutMenuItem_actionPerformed(e);
                 }
             });
         documentationMenuItem.setText("Documentation");
-        documentationMenuItem.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        documentationMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     documentationMenuItem_actionPerformed(e);
                 }
             });
         this.getContentPane().setLayout(flowLayout1);
         windowMenu.setText("Window");
         preferences.setText("Preferences...");
-        preferences.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        preferences.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     preferences_actionPerformed(e);
                 }
             });
         toolsMenu.setText("Tools");
         saveState.setMnemonic('S');
         saveState.setText("Save Project");
-        saveState.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        saveState.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     saveState_actionPerformed(e);
                 }
             });
         loadState.setMnemonic('L');
         loadState.setText("Load Project");
-        loadState.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        loadState.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     loadState_actionPerformed(e);
                 }
             });
@@ -139,36 +177,100 @@ public class GDesktop extends JFrame {
         jMenu1.add(inputTextboxMenuItem);
     }
 
-    protected void inputLocalFileMenuItem_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void inputURLMenuItem_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void inputURLMenuItem_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void inputTextboxMenuItem_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void quit() {
+    /**
+     * DOCUMENT ME!
+     */
+    protected void quit()
+    {
     }
 
-    protected void aboutMenuItem_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void aboutMenuItem_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void documentationMenuItem_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void documentationMenuItem_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void SaveState_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void SaveState_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void preferences_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void preferences_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void saveState_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveState_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void loadState_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void loadState_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void loadJalviewAlign_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void loadJalviewAlign_actionPerformed(ActionEvent e)
+    {
     }
 }
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 554d8bc..0f9f0d4 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,37 +1,37 @@
 /*
-* 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
-*/
+ * 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.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
-import javax.swing.event.CaretListener;
-import javax.swing.event.CaretEvent;
+import javax.swing.event.*;
 
-public class GFinder extends JPanel {
-    JLabel jLabel1 = new JLabel();
+public class GFinder
+    extends JPanel
+{
+  JLabel jLabel1 = new JLabel();
   protected JButton findAll = new JButton();
-    protected JButton findNext = new JButton();
-    JPanel jPanel1 = new JPanel();
-    GridLayout gridLayout1 = new GridLayout();
-    protected JButton createNewGroup = new JButton();
+  protected JButton findNext = new JButton();
+  JPanel jPanel1 = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
+  protected JButton createNewGroup = new JButton();
   JScrollPane jScrollPane1 = new JScrollPane();
   protected JTextArea textfield = new JTextArea();
   BorderLayout borderLayout1 = new BorderLayout();
@@ -41,47 +41,59 @@ public class GFinder extends JPanel {
   BorderLayout borderLayout2 = new BorderLayout();
   JPanel jPanel5 = new JPanel();
   JPanel jPanel6 = new JPanel();
-  public GFinder() {
-        try {
-            jbInit();
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
+  public GFinder()
+  {
+    try
+    {
+      jbInit();
     }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
 
-    private void jbInit() throws Exception {
-        jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
-        jLabel1.setText("Find");
+  private void jbInit()
+      throws Exception
+  {
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText("Find");
     this.setLayout(borderLayout1);
     findAll.setFont(new java.awt.Font("Verdana", 0, 12));
-        findAll.setText("Find all");
-        findAll.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    findAll_actionPerformed(e);
-                }
-            });
-        findNext.setEnabled(false);
-        findNext.setFont(new java.awt.Font("Verdana", 0, 12));
-        findNext.setText("Find Next");
-        findNext.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    findNext_actionPerformed(e);
-                }
-            });
+    findAll.setText("Find all");
+    findAll.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        findAll_actionPerformed(e);
+      }
+    });
+    findNext.setEnabled(false);
+    findNext.setFont(new java.awt.Font("Verdana", 0, 12));
+    findNext.setText("Find Next");
+    findNext.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        findNext_actionPerformed(e);
+      }
+    });
     jPanel1.setLayout(gridLayout1);
-        gridLayout1.setHgap(0);
-        gridLayout1.setRows(3);
-        gridLayout1.setVgap(2);
-        createNewGroup.setEnabled(false);
-        createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));
-        createNewGroup.setToolTipText("");
-        createNewGroup.setMargin(new Insets(0, 0, 0, 0));
-        createNewGroup.setText("Create new group");
-        createNewGroup.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    createNewGroup_actionPerformed(e);
-                }
-            });
+    gridLayout1.setHgap(0);
+    gridLayout1.setRows(3);
+    gridLayout1.setVgap(2);
+    createNewGroup.setEnabled(false);
+    createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));
+    createNewGroup.setToolTipText("");
+    createNewGroup.setMargin(new Insets(0, 0, 0, 0));
+    createNewGroup.setText("Create new group");
+    createNewGroup.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createNewGroup_actionPerformed(e);
+      }
+    });
     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 12));
     textfield.setText("");
     textfield.setLineWrap(true);
@@ -98,8 +110,8 @@ public class GFinder extends JPanel {
     jPanel2.setPreferredSize(new Dimension(10, 1));
     jPanel3.setPreferredSize(new Dimension(10, 1));
     jPanel1.add(findNext, null);
-        jPanel1.add(findAll, null);
-        jPanel1.add(createNewGroup, null);
+    jPanel1.add(findAll, null);
+    jPanel1.add(createNewGroup, null);
     this.add(jLabel1, java.awt.BorderLayout.WEST);
     this.add(jPanel1, java.awt.BorderLayout.EAST);
     this.add(jPanel2, java.awt.BorderLayout.SOUTH);
@@ -111,35 +123,40 @@ public class GFinder extends JPanel {
     jScrollPane1.getViewport().add(textfield);
   }
 
-    protected void findNext_actionPerformed(ActionEvent e) {
-    }
+  protected void findNext_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void findAll_actionPerformed(ActionEvent e) {
-    }
+  protected void findAll_actionPerformed(ActionEvent e)
+  {
+  }
 
-    protected void textfield_actionPerformed(ActionEvent e) {
-    }
+  protected void textfield_actionPerformed(ActionEvent e)
+  {
+  }
 
-    void textfield_keyTyped(KeyEvent e) {
-        findNext.setEnabled(true);
-    }
+  void textfield_keyTyped(KeyEvent e)
+  {
+    findNext.setEnabled(true);
+  }
 
-    public void createNewGroup_actionPerformed(ActionEvent e) {
-    }
+  public void createNewGroup_actionPerformed(ActionEvent e)
+  {
+  }
 
   public void textfield_caretUpdate(CaretEvent e)
   {
-    if (textfield.getText().indexOf("\t")>-1)
+    if (textfield.getText().indexOf("\t") > -1)
     {
       SwingUtilities.invokeLater(new Runnable()
       {
         public void run()
         {
-            String text = textfield.getText();
-            text = text.substring(text.lastIndexOf("\t") + 1).trim();
-            text = jalview.analysis.AlignSeq.extractGaps(
-                 jalview.util.Comparison.GapChars, text);
-            textfield.setText(text);
+          String text = textfield.getText();
+          text = text.substring(text.lastIndexOf("\t") + 1).trim();
+          text = jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, text);
+          textfield.setText(text);
         }
       });
     }
diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java
index 4ca3b42..f6a1e07 100755
--- a/src/jalview/jbgui/GFontChooser.java
+++ b/src/jalview/jbgui/GFontChooser.java
@@ -24,7 +24,14 @@ import java.awt.event.*;
 import javax.swing.*;
 
 
-public class GFontChooser extends JPanel {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GFontChooser extends JPanel
+{
     JLabel jLabel1 = new JLabel();
     protected JComboBox fontSize = new JComboBox();
     protected JComboBox fontStyle = new JComboBox();
@@ -42,15 +49,28 @@ public class GFontChooser extends JPanel {
     FlowLayout flowLayout1 = new FlowLayout();
     JButton defaultButton = new JButton();
 
-    public GFontChooser() {
-        try {
+    /**
+     * Creates a new GFontChooser object.
+     */
+    public GFontChooser()
+    {
+        try
+        {
             jbInit();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             e.printStackTrace();
         }
     }
 
-    private void jbInit() throws Exception {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
         jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
         jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
         jLabel1.setText("Font: ");
@@ -59,16 +79,20 @@ public class GFontChooser extends JPanel {
         fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
         fontSize.setOpaque(false);
         fontSize.setPreferredSize(new Dimension(50, 21));
-        fontSize.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        fontSize.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     fontSize_actionPerformed(e);
                 }
             });
         fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
         fontStyle.setOpaque(false);
         fontStyle.setPreferredSize(new Dimension(90, 21));
-        fontStyle.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        fontStyle.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     fontStyle_actionPerformed(e);
                 }
             });
@@ -85,22 +109,28 @@ public class GFontChooser extends JPanel {
         fontName.setMinimumSize(new Dimension(300, 21));
         fontName.setOpaque(false);
         fontName.setPreferredSize(new Dimension(180, 21));
-        fontName.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        fontName.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     fontName_actionPerformed(e);
                 }
             });
         ok.setFont(new java.awt.Font("Verdana", 0, 11));
         ok.setText("OK");
-        ok.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        ok.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     ok_actionPerformed(e);
                 }
             });
         cancel.setFont(new java.awt.Font("Verdana", 0, 11));
         cancel.setText("Cancel");
-        cancel.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        cancel.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     cancel_actionPerformed(e);
                 }
             });
@@ -114,8 +144,10 @@ public class GFontChooser extends JPanel {
         flowLayout1.setAlignment(FlowLayout.CENTER);
         flowLayout1.setVgap(5);
         defaultButton.setText("Set as Default");
-        defaultButton.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        defaultButton.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     defaultButton_actionPerformed(e);
                 }
             });
@@ -133,21 +165,57 @@ public class GFontChooser extends JPanel {
         this.add(defaultButton);
     }
 
-    protected void ok_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void ok_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void cancel_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cancel_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void fontName_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void fontName_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void fontSize_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void fontSize_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void fontStyle_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void fontStyle_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void defaultButton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void defaultButton_actionPerformed(ActionEvent e)
+    {
     }
 }
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 41d188e..7fc21a9 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -1,98 +1,114 @@
-/*
-* 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
-*/
+/*
+ * 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.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
+public class GPCAPanel
+    extends JPanel
+{
+  JPanel jPanel2 = new JPanel();
+  JLabel jLabel1 = new JLabel();
+  JLabel jLabel2 = new JLabel();
+  JLabel jLabel3 = new JLabel();
+  protected JComboBox xCombobox = new JComboBox();
+  protected JComboBox yCombobox = new JComboBox();
+  protected JComboBox zCombobox = new JComboBox();
+  FlowLayout flowLayout1 = new FlowLayout();
+  BorderLayout borderLayout1 = new BorderLayout();
 
-public class GPCAPanel extends JPanel {
-    JPanel jPanel2 = new JPanel();
-    JLabel jLabel1 = new JLabel();
-    JLabel jLabel2 = new JLabel();
-    JLabel jLabel3 = new JLabel();
-    protected JComboBox xCombobox = new JComboBox();
-    protected JComboBox yCombobox = new JComboBox();
-    protected JComboBox zCombobox = new JComboBox();
-    FlowLayout flowLayout1 = new FlowLayout();
-    BorderLayout borderLayout1 = new BorderLayout();
-
-    public GPCAPanel() {
-        try {
-            jbInit();
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-
-        for (int i = 1; i < 8; i++) {
-            xCombobox.addItem("dim " + i);
-            yCombobox.addItem("dim " + i);
-            zCombobox.addItem("dim " + i);
-        }
+  public GPCAPanel()
+  {
+    try
+    {
+      jbInit();
     }
-
-    private void jbInit() throws Exception {
-        this.setLayout(borderLayout1);
-        jPanel2.setLayout(flowLayout1);
-        jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
-        jLabel1.setText("x=");
-        jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
-        jLabel2.setText("y=");
-        jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
-        jLabel3.setText("z=");
-        jPanel2.setBackground(Color.white);
-        jPanel2.setBorder(null);
-        zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-        zCombobox.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    zCombobox_actionPerformed(e);
-                }
-            });
-        yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-        yCombobox.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    yCombobox_actionPerformed(e);
-                }
-            });
-        xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-        xCombobox.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    xCombobox_actionPerformed(e);
-                }
-            });
-        this.add(jPanel2, BorderLayout.SOUTH);
-        jPanel2.add(jLabel1, null);
-        jPanel2.add(xCombobox, null);
-        jPanel2.add(jLabel2, null);
-        jPanel2.add(yCombobox, null);
-        jPanel2.add(jLabel3, null);
-        jPanel2.add(zCombobox, null);
+    catch (Exception e)
+    {
+      e.printStackTrace();
     }
 
-    protected void xCombobox_actionPerformed(ActionEvent e) {
+    for (int i = 1; i < 8; i++)
+    {
+      xCombobox.addItem("dim " + i);
+      yCombobox.addItem("dim " + i);
+      zCombobox.addItem("dim " + i);
     }
+  }
 
-    protected void yCombobox_actionPerformed(ActionEvent e) {
-    }
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText("x=");
+    jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel2.setText("y=");
+    jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel3.setText("z=");
+    jPanel2.setBackground(Color.white);
+    jPanel2.setBorder(null);
+    zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    zCombobox.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zCombobox_actionPerformed(e);
+      }
+    });
+    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    yCombobox.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        yCombobox_actionPerformed(e);
+      }
+    });
+    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    xCombobox.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        xCombobox_actionPerformed(e);
+      }
+    });
+    this.add(jPanel2, BorderLayout.SOUTH);
+    jPanel2.add(jLabel1, null);
+    jPanel2.add(xCombobox, null);
+    jPanel2.add(jLabel2, null);
+    jPanel2.add(yCombobox, null);
+    jPanel2.add(jLabel3, null);
+    jPanel2.add(zCombobox, null);
+  }
 
-    protected void zCombobox_actionPerformed(ActionEvent e) {
-    }
+  protected void xCombobox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void yCombobox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void zCombobox_actionPerformed(ActionEvent e)
+  {
+  }
 }
diff --git a/src/jalview/jbgui/GPairwiseAlignPanel.java b/src/jalview/jbgui/GPairwiseAlignPanel.java
index 96a1a40..7f9eea2 100755
--- a/src/jalview/jbgui/GPairwiseAlignPanel.java
+++ b/src/jalview/jbgui/GPairwiseAlignPanel.java
@@ -24,30 +24,52 @@ import java.awt.event.*;
 import javax.swing.*;
 
 
-public class GPairwiseAlignPanel extends JPanel {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GPairwiseAlignPanel extends JPanel
+{
     protected JScrollPane scrollPane = new JScrollPane();
     protected JTextArea textarea = new JTextArea();
     protected JButton viewInEditorButton = new JButton();
     JPanel jPanel1 = new JPanel();
     BorderLayout borderLayout1 = new BorderLayout();
 
-    public GPairwiseAlignPanel() {
-        try {
+    /**
+     * Creates a new GPairwiseAlignPanel object.
+     */
+    public GPairwiseAlignPanel()
+    {
+        try
+        {
             jbInit();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             e.printStackTrace();
         }
     }
 
-    private void jbInit() throws Exception {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
         this.setLayout(borderLayout1);
         textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
         textarea.setText("");
         textarea.setWrapStyleWord(false);
         viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
         viewInEditorButton.setText("View in alignment editor");
-        viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        viewInEditorButton.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     viewInEditorButton_actionPerformed(e);
                 }
             });
@@ -57,6 +79,12 @@ public class GPairwiseAlignPanel extends JPanel {
         jPanel1.add(viewInEditorButton, null);
     }
 
-    protected void viewInEditorButton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void viewInEditorButton_actionPerformed(ActionEvent e)
+    {
     }
 }
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 04ac596..fd61014 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -28,7 +28,14 @@ import javax.swing.*;
 import javax.swing.border.TitledBorder;
 
 
-public class GPreferences extends JPanel {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GPreferences extends JPanel
+{
     JTabbedPane visaulTab = new JTabbedPane();
     JPanel visual = new JPanel();
     JButton ok = new JButton();
@@ -54,25 +61,42 @@ public class GPreferences extends JPanel {
     protected JCheckBox startupCheckbox = new JCheckBox();
     protected JTextField startupFileTextfield = new JTextField();
 
-    public GPreferences() {
-        try {
+    /**
+     * Creates a new GPreferences object.
+     */
+    public GPreferences()
+    {
+        try
+        {
             jbInit();
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             ex.printStackTrace();
         }
     }
 
-    private void jbInit() throws Exception {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
         this.setLayout(borderLayout1);
         ok.setText("OK");
-        ok.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        ok.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     ok_actionPerformed(e);
                 }
             });
         cancel.setText("Cancel");
-        cancel.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        cancel.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     cancel_actionPerformed(e);
                 }
             });
@@ -117,8 +141,10 @@ public class GPreferences extends JPanel {
         annotations.setSelected(true);
         annotations.setText("Show Annotations");
         annotations.setBounds(new Rectangle(10, 53, 128, 23));
-        annotations.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        annotations.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     annotations_actionPerformed(e);
                 }
             });
@@ -146,8 +172,10 @@ public class GPreferences extends JPanel {
         gapSymbolCB.setBounds(new Rectangle(121, 140, 67, 21));
         startupCheckbox.setText("Open file");
         startupCheckbox.setBounds(new Rectangle(4, 200, 115, 23));
-        startupCheckbox.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        startupCheckbox.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     jCheckBox1_actionPerformed(e);
                 }
             });
@@ -157,10 +185,14 @@ public class GPreferences extends JPanel {
         startupCheckbox.setSelected(true);
         startupFileTextfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
         startupFileTextfield.setBounds(new Rectangle(122, 202, 309, 20));
-        startupFileTextfield.addMouseListener(new MouseAdapter() {
-                public void mouseClicked(MouseEvent e) {
-                  if(e.getClickCount()>1)
-                    startupFileTextfield_mouseClicked();
+        startupFileTextfield.addMouseListener(new MouseAdapter()
+            {
+                public void mouseClicked(MouseEvent e)
+                {
+                    if (e.getClickCount() > 1)
+                    {
+                        startupFileTextfield_mouseClicked();
+                    }
                 }
             });
 
@@ -192,18 +224,46 @@ public class GPreferences extends JPanel {
         gapSymbolCB.setRenderer(dlcr);
     }
 
-    public void ok_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ok_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void cancel_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void cancel_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void annotations_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void annotations_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void jCheckBox1_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void jCheckBox1_actionPerformed(ActionEvent e)
+    {
     }
 
-    public void startupFileTextfield_mouseClicked() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void startupFileTextfield_mouseClicked()
+    {
     }
 }
diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java
index 341263f..c452d11 100755
--- a/src/jalview/jbgui/GSliderPanel.java
+++ b/src/jalview/jbgui/GSliderPanel.java
@@ -24,7 +24,14 @@ import java.awt.event.*;
 import javax.swing.*;
 
 
-public class GSliderPanel extends JPanel {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GSliderPanel extends JPanel
+{
     // this is used for conservation colours, PID colours and redundancy threshold
     protected JSlider slider = new JSlider();
     protected JTextField valueField = new JTextField();
@@ -38,15 +45,28 @@ public class GSliderPanel extends JPanel {
     protected JCheckBox allGroupsCheck = new JCheckBox();
     BorderLayout borderLayout1 = new BorderLayout();
 
-    public GSliderPanel() {
-        try {
+    /**
+     * Creates a new GSliderPanel object.
+     */
+    public GSliderPanel()
+    {
+        try
+        {
             jbInit();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             e.printStackTrace();
         }
     }
 
-    private void jbInit() throws Exception {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
         this.setLayout(gridLayout1);
         slider.setMajorTickSpacing(10);
         slider.setMinorTickSpacing(1);
@@ -59,8 +79,10 @@ public class GSliderPanel extends JPanel {
         valueField.setPreferredSize(new Dimension(50, 12));
         valueField.setText("");
         valueField.setHorizontalAlignment(SwingConstants.CENTER);
-        valueField.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        valueField.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     valueField_actionPerformed(e);
                 }
             });
@@ -74,8 +96,10 @@ public class GSliderPanel extends JPanel {
         applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
         applyButton.setOpaque(false);
         applyButton.setText("Apply");
-        applyButton.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        applyButton.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     applyButton_actionPerformed(e);
                 }
             });
@@ -83,8 +107,10 @@ public class GSliderPanel extends JPanel {
         undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
         undoButton.setOpaque(false);
         undoButton.setText("Undo");
-        undoButton.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        undoButton.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     undoButton_actionPerformed(e);
                 }
             });
@@ -92,8 +118,10 @@ public class GSliderPanel extends JPanel {
         allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
         allGroupsCheck.setOpaque(false);
         allGroupsCheck.setText("Apply to all Groups");
-        allGroupsCheck.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        allGroupsCheck.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     allGroupsCheck_actionPerformed(e);
                 }
             });
@@ -111,15 +139,39 @@ public class GSliderPanel extends JPanel {
         jPanel1.add(allGroupsCheck, BorderLayout.EAST);
     }
 
-    protected void valueField_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void valueField_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void applyButton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void applyButton_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void undoButton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void undoButton_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void allGroupsCheck_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void allGroupsCheck_actionPerformed(ActionEvent e)
+    {
     }
 }
diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index 088dbde..24e80b6 100755
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -1,170 +1,206 @@
 /*
-* 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
-*/
+ * 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.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
-
-public class GTreePanel extends JInternalFrame {
-    BorderLayout borderLayout1 = new BorderLayout();
-    public JScrollPane scrollPane = new JScrollPane();
-    JMenuBar jMenuBar1 = new JMenuBar();
-    JMenu jMenu1 = new JMenu();
-    JMenuItem saveAsNewick = new JMenuItem();
-    JMenuItem printMenu = new JMenuItem();
-    JMenu jMenu2 = new JMenu();
-    public JMenuItem fontSize = new JMenuItem();
-    public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
-    public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
-    public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
-    public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
-    JMenuItem pngTree = new JMenuItem();
-    JMenuItem epsTree = new JMenuItem();
-    JMenu saveAsMenu = new JMenu();
-    JMenuItem textbox = new JMenuItem();
-
-    public GTreePanel() {
-        try {
-            jbInit();
-            this.setJMenuBar(jMenuBar1);
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-    }
-
-    private void jbInit() throws Exception {
-        this.getContentPane().setLayout(borderLayout1);
-        this.setBackground(Color.white);
-        this.setFont(new java.awt.Font("Verdana", 0, 12));
-        scrollPane.setOpaque(false);
-        jMenu1.setText("File");
-        saveAsNewick.setText("Newick Format");
-        saveAsNewick.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    saveAsNewick_actionPerformed(e);
-                }
-            });
-        printMenu.setText("Print");
-        printMenu.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    printMenu_actionPerformed(e);
-                }
-            });
-        jMenu2.setText("View");
-        fontSize.setText("Font Size - 12");
-        fontSize.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    fontSize_actionPerformed(e);
-                }
-            });
-        bootstrapMenu.setText("Show Bootstrap Values");
-        bootstrapMenu.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    bootstrapMenu_actionPerformed(e);
-                }
-            });
-        distanceMenu.setText("Show Distances");
-        distanceMenu.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    distanceMenu_actionPerformed(e);
-                }
-            });
-        fitToWindow.setSelected(true);
-        fitToWindow.setText("Fit To Window");
-        fitToWindow.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    fitToWindow_actionPerformed(e);
-                }
-            });
-        epsTree.setText("EPS");
-        epsTree.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    epsTree_actionPerformed(e);
-                }
-            });
-        pngTree.setText("PNG");
-        pngTree.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    pngTree_actionPerformed(e);
-                }
-            });
-        saveAsMenu.setText("Save as");
-        placeholdersMenu.setToolTipText(
-            "Marks leaves of tree not associated with a sequence");
-        placeholdersMenu.setText("Mark Unlinked Leaves");
-        placeholdersMenu.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    placeholdersMenu_actionPerformed(e);
-                }
-            });
-        textbox.setText("Output to Textbox...");
-        textbox.addActionListener(new ActionListener() {
-                public void actionPerformed(ActionEvent e) {
-                    textbox_actionPerformed(e);
-                }
-            });
-        this.getContentPane().add(scrollPane, BorderLayout.CENTER);
-        jMenuBar1.add(jMenu1);
-        jMenuBar1.add(jMenu2);
-        jMenu1.add(saveAsMenu);
-        jMenu1.add(textbox);
-        jMenu1.add(printMenu);
-        jMenu2.add(fitToWindow);
-        jMenu2.add(fontSize);
-        jMenu2.add(distanceMenu);
-        jMenu2.add(bootstrapMenu);
-        jMenu2.add(placeholdersMenu);
-        saveAsMenu.add(saveAsNewick);
-        saveAsMenu.add(epsTree);
-        saveAsMenu.add(pngTree);
-    }
-
-    public void printMenu_actionPerformed(ActionEvent e) {
-    }
-
-    public void fontSize_actionPerformed(ActionEvent e) {
-    }
-
-    public void distanceMenu_actionPerformed(ActionEvent e) {
-    }
-
-    public void bootstrapMenu_actionPerformed(ActionEvent e) {
-    }
-
-    public void fitToWindow_actionPerformed(ActionEvent e) {
-    }
-
-    public void pngTree_actionPerformed(ActionEvent e) {
-    }
-
-    public void epsTree_actionPerformed(ActionEvent e) {
-    }
-
-    public void saveAsNewick_actionPerformed(ActionEvent e) {
+public class GTreePanel
+    extends JInternalFrame
+{
+  BorderLayout borderLayout1 = new BorderLayout();
+  public JScrollPane scrollPane = new JScrollPane();
+  JMenuBar jMenuBar1 = new JMenuBar();
+  JMenu jMenu1 = new JMenu();
+  JMenuItem saveAsNewick = new JMenuItem();
+  JMenuItem printMenu = new JMenuItem();
+  JMenu jMenu2 = new JMenu();
+  public JMenuItem fontSize = new JMenuItem();
+  public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
+  JMenuItem pngTree = new JMenuItem();
+  JMenuItem epsTree = new JMenuItem();
+  JMenu saveAsMenu = new JMenu();
+  JMenuItem textbox = new JMenuItem();
+
+  public GTreePanel()
+  {
+    try
+    {
+      jbInit();
+      this.setJMenuBar(jMenuBar1);
     }
-
-    public void placeholdersMenu_actionPerformed(ActionEvent e) {
-    }
-
-    public void textbox_actionPerformed(ActionEvent e) {
+    catch (Exception e)
+    {
+      e.printStackTrace();
     }
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    this.getContentPane().setLayout(borderLayout1);
+    this.setBackground(Color.white);
+    this.setFont(new java.awt.Font("Verdana", 0, 12));
+    scrollPane.setOpaque(false);
+    jMenu1.setText("File");
+    saveAsNewick.setText("Newick Format");
+    saveAsNewick.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveAsNewick_actionPerformed(e);
+      }
+    });
+    printMenu.setText("Print");
+    printMenu.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        printMenu_actionPerformed(e);
+      }
+    });
+    jMenu2.setText("View");
+    fontSize.setText("Font Size - 12");
+    fontSize.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fontSize_actionPerformed(e);
+      }
+    });
+    bootstrapMenu.setText("Show Bootstrap Values");
+    bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        bootstrapMenu_actionPerformed(e);
+      }
+    });
+    distanceMenu.setText("Show Distances");
+    distanceMenu.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        distanceMenu_actionPerformed(e);
+      }
+    });
+    fitToWindow.setSelected(true);
+    fitToWindow.setText("Fit To Window");
+    fitToWindow.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fitToWindow_actionPerformed(e);
+      }
+    });
+    epsTree.setText("EPS");
+    epsTree.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        epsTree_actionPerformed(e);
+      }
+    });
+    pngTree.setText("PNG");
+    pngTree.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pngTree_actionPerformed(e);
+      }
+    });
+    saveAsMenu.setText("Save as");
+    placeholdersMenu.setToolTipText(
+        "Marks leaves of tree not associated with a sequence");
+    placeholdersMenu.setText("Mark Unlinked Leaves");
+    placeholdersMenu.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        placeholdersMenu_actionPerformed(e);
+      }
+    });
+    textbox.setText("Output to Textbox...");
+    textbox.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textbox_actionPerformed(e);
+      }
+    });
+    this.getContentPane().add(scrollPane, BorderLayout.CENTER);
+    jMenuBar1.add(jMenu1);
+    jMenuBar1.add(jMenu2);
+    jMenu1.add(saveAsMenu);
+    jMenu1.add(textbox);
+    jMenu1.add(printMenu);
+    jMenu2.add(fitToWindow);
+    jMenu2.add(fontSize);
+    jMenu2.add(distanceMenu);
+    jMenu2.add(bootstrapMenu);
+    jMenu2.add(placeholdersMenu);
+    saveAsMenu.add(saveAsNewick);
+    saveAsMenu.add(epsTree);
+    saveAsMenu.add(pngTree);
+  }
+
+  public void printMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void fontSize_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void distanceMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void bootstrapMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void fitToWindow_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void pngTree_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void epsTree_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void saveAsNewick_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void placeholdersMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void textbox_actionPerformed(ActionEvent e)
+  {
+  }
 }
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 3cd9f51..49174a0 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -24,7 +24,14 @@ import java.awt.event.*;
 import javax.swing.*;
 
 
-public class GUserDefinedColours extends JPanel {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GUserDefinedColours extends JPanel
+{
     protected JColorChooser colorChooser = new JColorChooser();
     protected JPanel buttonPanel = new JPanel();
     protected GridLayout gridLayout = new GridLayout();
@@ -36,51 +43,74 @@ public class GUserDefinedColours extends JPanel {
     protected JButton cancelButton = new JButton();
     FlowLayout flowLayout1 = new FlowLayout();
 
-    public GUserDefinedColours() {
-        try {
+    /**
+     * Creates a new GUserDefinedColours object.
+     */
+    public GUserDefinedColours()
+    {
+        try
+        {
             jbInit();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             e.printStackTrace();
         }
     }
 
-    private void jbInit() throws Exception {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
         this.setLayout(flowLayout1);
         buttonPanel.setLayout(gridLayout);
         gridLayout.setColumns(6);
         gridLayout.setRows(4);
         okButton.setFont(new java.awt.Font("Verdana", 0, 11));
         okButton.setText("OK");
-        okButton.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        okButton.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     okButton_actionPerformed(e);
                 }
             });
         applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
         applyButton.setText("Apply");
-        applyButton.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        applyButton.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     applyButton_actionPerformed(e);
                 }
             });
         loadbutton.setFont(new java.awt.Font("Verdana", 0, 11));
         loadbutton.setText("Load scheme");
-        loadbutton.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        loadbutton.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     loadbutton_actionPerformed(e);
                 }
             });
         savebutton.setFont(new java.awt.Font("Verdana", 0, 11));
         savebutton.setText("Save scheme");
-        savebutton.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        savebutton.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     savebutton_actionPerformed(e);
                 }
             });
         cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
         cancelButton.setText("Cancel");
-        cancelButton.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        cancelButton.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     cancelButton_actionPerformed(e);
                 }
             });
@@ -97,18 +127,48 @@ public class GUserDefinedColours extends JPanel {
         jPanel2.add(cancelButton, null);
     }
 
-    protected void okButton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void okButton_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void applyButton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void applyButton_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void loadbutton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void loadbutton_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void savebutton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void savebutton_actionPerformed(ActionEvent e)
+    {
     }
 
-    protected void cancelButton_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cancelButton_actionPerformed(ActionEvent e)
+    {
     }
 }
diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java
index 54eab04..6f8bbd7 100755
--- a/src/jalview/jbgui/GWebserviceInfo.java
+++ b/src/jalview/jbgui/GWebserviceInfo.java
@@ -24,7 +24,14 @@ import java.awt.event.*;
 import javax.swing.*;
 
 
-public class GWebserviceInfo extends JPanel {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GWebserviceInfo extends JPanel
+{
     protected JTextArea infoText = new JTextArea();
     JScrollPane jScrollPane1 = new JScrollPane();
     JScrollPane jScrollPane2 = new JScrollPane();
@@ -38,15 +45,28 @@ public class GWebserviceInfo extends JPanel {
     protected JButton cancel = new JButton();
     GridBagLayout gridBagLayout1 = new GridBagLayout();
 
-    public GWebserviceInfo() {
-        try {
+    /**
+     * Creates a new GWebserviceInfo object.
+     */
+    public GWebserviceInfo()
+    {
+        try
+        {
             jbInit();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             e.printStackTrace();
         }
     }
 
-    private void jbInit() throws Exception {
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws Exception DOCUMENT ME!
+     */
+    private void jbInit() throws Exception
+    {
         infoText.setFont(new java.awt.Font("Verdana", 0, 10));
         infoText.setBorder(null);
         infoText.setEditable(false);
@@ -69,8 +89,10 @@ public class GWebserviceInfo extends JPanel {
         jScrollPane1.setPreferredSize(new Dimension(400, 70));
         cancel.setFont(new java.awt.Font("Verdana", 0, 11));
         cancel.setText("Cancel");
-        cancel.addActionListener(new java.awt.event.ActionListener() {
-                public void actionPerformed(ActionEvent e) {
+        cancel.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
                     cancel_actionPerformed(e);
                 }
             });
@@ -89,6 +111,12 @@ public class GWebserviceInfo extends JPanel {
                 new Insets(24, 5, 21, 5), 0, 0));
     }
 
-    protected void cancel_actionPerformed(ActionEvent e) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cancel_actionPerformed(ActionEvent e)
+    {
     }
 }
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 30c534b..81d520a 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -23,27 +23,58 @@ import jalview.util.*;
 import java.io.*;
 
 
-public class Matrix {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Matrix
+{
     /**
      * SMJSPUBLIC
      */
     public double[][] value;
+
+    /** DOCUMENT ME!! */
     public int rows;
+
+    /** DOCUMENT ME!! */
     public int cols;
+
+    /** DOCUMENT ME!! */
     public double[] d; // Diagonal
+
+    /** DOCUMENT ME!! */
     public double[] e; // off diagonal
 
-    public Matrix(double[][] value, int rows, int cols) {
+    /**
+     * Creates a new Matrix object.
+     *
+     * @param value DOCUMENT ME!
+     * @param rows DOCUMENT ME!
+     * @param cols DOCUMENT ME!
+     */
+    public Matrix(double[][] value, int rows, int cols)
+    {
         this.rows = rows;
         this.cols = cols;
         this.value = value;
     }
 
-    public Matrix transpose() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Matrix transpose()
+    {
         double[][] out = new double[cols][rows];
 
-        for (int i = 0; i < cols; i++) {
-            for (int j = 0; j < rows; j++) {
+        for (int i = 0; i < cols; i++)
+        {
+            for (int j = 0; j < rows; j++)
+            {
                 out[i][j] = value[j][i];
             }
         }
@@ -51,9 +82,17 @@ public class Matrix {
         return new Matrix(out, cols, rows);
     }
 
-    public void print(PrintStream ps) {
-        for (int i = 0; i < rows; i++) {
-            for (int j = 0; j < cols; j++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ps DOCUMENT ME!
+     */
+    public void print(PrintStream ps)
+    {
+        for (int i = 0; i < rows; i++)
+        {
+            for (int j = 0; j < cols; j++)
+            {
                 Format.print(ps, "%8.2f", value[i][j]);
             }
 
@@ -61,14 +100,25 @@ public class Matrix {
         }
     }
 
-    public Matrix preMultiply(Matrix in) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param in DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Matrix preMultiply(Matrix in)
+    {
         double[][] tmp = new double[in.rows][this.cols];
 
-        for (int i = 0; i < in.rows; i++) {
-            for (int j = 0; j < this.cols; j++) {
+        for (int i = 0; i < in.rows; i++)
+        {
+            for (int j = 0; j < this.cols; j++)
+            {
                 tmp[i][j] = 0.0;
 
-                for (int k = 0; k < in.cols; k++) {
+                for (int k = 0; k < in.cols; k++)
+                {
                     tmp[i][j] += (in.value[i][k] * this.value[k][j]);
                 }
             }
@@ -77,13 +127,23 @@ public class Matrix {
         return new Matrix(tmp, in.rows, this.cols);
     }
 
-    public double[] vectorPostMultiply(double[] in) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param in DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public double[] vectorPostMultiply(double[] in)
+    {
         double[] out = new double[in.length];
 
-        for (int i = 0; i < in.length; i++) {
+        for (int i = 0; i < in.length; i++)
+        {
             out[i] = 0.0;
 
-            for (int k = 0; k < in.length; k++) {
+            for (int k = 0; k < in.length; k++)
+            {
                 out[i] += (value[i][k] * in[k]);
             }
         }
@@ -91,14 +151,25 @@ public class Matrix {
         return out;
     }
 
-    public Matrix postMultiply(Matrix in) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param in DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Matrix postMultiply(Matrix in)
+    {
         double[][] out = new double[this.rows][in.cols];
 
-        for (int i = 0; i < this.rows; i++) {
-            for (int j = 0; j < in.cols; j++) {
+        for (int i = 0; i < this.rows; i++)
+        {
+            for (int j = 0; j < in.cols; j++)
+            {
                 out[i][j] = 0.0;
 
-                for (int k = 0; k < rows; k++) {
+                for (int k = 0; k < rows; k++)
+                {
                     out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
                 }
             }
@@ -107,11 +178,19 @@ public class Matrix {
         return new Matrix(out, this.cols, in.rows);
     }
 
-    public Matrix copy() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Matrix copy()
+    {
         double[][] newmat = new double[rows][cols];
 
-        for (int i = 0; i < rows; i++) {
-            for (int j = 0; j < cols; j++) {
+        for (int i = 0; i < rows; i++)
+        {
+            for (int j = 0; j < cols; j++)
+            {
                 newmat[i][j] = value[i][j];
             }
         }
@@ -119,7 +198,11 @@ public class Matrix {
         return new Matrix(newmat, rows, cols);
     }
 
-    public void tred() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void tred()
+    {
         int n = rows;
         int l;
         int k;
@@ -135,29 +218,39 @@ public class Matrix {
         this.d = new double[rows];
         this.e = new double[rows];
 
-        for (i = n; i >= 2; i--) {
+        for (i = n; i >= 2; i--)
+        {
             l = i - 1;
             h = 0.0;
             scale = 0.0;
 
-            if (l > 1) {
-                for (k = 1; k <= l; k++) {
+            if (l > 1)
+            {
+                for (k = 1; k <= l; k++)
+                {
                     scale += Math.abs(value[i - 1][k - 1]);
                 }
 
-                if (scale == 0.0) {
+                if (scale == 0.0)
+                {
                     e[i - 1] = value[i - 1][l - 1];
-                } else {
-                    for (k = 1; k <= l; k++) {
+                }
+                else
+                {
+                    for (k = 1; k <= l; k++)
+                    {
                         value[i - 1][k - 1] /= scale;
                         h += (value[i - 1][k - 1] * value[i - 1][k - 1]);
                     }
 
                     f = value[i - 1][l - 1];
 
-                    if (f > 0) {
+                    if (f > 0)
+                    {
                         g = -1.0 * Math.sqrt(h);
-                    } else {
+                    }
+                    else
+                    {
                         g = Math.sqrt(h);
                     }
 
@@ -166,15 +259,18 @@ public class Matrix {
                     value[i - 1][l - 1] = f - g;
                     f = 0.0;
 
-                    for (j = 1; j <= l; j++) {
+                    for (j = 1; j <= l; j++)
+                    {
                         value[j - 1][i - 1] = value[i - 1][j - 1] / h;
                         g = 0.0;
 
-                        for (k = 1; k <= j; k++) {
+                        for (k = 1; k <= j; k++)
+                        {
                             g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
                         }
 
-                        for (k = j + 1; k <= l; k++) {
+                        for (k = j + 1; k <= l; k++)
+                        {
                             g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
                         }
 
@@ -184,18 +280,22 @@ public class Matrix {
 
                     hh = f / (h + h);
 
-                    for (j = 1; j <= l; j++) {
+                    for (j = 1; j <= l; j++)
+                    {
                         f = value[i - 1][j - 1];
                         g = e[j - 1] - (hh * f);
                         e[j - 1] = g;
 
-                        for (k = 1; k <= j; k++) {
+                        for (k = 1; k <= j; k++)
+                        {
                             value[j - 1][k - 1] -= ((f * e[k - 1]) +
                             (g * value[i - 1][k - 1]));
                         }
                     }
                 }
-            } else {
+            }
+            else
+            {
                 e[i - 1] = value[i - 1][l - 1];
             }
 
@@ -205,18 +305,23 @@ public class Matrix {
         d[0] = 0.0;
         e[0] = 0.0;
 
-        for (i = 1; i <= n; i++) {
+        for (i = 1; i <= n; i++)
+        {
             l = i - 1;
 
-            if (d[i - 1] != 0.0) {
-                for (j = 1; j <= l; j++) {
+            if (d[i - 1] != 0.0)
+            {
+                for (j = 1; j <= l; j++)
+                {
                     g = 0.0;
 
-                    for (k = 1; k <= l; k++) {
+                    for (k = 1; k <= l; k++)
+                    {
                         g += (value[i - 1][k - 1] * value[k - 1][j - 1]);
                     }
 
-                    for (k = 1; k <= l; k++) {
+                    for (k = 1; k <= l; k++)
+                    {
                         value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
                     }
                 }
@@ -225,14 +330,19 @@ public class Matrix {
             d[i - 1] = value[i - 1][i - 1];
             value[i - 1][i - 1] = 1.0;
 
-            for (j = 1; j <= l; j++) {
+            for (j = 1; j <= l; j++)
+            {
                 value[j - 1][i - 1] = 0.0;
                 value[i - 1][j - 1] = 0.0;
             }
         }
     }
 
-    public void tqli() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void tqli()
+    {
         int n = rows;
 
         int m;
@@ -251,31 +361,40 @@ public class Matrix {
         double c;
         double b;
 
-        for (i = 2; i <= n; i++) {
+        for (i = 2; i <= n; i++)
+        {
             e[i - 2] = e[i - 1];
         }
 
         e[n - 1] = 0.0;
 
-        for (l = 1; l <= n; l++) {
+        for (l = 1; l <= n; l++)
+        {
             iter = 0;
 
-            do {
-                for (m = l; m <= (n - 1); m++) {
+            do
+            {
+                for (m = l; m <= (n - 1); m++)
+                {
                     dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
 
-                    if ((Math.abs(e[m - 1]) + dd) == dd) {
+                    if ((Math.abs(e[m - 1]) + dd) == dd)
+                    {
                         break;
                     }
                 }
 
-                if (m != l) {
+                if (m != l)
+                {
                     iter++;
 
-                    if (iter == 30) {
+                    if (iter == 30)
+                    {
                         System.err.print("Too many iterations in tqli");
                         System.exit(0); // JBPNote - should this really be here ???
-                    } else {
+                    }
+                    else
+                    {
                         //	    System.out.println("Iteration " + iter);
                     }
 
@@ -286,17 +405,21 @@ public class Matrix {
                     s = c;
                     p = 0.0;
 
-                    for (i = m - 1; i >= l; i--) {
+                    for (i = m - 1; i >= l; i--)
+                    {
                         f = s * e[i - 1];
                         b = c * e[i - 1];
 
-                        if (Math.abs(f) >= Math.abs(g)) {
+                        if (Math.abs(f) >= Math.abs(g))
+                        {
                             c = g / f;
                             r = Math.sqrt((c * c) + 1.0);
                             e[i] = f * r;
                             s = 1.0 / r;
                             c *= s;
-                        } else {
+                        }
+                        else
+                        {
                             s = f / g;
                             r = Math.sqrt((s * s) + 1.0);
                             e[i] = g * r;
@@ -310,7 +433,8 @@ public class Matrix {
                         d[i] = g + p;
                         g = (c * r) - b;
 
-                        for (k = 1; k <= n; k++) {
+                        for (k = 1; k <= n; k++)
+                        {
                             f = value[k - 1][i];
                             value[k - 1][i] = (s * value[k - 1][i - 1]) +
                                 (c * f);
@@ -323,11 +447,16 @@ public class Matrix {
                     e[l - 1] = g;
                     e[m - 1] = 0.0;
                 }
-            } while (m != l);
+            }
+            while (m != l);
         }
     }
 
-    public void tred2() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void tred2()
+    {
         int n = rows;
         int l;
         int k;
@@ -343,29 +472,39 @@ public class Matrix {
         this.d = new double[rows];
         this.e = new double[rows];
 
-        for (i = n - 1; i >= 1; i--) {
+        for (i = n - 1; i >= 1; i--)
+        {
             l = i - 1;
             h = 0.0;
             scale = 0.0;
 
-            if (l > 0) {
-                for (k = 0; k < l; k++) {
+            if (l > 0)
+            {
+                for (k = 0; k < l; k++)
+                {
                     scale += Math.abs(value[i][k]);
                 }
 
-                if (scale == 0.0) {
+                if (scale == 0.0)
+                {
                     e[i] = value[i][l];
-                } else {
-                    for (k = 0; k < l; k++) {
+                }
+                else
+                {
+                    for (k = 0; k < l; k++)
+                    {
                         value[i][k] /= scale;
                         h += (value[i][k] * value[i][k]);
                     }
 
                     f = value[i][l];
 
-                    if (f > 0) {
+                    if (f > 0)
+                    {
                         g = -1.0 * Math.sqrt(h);
-                    } else {
+                    }
+                    else
+                    {
                         g = Math.sqrt(h);
                     }
 
@@ -374,15 +513,18 @@ public class Matrix {
                     value[i][l] = f - g;
                     f = 0.0;
 
-                    for (j = 0; j < l; j++) {
+                    for (j = 0; j < l; j++)
+                    {
                         value[j][i] = value[i][j] / h;
                         g = 0.0;
 
-                        for (k = 0; k < j; k++) {
+                        for (k = 0; k < j; k++)
+                        {
                             g += (value[j][k] * value[i][k]);
                         }
 
-                        for (k = j; k < l; k++) {
+                        for (k = j; k < l; k++)
+                        {
                             g += (value[k][j] * value[i][k]);
                         }
 
@@ -392,17 +534,21 @@ public class Matrix {
 
                     hh = f / (h + h);
 
-                    for (j = 0; j < l; j++) {
+                    for (j = 0; j < l; j++)
+                    {
                         f = value[i][j];
                         g = e[j] - (hh * f);
                         e[j] = g;
 
-                        for (k = 0; k < j; k++) {
+                        for (k = 0; k < j; k++)
+                        {
                             value[j][k] -= ((f * e[k]) + (g * value[i][k]));
                         }
                     }
                 }
-            } else {
+            }
+            else
+            {
                 e[i] = value[i][l];
             }
 
@@ -412,18 +558,23 @@ public class Matrix {
         d[0] = 0.0;
         e[0] = 0.0;
 
-        for (i = 0; i < n; i++) {
+        for (i = 0; i < n; i++)
+        {
             l = i - 1;
 
-            if (d[i] != 0.0) {
-                for (j = 0; j < l; j++) {
+            if (d[i] != 0.0)
+            {
+                for (j = 0; j < l; j++)
+                {
                     g = 0.0;
 
-                    for (k = 0; k < l; k++) {
+                    for (k = 0; k < l; k++)
+                    {
                         g += (value[i][k] * value[k][j]);
                     }
 
-                    for (k = 0; k < l; k++) {
+                    for (k = 0; k < l; k++)
+                    {
                         value[k][j] -= (g * value[k][i]);
                     }
                 }
@@ -432,14 +583,19 @@ public class Matrix {
             d[i] = value[i][i];
             value[i][i] = 1.0;
 
-            for (j = 0; j < l; j++) {
+            for (j = 0; j < l; j++)
+            {
                 value[j][i] = 0.0;
                 value[i][j] = 0.0;
             }
         }
     }
 
-    public void tqli2() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void tqli2()
+    {
         int n = rows;
 
         int m;
@@ -458,31 +614,40 @@ public class Matrix {
         double c;
         double b;
 
-        for (i = 2; i <= n; i++) {
+        for (i = 2; i <= n; i++)
+        {
             e[i - 2] = e[i - 1];
         }
 
         e[n - 1] = 0.0;
 
-        for (l = 1; l <= n; l++) {
+        for (l = 1; l <= n; l++)
+        {
             iter = 0;
 
-            do {
-                for (m = l; m <= (n - 1); m++) {
+            do
+            {
+                for (m = l; m <= (n - 1); m++)
+                {
                     dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
 
-                    if ((Math.abs(e[m - 1]) + dd) == dd) {
+                    if ((Math.abs(e[m - 1]) + dd) == dd)
+                    {
                         break;
                     }
                 }
 
-                if (m != l) {
+                if (m != l)
+                {
                     iter++;
 
-                    if (iter == 30) {
+                    if (iter == 30)
+                    {
                         System.err.print("Too many iterations in tqli");
                         System.exit(0); // JBPNote - same as above - not a graceful exit!
-                    } else {
+                    }
+                    else
+                    {
                         //	    System.out.println("Iteration " + iter);
                     }
 
@@ -493,17 +658,21 @@ public class Matrix {
                     s = c;
                     p = 0.0;
 
-                    for (i = m - 1; i >= l; i--) {
+                    for (i = m - 1; i >= l; i--)
+                    {
                         f = s * e[i - 1];
                         b = c * e[i - 1];
 
-                        if (Math.abs(f) >= Math.abs(g)) {
+                        if (Math.abs(f) >= Math.abs(g))
+                        {
                             c = g / f;
                             r = Math.sqrt((c * c) + 1.0);
                             e[i] = f * r;
                             s = 1.0 / r;
                             c *= s;
-                        } else {
+                        }
+                        else
+                        {
                             s = f / g;
                             r = Math.sqrt((s * s) + 1.0);
                             e[i] = g * r;
@@ -517,7 +686,8 @@ public class Matrix {
                         d[i] = g + p;
                         g = (c * r) - b;
 
-                        for (k = 1; k <= n; k++) {
+                        for (k = 1; k <= n; k++)
+                        {
                             f = value[k - 1][i];
                             value[k - 1][i] = (s * value[k - 1][i - 1]) +
                                 (c * f);
@@ -530,46 +700,90 @@ public class Matrix {
                     e[l - 1] = g;
                     e[m - 1] = 0.0;
                 }
-            } while (m != l);
+            }
+            while (m != l);
         }
     }
 
-    public double sign(double a, double b) {
-        if (b < 0) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param a DOCUMENT ME!
+     * @param b DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public double sign(double a, double b)
+    {
+        if (b < 0)
+        {
             return -Math.abs(a);
-        } else {
+        }
+        else
+        {
             return Math.abs(a);
         }
     }
 
-    public double[] getColumn(int n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public double[] getColumn(int n)
+    {
         double[] out = new double[rows];
 
-        for (int i = 0; i < rows; i++) {
+        for (int i = 0; i < rows; i++)
+        {
             out[i] = value[i][n];
         }
 
         return out;
     }
 
-    public void printD(PrintStream ps) {
-        for (int j = 0; j < rows; j++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ps DOCUMENT ME!
+     */
+    public void printD(PrintStream ps)
+    {
+        for (int j = 0; j < rows; j++)
+        {
             Format.print(ps, "%15.4e", d[j]);
         }
     }
 
-    public void printE(PrintStream ps) {
-        for (int j = 0; j < rows; j++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ps DOCUMENT ME!
+     */
+    public void printE(PrintStream ps)
+    {
+        for (int j = 0; j < rows; j++)
+        {
             Format.print(ps, "%15.4e", e[j]);
         }
     }
 
-    public static void main(String[] args) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param args DOCUMENT ME!
+     */
+    public static void main(String[] args)
+    {
         int n = Integer.parseInt(args[0]);
         double[][] in = new double[n][n];
 
-        for (int i = 0; i < n; i++) {
-            for (int j = 0; j < n; j++) {
+        for (int i = 0; i < n; i++)
+        {
+            for (int j = 0; j < n; j++)
+            {
                 in[i][j] = (double) Math.random();
             }
         }
diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java
index c0ec1c9..2385288 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -18,12 +18,27 @@
 */
 package jalview.math;
 
-public class RotatableMatrix {
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RotatableMatrix
+{
     float[][] matrix;
     float[] temp;
     float[][] rot;
 
-    public RotatableMatrix(int rows, int cols) {
+    /**
+     * Creates a new RotatableMatrix object.
+     *
+     * @param rows DOCUMENT ME!
+     * @param cols DOCUMENT ME!
+     */
+    public RotatableMatrix(int rows, int cols)
+    {
         matrix = new float[rows][cols];
 
         temp = new float[3];
@@ -31,11 +46,23 @@ public class RotatableMatrix {
         rot = new float[3][3];
     }
 
-    public void addElement(int i, int j, float value) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     * @param value DOCUMENT ME!
+     */
+    public void addElement(int i, int j, float value)
+    {
         matrix[i][j] = value;
     }
 
-    public void print() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void print()
+    {
         System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +
             matrix[0][2]);
 
@@ -46,12 +73,20 @@ public class RotatableMatrix {
             matrix[2][2]);
     }
 
-    public void rotate(float degrees, char axis) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param degrees DOCUMENT ME!
+     * @param axis DOCUMENT ME!
+     */
+    public void rotate(float degrees, char axis)
+    {
         float costheta = (float) Math.cos((degrees * Math.PI) / (float) 180.0);
 
         float sintheta = (float) Math.sin((degrees * Math.PI) / (float) 180.0);
 
-        if (axis == 'z') {
+        if (axis == 'z')
+        {
             rot[0][0] = (float) costheta;
 
             rot[0][1] = (float) -sintheta;
@@ -73,7 +108,8 @@ public class RotatableMatrix {
             preMultiply(rot);
         }
 
-        if (axis == 'x') {
+        if (axis == 'x')
+        {
             rot[0][0] = (float) 1.0;
 
             rot[0][1] = (float) 0.0;
@@ -95,7 +131,8 @@ public class RotatableMatrix {
             preMultiply(rot);
         }
 
-        if (axis == 'y') {
+        if (axis == 'y')
+        {
             rot[0][0] = (float) costheta;
 
             rot[0][1] = (float) 0.0;
@@ -118,14 +155,23 @@ public class RotatableMatrix {
         }
     }
 
-    public float[] vectorMultiply(float[] vect) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param vect DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float[] vectorMultiply(float[] vect)
+    {
         temp[0] = vect[0];
 
         temp[1] = vect[1];
 
         temp[2] = vect[2];
 
-        for (int i = 0; i < 3; i++) {
+        for (int i = 0; i < 3; i++)
+        {
             temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +
                 (matrix[i][2] * vect[2]);
         }
@@ -139,41 +185,67 @@ public class RotatableMatrix {
         return vect;
     }
 
-    public void preMultiply(float[][] mat) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param mat DOCUMENT ME!
+     */
+    public void preMultiply(float[][] mat)
+    {
         float[][] tmp = new float[3][3];
 
-        for (int i = 0; i < 3; i++) {
-            for (int j = 0; j < 3; j++) {
+        for (int i = 0; i < 3; i++)
+        {
+            for (int j = 0; j < 3; j++)
+            {
                 tmp[i][j] = (mat[i][0] * matrix[0][j]) +
                     (mat[i][1] * matrix[1][j]) + (mat[i][2] * matrix[2][j]);
             }
         }
 
-        for (int i = 0; i < 3; i++) {
-            for (int j = 0; j < 3; j++) {
+        for (int i = 0; i < 3; i++)
+        {
+            for (int j = 0; j < 3; j++)
+            {
                 matrix[i][j] = tmp[i][j];
             }
         }
     }
 
-    public void postMultiply(float[][] mat) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param mat DOCUMENT ME!
+     */
+    public void postMultiply(float[][] mat)
+    {
         float[][] tmp = new float[3][3];
 
-        for (int i = 0; i < 3; i++) {
-            for (int j = 0; j < 3; j++) {
+        for (int i = 0; i < 3; i++)
+        {
+            for (int j = 0; j < 3; j++)
+            {
                 tmp[i][j] = (matrix[i][0] * mat[0][j]) +
                     (matrix[i][1] * mat[1][j]) + (matrix[i][2] * mat[2][j]);
             }
         }
 
-        for (int i = 0; i < 3; i++) {
-            for (int j = 0; j < 3; j++) {
+        for (int i = 0; i < 3; i++)
+        {
+            for (int j = 0; j < 3; j++)
+            {
                 matrix[i][j] = tmp[i][j];
             }
         }
     }
 
-    public static void main(String[] args) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param args DOCUMENT ME!
+     */
+    public static void main(String[] args)
+    {
         RotatableMatrix m = new RotatableMatrix(3, 3);
 
         m.addElement(0, 0, 1);
@@ -234,7 +306,11 @@ public class RotatableMatrix {
         System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
     }
 
-    public void setIdentity() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void setIdentity()
+    {
         matrix[0][0] = (float) 1.0;
 
         matrix[1][1] = (float) 1.0;
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 9c720ee..1aea477 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,63 +1,78 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
-import java.awt.*;
-
 import java.util.*;
 
+import java.awt.*;
 
-public class Blosum62ColourScheme extends ResidueColourScheme {
-    public Blosum62ColourScheme() {
-        super();
+public class Blosum62ColourScheme
+    extends ResidueColourScheme
+{
+  public Blosum62ColourScheme()
+  {
+    super();
+  }
+
+  public Color findColour(String s, int j)
+  {
+    if ( (threshold != 0) && !aboveThreshold(s, j))
+    {
+      return Color.white;
     }
 
-    public Color findColour(String s, int j) {
-        if ((threshold != 0) && !aboveThreshold(s, j)) {
-            return Color.white;
+    Hashtable hash = (Hashtable) consensus.elementAt(j);
+
+    if (!jalview.util.Comparison.isGap( (s.charAt(0))))
+    {
+      String max = (String) hash.get("maxResidue");
+
+      if (max.indexOf(s) > -1)
+      {
+        return new Color(154, 154, 255);
+      }
+      else
+      {
+        int c = 0;
+        int max_aa = 0;
+        int n = max.length();
+
+        do
+        {
+          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
+              max_aa + 1), s);
         }
+        while (++max_aa < n);
 
-        Hashtable hash = (Hashtable) consensus.elementAt(j);
-
-        if (!jalview.util.Comparison.isGap((s.charAt(0)))) {
-            String max = (String) hash.get("maxResidue");
-
-            if (max.indexOf(s) > -1) {
-                return new Color(154, 154, 255);
-            } else {
-                int c = 0;
-                int max_aa = 0;
-                int n = max.length();
-
-                do {
-                    c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
-                            max_aa + 1), s);
-                } while (++max_aa < n);
-
-                if (c > 0) {
-                    return new Color(204, 204, 255);
-                } else {
-                    return Color.white;
-                }
-            }
-        } else {
-            return Color.white;
+        if (c > 0)
+        {
+          return new Color(204, 204, 255);
         }
+        else
+        {
+          return Color.white;
+        }
+      }
+    }
+    else
+    {
+      return Color.white;
     }
+  }
 }
diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index 186b98a..691cd02 100755
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -21,13 +21,32 @@ package jalview.schemes;
 import java.awt.*;
 
 
-public class BuriedColourScheme extends ScoreColourScheme {
-    public BuriedColourScheme() {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BuriedColourScheme extends ScoreColourScheme
+{
+    /**
+     * Creates a new BuriedColourScheme object.
+     */
+    public BuriedColourScheme()
+    {
         super(ResidueProperties.buried, ResidueProperties.buriedmin,
             ResidueProperties.buriedmax);
     }
 
-    public Color makeColour(float c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color makeColour(float c)
+    {
         return new Color(0, (float) (1.0 - c), c);
     }
 }
diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 17398fc..addf00f 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,274 +1,297 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
-import jalview.datamodel.*;
-
-import java.awt.*;
-
 import java.util.*;
 
+import java.awt.*;
 
-public class ClustalxColourScheme extends ResidueColourScheme {
-    public static Hashtable colhash = new Hashtable();
-    Hashtable[] cons;
-    int[][] cons2;
-    ConsensusColour[] colours;
-    ConsensusColour[] ResidueColour;
-    int size;
-    Consensus[] conses = new Consensus[32];
-    Vector colourTable = new Vector();
+import jalview.datamodel.*;
 
+public class ClustalxColourScheme
+    extends ResidueColourScheme
+{
+  public static Hashtable colhash = new Hashtable();
+  Hashtable[] cons;
+  int[][] cons2;
+  ConsensusColour[] colours;
+  ConsensusColour[] ResidueColour;
+  int size;
+  Consensus[] conses = new Consensus[32];
+  Vector colourTable = new Vector();
+
+  {
+    colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1));
+    colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9));
+    colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1));
+    colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3));
+    colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7));
+    colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5));
+    colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8));
+    colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0));
+  }
+
+  public ClustalxColourScheme(Vector seqs, int maxWidth)
+  {
+    resetClustalX(seqs, maxWidth);
+  }
+
+  public void resetClustalX(Vector seqs, int maxWidth)
+  {
+    cons2 = new int[maxWidth][24];
+
+    int start = 0;
+
+    // Initialize the array
+    for (int j = 0; j < 24; j++)
     {
-        colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
-        colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
-        colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
-        colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
-        colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
-        colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
-        colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
-        colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
-    }
-
-    public ClustalxColourScheme(Vector seqs, int maxWidth) {
-        resetClustalX(seqs, maxWidth);
+      for (int i = 0; i < maxWidth; i++)
+      {
+        cons2[i][j] = 0;
+      }
     }
 
-    public void resetClustalX(Vector seqs, int maxWidth) {
-        cons2 = new int[maxWidth][24];
+    int res;
+    int i;
+    int j = 0;
+    String seq;
 
-        int start = 0;
-
-        // Initialize the array
-        for (int j = 0; j < 24; j++)
-            for (int i = 0; i < maxWidth; i++)
-                cons2[i][j] = 0;
-
-        int res;
-        int i;
-        int j = 0;
-        String seq;
-
-        while (j < seqs.size()) {
-            seq = ((SequenceI) seqs.elementAt(j)).getSequence();
-
-            int end_j = seq.length() - 1;
-
-            for (i = start; i <= end_j; i++) {
-                if ((seq.length() - 1) < i) {
-                    res = 23;
-                } else {
-                    res = ((Integer) ResidueProperties.aaHash.get(seq.charAt(i) +
-                            "")).intValue();
-                }
+    while (j < seqs.size())
+    {
+      seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
 
-                cons2[i][res]++;
-            }
+      int end_j = seq.length() - 1;
 
-            j++;
+      for (i = start; i <= end_j; i++)
+      {
+        if ( (seq.length() - 1) < i)
+        {
+          res = 23;
+        }
+        else
+        {
+          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +
+              "")).intValue();
         }
 
-        this.size = seqs.size();
-        makeColours();
-    }
+        cons2[i][res]++;
+      }
 
-    public void makeColours() {
-        conses[0] = new Consensus("WLVIMAFCYHP", 60);
-        conses[1] = new Consensus("WLVIMAFCYHP", 80);
-        conses[2] = new Consensus("ED", 50);
-        conses[3] = new Consensus("KR", 60);
-        conses[4] = new Consensus("G", 50);
-        conses[5] = new Consensus("N", 50);
-        conses[6] = new Consensus("QE", 50);
-        conses[7] = new Consensus("P", 50);
-        conses[8] = new Consensus("TS", 50);
-
-        conses[26] = new Consensus("A", 85);
-        conses[27] = new Consensus("C", 85);
-        conses[10] = new Consensus("E", 85);
-        conses[11] = new Consensus("F", 85);
-        conses[12] = new Consensus("G", 85);
-        conses[13] = new Consensus("H", 85);
-        conses[14] = new Consensus("I", 85);
-        conses[15] = new Consensus("L", 85);
-        conses[16] = new Consensus("M", 85);
-        conses[17] = new Consensus("N", 85);
-        conses[18] = new Consensus("P", 85);
-        conses[19] = new Consensus("Q", 85);
-        conses[20] = new Consensus("R", 85);
-        conses[21] = new Consensus("S", 85);
-        conses[22] = new Consensus("T", 85);
-        conses[23] = new Consensus("V", 85);
-        conses[24] = new Consensus("W", 85);
-        conses[25] = new Consensus("Y", 85);
-        conses[28] = new Consensus("K", 85);
-        conses[29] = new Consensus("D", 85);
-
-        conses[30] = new Consensus("G", 0);
-        conses[31] = new Consensus("P", 0);
-
-        // We now construct the colours
-        colours = new ConsensusColour[11];
-
-        Consensus[] tmp8 = new Consensus[1];
-        tmp8[0] = conses[30]; //G
-        colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
-
-        Consensus[] tmp9 = new Consensus[1];
-        tmp9[0] = conses[31]; //P
-        colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
-
-        Consensus[] tmp10 = new Consensus[1];
-        tmp10[0] = conses[27]; //C
-        colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
-
-        Consensus[] tmp1 = new Consensus[14];
-        tmp1[0] = conses[0]; //%
-        tmp1[1] = conses[1]; //#
-        tmp1[2] = conses[26]; //A
-        tmp1[3] = conses[27]; //C
-        tmp1[4] = conses[11]; //F
-        tmp1[5] = conses[13]; //H
-        tmp1[6] = conses[14]; //I
-        tmp1[7] = conses[15]; //L
-        tmp1[8] = conses[16]; //M
-        tmp1[9] = conses[23]; //V
-        tmp1[10] = conses[24]; //W
-        tmp1[11] = conses[25]; //Y
-        tmp1[12] = conses[18]; //P
-        tmp1[13] = conses[19]; //p
-        colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
-
-        colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
-
-        Consensus[] tmp2 = new Consensus[5];
-        tmp2[0] = conses[8]; //t
-        tmp2[1] = conses[21]; //S
-        tmp2[2] = conses[22]; //T
-        tmp2[3] = conses[0]; //%
-        tmp2[4] = conses[1]; //#
-        colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
-
-        Consensus[] tmp3 = new Consensus[3];
-
-        tmp3[0] = conses[17]; //N
-        tmp3[1] = conses[29]; //D
-        tmp3[2] = conses[5]; //n
-        colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
-
-        Consensus[] tmp4 = new Consensus[6];
-        tmp4[0] = conses[6]; // q = QE
-        tmp4[1] = conses[19]; //Q
-        tmp4[2] = conses[22]; //E
-        tmp4[3] = conses[3]; //+
-        tmp4[4] = conses[28]; //K
-        tmp4[5] = conses[20]; //R
-        colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
-
-        Consensus[] tmp5 = new Consensus[4];
-        tmp5[0] = conses[3]; //+
-        tmp5[1] = conses[28]; //K
-        tmp5[2] = conses[20]; //R
-        tmp5[3] = conses[19]; //Q
-        colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
-
-        Consensus[] tmp6 = new Consensus[5];
-        tmp6[0] = conses[3]; //-
-        tmp6[1] = conses[29]; //D
-        tmp6[2] = conses[10]; //E
-        tmp6[3] = conses[6]; //q
-        tmp6[4] = conses[19]; //Q
-        colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
-
-        Consensus[] tmp7 = new Consensus[5];
-        tmp7[0] = conses[3]; //-
-        tmp7[1] = conses[29]; //D
-        tmp7[2] = conses[10]; //E
-        tmp7[3] = conses[17]; //N
-        tmp7[4] = conses[2]; //DE
-        colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
-
-        // Now attach the ConsensusColours to the residue letters
-        ResidueColour = new ConsensusColour[20];
-        ResidueColour[0] = colours[0]; // A
-        ResidueColour[1] = colours[4]; // R
-        ResidueColour[2] = colours[2]; // N
-        ResidueColour[3] = colours[6]; // D
-        ResidueColour[4] = colours[0]; // C
-        ResidueColour[5] = colours[3]; // Q
-        ResidueColour[6] = colours[5]; // E
-        ResidueColour[7] = colours[7]; // G
-        ResidueColour[8] = colours[10]; // H
-        ResidueColour[9] = colours[0]; // I
-        ResidueColour[10] = colours[0]; // L
-        ResidueColour[11] = colours[4]; // K
-        ResidueColour[12] = colours[0]; // M
-        ResidueColour[13] = colours[0]; // F
-        ResidueColour[14] = colours[8]; // P
-        ResidueColour[15] = colours[1]; // S
-        ResidueColour[16] = colours[1]; // T
-        ResidueColour[17] = colours[0]; // W
-        ResidueColour[18] = colours[10]; // Y
-        ResidueColour[19] = colours[0]; // V
+      j++;
     }
 
-    public Color findColour(String s) {
-        return Color.pink;
+    this.size = seqs.size();
+    makeColours();
+  }
+
+  public void makeColours()
+  {
+    conses[0] = new Consensus("WLVIMAFCYHP", 60);
+    conses[1] = new Consensus("WLVIMAFCYHP", 80);
+    conses[2] = new Consensus("ED", 50);
+    conses[3] = new Consensus("KR", 60);
+    conses[4] = new Consensus("G", 50);
+    conses[5] = new Consensus("N", 50);
+    conses[6] = new Consensus("QE", 50);
+    conses[7] = new Consensus("P", 50);
+    conses[8] = new Consensus("TS", 50);
+
+    conses[26] = new Consensus("A", 85);
+    conses[27] = new Consensus("C", 85);
+    conses[10] = new Consensus("E", 85);
+    conses[11] = new Consensus("F", 85);
+    conses[12] = new Consensus("G", 85);
+    conses[13] = new Consensus("H", 85);
+    conses[14] = new Consensus("I", 85);
+    conses[15] = new Consensus("L", 85);
+    conses[16] = new Consensus("M", 85);
+    conses[17] = new Consensus("N", 85);
+    conses[18] = new Consensus("P", 85);
+    conses[19] = new Consensus("Q", 85);
+    conses[20] = new Consensus("R", 85);
+    conses[21] = new Consensus("S", 85);
+    conses[22] = new Consensus("T", 85);
+    conses[23] = new Consensus("V", 85);
+    conses[24] = new Consensus("W", 85);
+    conses[25] = new Consensus("Y", 85);
+    conses[28] = new Consensus("K", 85);
+    conses[29] = new Consensus("D", 85);
+
+    conses[30] = new Consensus("G", 0);
+    conses[31] = new Consensus("P", 0);
+
+    // We now construct the colours
+    colours = new ConsensusColour[11];
+
+    Consensus[] tmp8 = new Consensus[1];
+    tmp8[0] = conses[30]; //G
+    colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);
+
+    Consensus[] tmp9 = new Consensus[1];
+    tmp9[0] = conses[31]; //P
+    colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);
+
+    Consensus[] tmp10 = new Consensus[1];
+    tmp10[0] = conses[27]; //C
+    colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);
+
+    Consensus[] tmp1 = new Consensus[14];
+    tmp1[0] = conses[0]; //%
+    tmp1[1] = conses[1]; //#
+    tmp1[2] = conses[26]; //A
+    tmp1[3] = conses[27]; //C
+    tmp1[4] = conses[11]; //F
+    tmp1[5] = conses[13]; //H
+    tmp1[6] = conses[14]; //I
+    tmp1[7] = conses[15]; //L
+    tmp1[8] = conses[16]; //M
+    tmp1[9] = conses[23]; //V
+    tmp1[10] = conses[24]; //W
+    tmp1[11] = conses[25]; //Y
+    tmp1[12] = conses[18]; //P
+    tmp1[13] = conses[19]; //p
+    colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);
+
+    colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);
+
+    Consensus[] tmp2 = new Consensus[5];
+    tmp2[0] = conses[8]; //t
+    tmp2[1] = conses[21]; //S
+    tmp2[2] = conses[22]; //T
+    tmp2[3] = conses[0]; //%
+    tmp2[4] = conses[1]; //#
+    colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);
+
+    Consensus[] tmp3 = new Consensus[3];
+
+    tmp3[0] = conses[17]; //N
+    tmp3[1] = conses[29]; //D
+    tmp3[2] = conses[5]; //n
+    colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);
+
+    Consensus[] tmp4 = new Consensus[6];
+    tmp4[0] = conses[6]; // q = QE
+    tmp4[1] = conses[19]; //Q
+    tmp4[2] = conses[22]; //E
+    tmp4[3] = conses[3]; //+
+    tmp4[4] = conses[28]; //K
+    tmp4[5] = conses[20]; //R
+    colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);
+
+    Consensus[] tmp5 = new Consensus[4];
+    tmp5[0] = conses[3]; //+
+    tmp5[1] = conses[28]; //K
+    tmp5[2] = conses[20]; //R
+    tmp5[3] = conses[19]; //Q
+    colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);
+
+    Consensus[] tmp6 = new Consensus[5];
+    tmp6[0] = conses[3]; //-
+    tmp6[1] = conses[29]; //D
+    tmp6[2] = conses[10]; //E
+    tmp6[3] = conses[6]; //q
+    tmp6[4] = conses[19]; //Q
+    colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);
+
+    Consensus[] tmp7 = new Consensus[5];
+    tmp7[0] = conses[3]; //-
+    tmp7[1] = conses[29]; //D
+    tmp7[2] = conses[10]; //E
+    tmp7[3] = conses[17]; //N
+    tmp7[4] = conses[2]; //DE
+    colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);
+
+    // Now attach the ConsensusColours to the residue letters
+    ResidueColour = new ConsensusColour[20];
+    ResidueColour[0] = colours[0]; // A
+    ResidueColour[1] = colours[4]; // R
+    ResidueColour[2] = colours[2]; // N
+    ResidueColour[3] = colours[6]; // D
+    ResidueColour[4] = colours[0]; // C
+    ResidueColour[5] = colours[3]; // Q
+    ResidueColour[6] = colours[5]; // E
+    ResidueColour[7] = colours[7]; // G
+    ResidueColour[8] = colours[10]; // H
+    ResidueColour[9] = colours[0]; // I
+    ResidueColour[10] = colours[0]; // L
+    ResidueColour[11] = colours[4]; // K
+    ResidueColour[12] = colours[0]; // M
+    ResidueColour[13] = colours[0]; // F
+    ResidueColour[14] = colours[8]; // P
+    ResidueColour[15] = colours[1]; // S
+    ResidueColour[16] = colours[1]; // T
+    ResidueColour[17] = colours[0]; // W
+    ResidueColour[18] = colours[10]; // Y
+    ResidueColour[19] = colours[0]; // V
+  }
+
+  public Color findColour(String s)
+  {
+    return Color.pink;
+  }
+
+  public Color findColour(String s, int j)
+  {
+    if ( (threshold != 0) && !aboveThreshold(s, j))
+    {
+      return Color.white;
     }
 
-    public Color findColour(String s, int j) {
-        if ((threshold != 0) && !aboveThreshold(s, j)) {
-            return Color.white;
-        }
-
-        int i = ((Integer) ResidueProperties.aaHash.get(s)).intValue();
+    int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();
 
-        Color c = Color.white;
+    Color c = Color.white;
 
-        if (i > 19) {
-            return c;
-        }
-
-        for (int k = 0; k < ResidueColour[i].conses.length; k++)
-            if (ResidueColour[i].conses[k].isConserved(cons2, j, size)) {
-                c = ResidueColour[i].c;
-            }
+    if (i > 19)
+    {
+      return c;
+    }
 
-        if (i == 4) {
-            if (conses[27].isConserved(cons2, j, size)) {
-                c = (Color) colhash.get("PINK");
-            }
-        }
+    for (int k = 0; k < ResidueColour[i].conses.length; k++)
+    {
+      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
+      {
+        c = ResidueColour[i].c;
+      }
+    }
 
-        return c;
+    if (i == 4)
+    {
+      if (conses[27].isConserved(cons2, j, size))
+      {
+        c = (Color) colhash.get("PINK");
+      }
     }
-}
 
+    return c;
+  }
+}
 
-class ConsensusColour {
-    Consensus[] conses;
-    Color c;
+class ConsensusColour
+{
+  Consensus[] conses;
+  Color c;
 
-    public ConsensusColour(Color c, Consensus[] conses) {
-        this.conses = conses;
+  public ConsensusColour(Color c, Consensus[] conses)
+  {
+    this.conses = conses;
 
-        //    this.list = list;
-        this.c = c;
-    }
+    //    this.list = list;
+    this.c = c;
+  }
 }
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 2e28695..9cc74f1 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,32 +1,32 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
-import java.awt.*;
-
 import java.util.*;
 
+import java.awt.*;
 
-public interface ColourSchemeI {
-    public Color findColour(String aa);
+public interface ColourSchemeI
+{
+  public Color findColour(String aa);
 
-    public Color findColour(String s, int j);
+  public Color findColour(String s, int j);
 
-    public void setConsensus(Vector v);
+  public void setConsensus(Vector v);
 }
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 0d5ecc7..d27dcf0 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -18,88 +18,187 @@
 */
 package jalview.schemes;
 
-public class ColourSchemeProperty {
+import java.awt.*;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ColourSchemeProperty
+{
+    /** DOCUMENT ME!! */
     public static final int CLUSTAL = 0;
+
+    /** DOCUMENT ME!! */
     public static final int BLOSUM = 1;
+
+    /** DOCUMENT ME!! */
     public static final int PID = 2;
+
+    /** DOCUMENT ME!! */
     public static final int ZAPPO = 3;
+
+    /** DOCUMENT ME!! */
     public static final int HYDROPHOBIC = 4;
+
+    /** DOCUMENT ME!! */
     public static final int HELIX = 5;
+
+    /** DOCUMENT ME!! */
     public static final int STRAND = 6;
+
+    /** DOCUMENT ME!! */
     public static final int TURN = 7;
+
+    /** DOCUMENT ME!! */
     public static final int BURIED = 8;
+
+    /** DOCUMENT ME!! */
     public static final int NUCLEOTIDE = 9;
+
+    /** DOCUMENT ME!! */
     public static final int USER_DEFINED = 10;
+
+    /** DOCUMENT ME!! */
     public static final int NONE = 11;
 
-    public static int getColourIndexFromName(String name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static int getColourIndexFromName(String name)
+    {
         int ret = 11;
 
-        if (name.equalsIgnoreCase("Clustal")) {
+        if (name.equalsIgnoreCase("Clustal"))
+        {
             ret = CLUSTAL;
-        } else if (name.equalsIgnoreCase("Blosum62")) {
+        }
+        else if (name.equalsIgnoreCase("Blosum62"))
+        {
             ret = BLOSUM;
-        } else if (name.equalsIgnoreCase("% Identity")) {
+        }
+        else if (name.equalsIgnoreCase("% Identity"))
+        {
             ret = PID;
-        } else if (name.equalsIgnoreCase("Zappo")) {
+        }
+        else if (name.equalsIgnoreCase("Zappo"))
+        {
             ret = ZAPPO;
-        } else if (name.equalsIgnoreCase("Hydrophobic")) {
+        }
+        else if (name.equalsIgnoreCase("Hydrophobic"))
+        {
             ret = HYDROPHOBIC;
-        } else if (name.equalsIgnoreCase("Helix Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Helix Propensity"))
+        {
             ret = HELIX;
-        } else if (name.equalsIgnoreCase("Strand Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Strand Propensity"))
+        {
             ret = STRAND;
-        } else if (name.equalsIgnoreCase("Turn Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Turn Propensity"))
+        {
             ret = TURN;
-        } else if (name.equalsIgnoreCase("Buried Index")) {
+        }
+        else if (name.equalsIgnoreCase("Buried Index"))
+        {
             ret = BURIED;
-        } else if (name.equalsIgnoreCase("Nucleotide")) {
+        }
+        else if (name.equalsIgnoreCase("Nucleotide"))
+        {
             ret = NUCLEOTIDE;
-        } else if (name.equalsIgnoreCase("User Defined")) {
+        }
+        else if (name.equalsIgnoreCase("User Defined"))
+        {
             ret = USER_DEFINED;
         }
 
         return ret;
     }
 
-    public static String getColourName(ColourSchemeI cs) {
-        if (cs instanceof ConservationColourScheme) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String getColourName(ColourSchemeI cs)
+    {
+        if (cs instanceof ConservationColourScheme)
+        {
             cs = ((ConservationColourScheme) cs).cs;
         }
 
         int index = 11;
 
-        if (cs instanceof ClustalxColourScheme) {
+        if (cs instanceof ClustalxColourScheme)
+        {
             index = CLUSTAL;
-        } else if (cs instanceof Blosum62ColourScheme) {
+        }
+        else if (cs instanceof Blosum62ColourScheme)
+        {
             index = BLOSUM;
-        } else if (cs instanceof PIDColourScheme) {
+        }
+        else if (cs instanceof PIDColourScheme)
+        {
             index = PID;
-        } else if (cs instanceof ZappoColourScheme) {
+        }
+        else if (cs instanceof ZappoColourScheme)
+        {
             index = ZAPPO;
-        } else if (cs instanceof HydrophobicColourScheme) {
+        }
+        else if (cs instanceof HydrophobicColourScheme)
+        {
             index = HYDROPHOBIC;
-        } else if (cs instanceof HelixColourScheme) {
+        }
+        else if (cs instanceof HelixColourScheme)
+        {
             index = HELIX;
-        } else if (cs instanceof StrandColourScheme) {
+        }
+        else if (cs instanceof StrandColourScheme)
+        {
             index = STRAND;
-        } else if (cs instanceof TurnColourScheme) {
+        }
+        else if (cs instanceof TurnColourScheme)
+        {
             index = TURN;
-        } else if (cs instanceof BuriedColourScheme) {
+        }
+        else if (cs instanceof BuriedColourScheme)
+        {
             index = BURIED;
-        } else if (cs instanceof NucleotideColourScheme) {
+        }
+        else if (cs instanceof NucleotideColourScheme)
+        {
             index = NUCLEOTIDE;
-        } else if (cs instanceof UserColourScheme) {
+        }
+        else if (cs instanceof UserColourScheme)
+        {
             index = USER_DEFINED;
         }
 
         return getColourName(index);
     }
 
-    public static String getColourName(int index) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param index DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String getColourName(int index)
+    {
         String ret = null;
 
-        switch (index) {
+        switch (index)
+        {
         case CLUSTAL:
             ret = "Clustal";
 
@@ -164,21 +263,51 @@ public class ColourSchemeProperty {
         return ret;
     }
 
-    public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param al DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
+        String name)
     {
-     return getColour(al.getSequences(), al.getWidth(), name);
+        return getColour(al.getSequences(), al.getWidth(), name);
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seqs DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public static ColourSchemeI getColour(java.util.Vector seqs, int width,
-        String name) {
+        String name)
+    {
         return getColour(seqs, width, getColourIndexFromName(name));
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seqs DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param index DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public static ColourSchemeI getColour(java.util.Vector seqs, int width,
-        int index) {
+        int index)
+    {
         ColourSchemeI cs = null;
 
-        switch (index) {
+        switch (index)
+        {
         case CLUSTAL:
             cs = new ClustalxColourScheme(seqs, width);
 
@@ -230,7 +359,7 @@ public class ColourSchemeProperty {
             break;
 
         case USER_DEFINED:
-            cs = new UserColourScheme(null);
+            cs = new UserColourScheme(new Color[0]);
 
             break;
 
@@ -240,4 +369,38 @@ public class ColourSchemeProperty {
 
         return cs;
     }
+
+    public static Color getAWTColorFromName(String name)
+    {
+      Color col = null;
+      name = name.toLowerCase();
+      if(name.equals("black"))
+        col = Color.black;
+      else if(name.equals("blue"))
+        col = Color.blue;
+      else if(name.equals("cyan"))
+        col = Color.cyan;
+      else if(name.equals("darkGray"))
+        col = Color.darkGray;
+      else if(name.equals("gray"))
+        col = Color.gray;
+      else if(name.equals("green"))
+        col = Color.green;
+      else if(name.equals("lightGray"))
+        col = Color.lightGray;
+      else if(name.equals("magenta"))
+        col = Color.magenta;
+      else if(name.equals("orange"))
+        col = Color.orange;
+      else if(name.equals("pink"))
+        col = Color.pink;
+      else if(name.equals("red"))
+        col = Color.red;
+      else if(name.equals("white"))
+        col = Color.white;
+      else if(name.equals("yellow"))
+        col = Color.yellow;
+
+      return col;
+    }
 }
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 8ca0223..ac895bb 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,72 +1,80 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
-
 ////////////////////////////////////////////
 // This does nothing at all at the moment!!!!!!!!!!
 // AW 15th Dec 2004
 /////////////////////////////////////////
-public class Consensus {
-    int[] mask;
-    double threshold;
-    String maskstr;
-
-    public Consensus(String mask, double threshold) {
-        // this.id = id;
-        //    this.mask = mask;
-        this.maskstr = mask;
-        setMask(mask);
-        this.threshold = threshold;
-    }
+public class Consensus
+{
+  int[] mask;
+  double threshold;
+  String maskstr;
 
-    public void setMask(String s) {
-        this.mask = setNums(s);
+  public Consensus(String mask, double threshold)
+  {
+    // this.id = id;
+    //    this.mask = mask;
+    this.maskstr = mask;
+    setMask(mask);
+    this.threshold = threshold;
+  }
 
-        //   for (int i=0; i < mask.length; i++) {
-        //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
-        // }
-    }
+  public void setMask(String s)
+  {
+    this.mask = setNums(s);
 
-    public boolean isConserved(int[][] cons2, int col, int size) {
-        int tot = 0;
+    //   for (int i=0; i < mask.length; i++) {
+    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // }
+  }
 
-        for (int i = 0; i < mask.length; i++)
-            tot += cons2[col][mask[i]];
+  public boolean isConserved(int[][] cons2, int col, int size)
+  {
+    int tot = 0;
 
-        if ((double) tot > ((threshold * size) / 100)) {
-            return true;
-        }
+    for (int i = 0; i < mask.length; i++)
+    {
+      tot += cons2[col][mask[i]];
+    }
 
-        return false;
+    if ( (double) tot > ( (threshold * size) / 100))
+    {
+      return true;
     }
 
-    int[] setNums(String s) {
-        int[] out = new int[s.length()];
-        int i = 0;
+    return false;
+  }
 
-        while (i < s.length()) {
-            out[i] = ((Integer) ResidueProperties.aaHash.get(s.substring(i,
-                        i + 1))).intValue();
-            i++;
-        }
+  int[] setNums(String s)
+  {
+    int[] out = new int[s.length()];
+    int i = 0;
 
-        return out;
+    while (i < s.length())
+    {
+      out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i,
+          i + 1))).intValue();
+      i++;
     }
+
+    return out;
+  }
 }
diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index bbc0edd..5d0d1f6 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -25,47 +25,88 @@ import java.awt.*;
 import java.util.Vector;
 
 
-public class ConservationColourScheme extends ResidueColourScheme {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ConservationColourScheme extends ResidueColourScheme
+{
+    /** DOCUMENT ME!! */
     public Conservation conserve;
+
+    /** DOCUMENT ME!! */
     public ColourSchemeI cs;
+
+    /** DOCUMENT ME!! */
     public int inc = 30;
 
-    public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs) {
+    /**
+     * Creates a new ConservationColourScheme object.
+     *
+     * @param cons DOCUMENT ME!
+     * @param oldcs DOCUMENT ME!
+     */
+    public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
+    {
         super();
         conserve = cons;
         cs = oldcs;
     }
 
-    public void setConsensus(Vector consensus) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Vector consensus)
+    {
         this.consensus = consensus;
 
-        if (cs != null) {
+        if (cs != null)
+        {
             cs.setConsensus(consensus);
         }
     }
 
-    public Color findColour(String s, int i) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String s, int i)
+    {
         Color c = Color.white;
 
-        if (cs == null) {
+        if (cs == null)
+        {
             return c;
         }
 
         char ch = conserve.getConsSequence().getSequence().charAt(i);
 
-        if ((ch == '*') || (ch == '+')) {
+        if ((ch == '*') || (ch == '+'))
+        {
             c = cs.findColour(s, i);
-        } else {
+        }
+        else
+        {
             int tmp = 10;
             int t = 0;
 
-            if (!jalview.util.Comparison.isGap(ch)) {
+            if (!jalview.util.Comparison.isGap(ch))
+            {
                 t = Integer.parseInt(ch + "");
             }
 
             c = cs.findColour(s, i);
 
-            while (tmp >= t) {
+            while (tmp >= t)
+            {
                 c = lighter(c, inc);
                 tmp--;
             }
@@ -74,26 +115,44 @@ public class ConservationColourScheme extends ResidueColourScheme {
         return c;
     }
 
-    public Color lighter(Color c, int inc) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     * @param inc DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color lighter(Color c, int inc)
+    {
         int red = c.getRed();
         int blue = c.getBlue();
         int green = c.getGreen();
 
-        if (red < (255 - inc)) {
+        if (red < (255 - inc))
+        {
             red = red + inc;
-        } else {
+        }
+        else
+        {
             red = 255;
         }
 
-        if (blue < (255 - inc)) {
+        if (blue < (255 - inc))
+        {
             blue = blue + inc;
-        } else {
+        }
+        else
+        {
             blue = 255;
         }
 
-        if (green < (255 - inc)) {
+        if (green < (255 - inc))
+        {
             green = green + inc;
-        } else {
+        }
+        else
+        {
             green = 255;
         }
 
diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index a25f014..43ddcdc 100755
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -1,33 +1,36 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
 import java.awt.*;
 
+public class HelixColourScheme
+    extends ScoreColourScheme
+{
+  public HelixColourScheme()
+  {
+    super(ResidueProperties.helix, ResidueProperties.helixmin,
+          ResidueProperties.helixmax);
+  }
 
-public class HelixColourScheme extends ScoreColourScheme {
-    public HelixColourScheme() {
-        super(ResidueProperties.helix, ResidueProperties.helixmin,
-            ResidueProperties.helixmax);
-    }
-
-    public Color makeColour(float c) {
-        return new Color(c, (float) 1.0 - c, c);
-    }
+  public Color makeColour(float c)
+  {
+    return new Color(c, (float) 1.0 - c, c);
+  }
 }
diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index eeb43a3..aa04a6c 100755
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -21,13 +21,32 @@ package jalview.schemes;
 import java.awt.*;
 
 
-public class HydrophobicColourScheme extends ScoreColourScheme {
-    public HydrophobicColourScheme() {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class HydrophobicColourScheme extends ScoreColourScheme
+{
+    /**
+     * Creates a new HydrophobicColourScheme object.
+     */
+    public HydrophobicColourScheme()
+    {
         super(ResidueProperties.hyd, ResidueProperties.hydmin,
             ResidueProperties.hydmax);
     }
 
-    public Color makeColour(float c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color makeColour(float c)
+    {
         return new Color(c, (float) 0.0, (float) 1.0 - c);
     }
 }
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 0cca608..8785954 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -21,24 +21,58 @@ package jalview.schemes;
 import java.awt.*;
 
 
-public class NucleotideColourScheme extends ResidueColourScheme {
-    public NucleotideColourScheme() {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme extends ResidueColourScheme
+{
+    /**
+     * Creates a new NucleotideColourScheme object.
+     */
+    public NucleotideColourScheme()
+    {
         super(ResidueProperties.nucleotide, 0);
     }
 
-    public Color findColour(String n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n)
+    {
         // System.out.println("called"); log.debug
         return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
     }
 
-    public Color findColour(String n, int j) {
-        if ((threshold == 0) || aboveThreshold(n, j)) {
-            try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n, int j)
+    {
+        if ((threshold == 0) || aboveThreshold(n, j))
+        {
+            try
+            {
                 return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
-            } catch (Exception ex) {
+            }
+            catch (Exception ex)
+            {
                 return Color.white;
             }
-        } else {
+        }
+        else
+        {
             return Color.white;
         }
     }
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 2535154..cfc9f94 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,67 +1,76 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
+import jalview.datamodel.*;
 
+public class PIDColourScheme
+    extends ResidueColourScheme
+{
+  public Color[] pidColours;
+  public float[] thresholds;
+  SequenceGroup group;
 
-public class PIDColourScheme extends ResidueColourScheme {
-    public Color[] pidColours;
-    public float[] thresholds;
-    SequenceGroup group;
+  public PIDColourScheme()
+  {
+    this.pidColours = ResidueProperties.pidColours;
+    this.thresholds = ResidueProperties.pidThresholds;
+  }
 
-    public PIDColourScheme() {
-        this.pidColours = ResidueProperties.pidColours;
-        this.thresholds = ResidueProperties.pidThresholds;
+  public Color findColour(String s, int j)
+  {
+    if ( (threshold != 0) && !aboveThreshold(s, j))
+    {
+      return Color.white;
     }
 
-    public Color findColour(String s, int j) {
-        if ((threshold != 0) && !aboveThreshold(s, j)) {
-            return Color.white;
-        }
-
-        Color c = Color.white;
-        Hashtable hash = (Hashtable) consensus.elementAt(j);
+    Color c = Color.white;
+    Hashtable hash = (Hashtable) consensus.elementAt(j);
 
-        double sc = 0;
+    double sc = 0;
 
-        if ((Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
-                hash.contains(s)) {
-            sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
-                    "size")).intValue();
+    if ( (Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
+        hash.contains(s))
+    {
+      sc = ( ( (Integer) hash.get(s)).intValue() * 100.0) /
+          ( (Integer) hash.get(
+              "size")).intValue();
 
-            // MC Should be isGap
-            if (!jalview.util.Comparison.isGap((s.charAt(0)))) {
-                for (int i = 0; i < thresholds.length; i++) {
-                    if (sc > thresholds[i]) {
-                        c = pidColours[i];
+      // MC Should be isGap
+      if (!jalview.util.Comparison.isGap( (s.charAt(0))))
+      {
+        for (int i = 0; i < thresholds.length; i++)
+        {
+          if (sc > thresholds[i])
+          {
+            c = pidColours[i];
 
-                        break;
-                    }
-                }
-            }
+            break;
+          }
         }
-
-        return c;
+      }
     }
+
+    return c;
+  }
 }
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index a688593..9c10e7d 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -23,53 +23,122 @@ import java.awt.*;
 import java.util.*;
 
 
-public class ResidueColourScheme implements ColourSchemeI {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
     Color[] colors;
     int threshold = 0;
+
+    /** DOCUMENT ME!! */
     public Vector consensus;
 
-    public ResidueColourScheme(Color[] colors, int threshold) {
+    /**
+     * Creates a new ResidueColourScheme object.
+     *
+     * @param colors DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     */
+    public ResidueColourScheme(Color[] colors, int threshold)
+    {
         this.colors = colors;
         this.threshold = threshold;
     }
 
-    public ResidueColourScheme() {
+    /**
+     * Creates a new ResidueColourScheme object.
+     */
+    public ResidueColourScheme()
+    {
     }
 
-    public void setConsensus(Vector consensus) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Vector consensus)
+    {
         this.consensus = consensus;
     }
 
-    public Color findColour(String aa) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String aa)
+    {
         return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
     }
 
-    public Color findColour(String s, int j) {
-        if ((threshold == 0) || aboveThreshold(s, j)) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String s, int j)
+    {
+        if ((threshold == 0) || aboveThreshold(s, j))
+        {
             return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
-        } else {
+        }
+        else
+        {
             return Color.white;
         }
     }
 
-    public int getThreshold() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getThreshold()
+    {
         return threshold;
     }
 
-    public void setThreshold(int ct) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ct DOCUMENT ME!
+     */
+    public void setThreshold(int ct)
+    {
         threshold = ct;
     }
 
-    public boolean aboveThreshold(String s, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean aboveThreshold(String s, int j)
+    {
         Hashtable hash = (Hashtable) consensus.elementAt(j);
 
         if ((((Integer) hash.get("maxCount")).intValue() != -1) &&
-                hash.contains(s)) {
+                hash.contains(s))
+        {
             ////  resCount////////////////////                  ///////////////seq count////////////
             double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
                     "size")).intValue();
 
-            if (sc >= threshold) {
+            if (sc >= threshold)
+            {
                 return true;
             }
         }
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 552a463..14479a7 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,1131 +1,1199 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
-import java.awt.Color;
-
 import java.util.*;
 
-
-public class ResidueProperties {
-    //Stores residue codes/names and colours and other things
-    public static Hashtable aaHash = new Hashtable(); // stores the number value of the aa
-    public static Hashtable aa3Hash = new Hashtable();
-    public static Hashtable aa2Triplet = new Hashtable();
-    public static Hashtable nucleotideHash = new Hashtable();
-
-    static {
-        aaHash.put("A", new Integer(0));
-        aaHash.put("R", new Integer(1));
-        aaHash.put("N", new Integer(2));
-        aaHash.put("D", new Integer(3));
-        aaHash.put("C", new Integer(4));
-        aaHash.put("Q", new Integer(5));
-        aaHash.put("E", new Integer(6));
-        aaHash.put("G", new Integer(7));
-        aaHash.put("H", new Integer(8));
-        aaHash.put("I", new Integer(9));
-        aaHash.put("L", new Integer(10));
-        aaHash.put("K", new Integer(11));
-        aaHash.put("M", new Integer(12));
-        aaHash.put("F", new Integer(13));
-        aaHash.put("P", new Integer(14));
-        aaHash.put("S", new Integer(15));
-        aaHash.put("T", new Integer(16));
-        aaHash.put("W", new Integer(17));
-        aaHash.put("Y", new Integer(18));
-        aaHash.put("V", new Integer(19));
-        aaHash.put("B", new Integer(20));
-        aaHash.put("Z", new Integer(21));
-        aaHash.put("X", new Integer(22));
-        aaHash.put("a", new Integer(0));
-        aaHash.put("r", new Integer(1));
-        aaHash.put("n", new Integer(2));
-        aaHash.put("d", new Integer(3));
-        aaHash.put("c", new Integer(4));
-        aaHash.put("q", new Integer(5));
-        aaHash.put("e", new Integer(6));
-        aaHash.put("g", new Integer(7));
-        aaHash.put("h", new Integer(8));
-        aaHash.put("i", new Integer(9));
-        aaHash.put("l", new Integer(10));
-        aaHash.put("k", new Integer(11));
-        aaHash.put("m", new Integer(12));
-        aaHash.put("f", new Integer(13));
-        aaHash.put("p", new Integer(14));
-        aaHash.put("s", new Integer(15));
-        aaHash.put("t", new Integer(16));
-        aaHash.put("w", new Integer(17));
-        aaHash.put("y", new Integer(18));
-        aaHash.put("v", new Integer(19));
-        aaHash.put("b", new Integer(20));
-        aaHash.put("z", new Integer(21));
-        aaHash.put("x", new Integer(22));
-        aaHash.put("-", new Integer(23));
-        aaHash.put("*", new Integer(23));
-        aaHash.put(".", new Integer(23));
-        aaHash.put(" ", new Integer(23));
-    }
-
-    static {
-        nucleotideHash.put("A", new Integer(0));
-        nucleotideHash.put("C", new Integer(1));
-        nucleotideHash.put("G", new Integer(2));
-        nucleotideHash.put("T", new Integer(3));
-        nucleotideHash.put("U", new Integer(4));
-    }
-
-    // These numbers should correspond to the indices in the Color hashes
-    public static Hashtable aaSpecialsHash = new Hashtable();
-
-    static {
-        aaSpecialsHash.put("-", new Integer(23));
-        aaSpecialsHash.put("*", new Integer(24));
-        aaSpecialsHash.put(".", new Integer(25));
-        aaSpecialsHash.put(" ", new Integer(26));
-    }
-
-    static {
-        aa3Hash.put("ALA", new Integer(0));
-        aa3Hash.put("ARG", new Integer(1));
-        aa3Hash.put("ASN", new Integer(2));
-        aa3Hash.put("ASP", new Integer(3)); //D
-        aa3Hash.put("CYS", new Integer(4));
-        aa3Hash.put("GLN", new Integer(5)); //Q
-        aa3Hash.put("GLU", new Integer(6)); // E
-        aa3Hash.put("GLY", new Integer(7));
-        aa3Hash.put("HIS", new Integer(8));
-        aa3Hash.put("ILE", new Integer(9));
-        aa3Hash.put("LEU", new Integer(10));
-        aa3Hash.put("LYS", new Integer(11));
-        aa3Hash.put("MET", new Integer(12));
-        aa3Hash.put("PHE", new Integer(13));
-        aa3Hash.put("PRO", new Integer(14));
-        aa3Hash.put("SER", new Integer(15));
-        aa3Hash.put("THR", new Integer(16));
-        aa3Hash.put("TRP", new Integer(17));
-        aa3Hash.put("TYR", new Integer(18));
-        aa3Hash.put("VAL", new Integer(19));
-        aa3Hash.put("B", new Integer(20));
-        aa3Hash.put("Z", new Integer(21));
-        aa3Hash.put("X", new Integer(22));
-        aa3Hash.put("-", new Integer(23));
-        aa3Hash.put("*", new Integer(23));
-        aa3Hash.put(".", new Integer(23));
-        aa3Hash.put(" ", new Integer(23));
-    }
-
-    static {
-        aa2Triplet.put("A", "ALA");
-        aa2Triplet.put("R", "ARG");
-        aa2Triplet.put("N", "ASN");
-        aa2Triplet.put("D", "ASP");
-        aa2Triplet.put("C", "CYS");
-        aa2Triplet.put("Q", "GLN");
-        aa2Triplet.put("E", "GLU");
-        aa2Triplet.put("G", "GLY");
-        aa2Triplet.put("H", "HIS");
-        aa2Triplet.put("I", "ILE");
-        aa2Triplet.put("L", "LEU");
-        aa2Triplet.put("K", "LYS");
-        aa2Triplet.put("M", "MET");
-        aa2Triplet.put("F", "PHE");
-        aa2Triplet.put("P", "PRO");
-        aa2Triplet.put("S", "SER");
-        aa2Triplet.put("T", "THR");
-        aa2Triplet.put("W", "TRP");
-        aa2Triplet.put("Y", "TYR");
-        aa2Triplet.put("V", "VAL");
-    }
-
-    public static String[] aa = {
-        "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
-        "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "
-    };
-    public static Color midBlue = new Color(100, 100, 255);
-    public static Vector scaleColours = new Vector();
-
-    static {
-        scaleColours.addElement(new Color(114, 0, 147));
-        scaleColours.addElement(new Color(156, 0, 98));
-        scaleColours.addElement(new Color(190, 0, 0));
-        scaleColours.addElement(Color.red);
-        scaleColours.addElement(new Color(255, 125, 0));
-        scaleColours.addElement(Color.orange);
-        scaleColours.addElement(new Color(255, 194, 85));
-        scaleColours.addElement(Color.yellow);
-        scaleColours.addElement(new Color(255, 255, 181));
-        scaleColours.addElement(Color.white);
-    }
-
-    public static Color[] taylor = {
-        new Color(204, 255, 0), // A  Greenish-yellowy-yellow
-        new Color(0, 0, 255), // R  Blueish-bluey-blue
-        new Color(204, 0, 255), // N  Blueish-reddy-blue
-        new Color(255, 0, 0), // D  Reddish-reddy-red
-        new Color(255, 255, 0), // C  Yellowish-yellowy-yellow
-        new Color(255, 0, 204), // Q  Reddish-bluey-red
-        new Color(255, 0, 102), // E  Blueish-reddy-red
-        new Color(255, 153, 0), // G  Yellowy-reddy-yellow
-        new Color(0, 102, 255), // H  Greenish-bluey-blue
-        new Color(102, 255, 0), // I  Greenish-yellowy-green
-        new Color(51, 255, 0), // L  Yellowish-greeny-green
-        new Color(102, 0, 255), // K  Reddish-bluey-blue
-        new Color(0, 255, 0), // M  Greenish-greeny-green
-        new Color(0, 255, 102), // F  Blueish-greeny-green
-        new Color(255, 204, 0), // P  Reddish-yellowy-yellow
-        new Color(255, 51, 0), // S  Yellowish-reddy-red
-        new Color(255, 102, 0), // T  Reddish-yellowy-red
-        new Color(0, 204, 255), // W  Blueish-greeny-green
-        new Color(0, 255, 204), // Y  Greenish-bluey-green
-        new Color(153, 255, 0), // V  Yellowish-greeny-yellow
-        Color.white, // B
-        Color.white, // Z
-        Color.white, // X
-        Color.white, // -
-        Color.white, // *
-        Color.white // .
-    };
-    public static Color[] nucleotide = {
-        new Color(100, 247, 63), // A
-        new Color(255, 179, 64), // C
-        new Color(235, 65, 60), // G
-        new Color(60, 136, 238), // T
-        new Color(60, 136, 238) // U
-    };
-    public static Color[] color = {
-        Color.pink, // A
-        midBlue, // R
-        Color.green, // N
-        Color.red, // D
-        Color.yellow, // C
-        Color.green, // Q
-        Color.red, // E
-        Color.magenta, // G
-        Color.red, // H
-        Color.pink, // I
-        Color.pink, // L
-        midBlue, // K
-        Color.pink, // M
-        Color.orange, // F
-        Color.magenta, // P
-        Color.green, // S
-        Color.green, // T
-        Color.orange, // W
-        Color.orange, // Y
-        Color.pink, // V
-        Color.white, // B
-        Color.white, // Z
-        Color.white, // X
-        Color.white, // -
-        Color.white, // *
-        Color.white, // .
-        Color.white // ' '
-    };
-
-    // Dunno where I got these numbers from
-    public static double[] hyd2 = {
-        0.62, //A
-        0.29, //R
-        -0.90, //N
-        -0.74, //D
-        1.19, //C
-        0.48, //Q
-        -0.40, //E
-        1.38, //G
-        -1.50, //H
-        1.06, //I
-        0.64, //L
-        -0.78, //K
-        0.12, //M
-        -0.85, //F
-        -2.53, //P
-        -0.18, //S
-        -0.05, //T
-        1.08, //W
-        0.81, //Y
-        0.0, //V
-        0.26, //B
-        0.0, //Z
-        0.0 //X
-    };
-    public static double[] helix = {
-        1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
-        1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0
-    };
-    public static double helixmin = 0.57;
-    public static double helixmax = 1.51;
-    public static double[] strand = {
-        0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
-        1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0
-    };
-    public static double strandmin = 0.37;
-    public static double strandmax = 1.7;
-    public static double[] turn = {
-        0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
-        0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0
-    };
-    public static double turnmin = 0.47;
-    public static double turnmax = 1.56;
-    public static double[] buried = {
-        1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
-        0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00
-    };
-    public static double buriedmin = 0.05;
-    public static double buriedmax = 4.6;
-
-    // This is hydropathy index
-    // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
-    // 1157, 105-132, 1982
-    public static double[] hyd = {
-        1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9,
-        2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0
-    };
-    public static final double hydmax = 4.5;
-    public static final double hydmin = -3.9;
-
-    //public static final double hydmax = 1.38;
-    //public static final double hydmin = -2.53;
-    static final int[][] BLOSUM62 = {
-        {
-            4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
-            -2, 0, -2, -1, 0, -4
-        },
-        {
-            -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,
-            -3, -1, 0, -1, -4
-        },
-        {
-            -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,
-            3, 0, -1, -4
-        },
-        {
-            -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
-            -3, -3, 4, 1, -1, -4
-        },
-        {
-            0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,
-            -2, -1, -3, -3, -2, -4
-        },
-        {
-            -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
-            -2, 0, 3, -1, -4
-        },
-        {
-            -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
-            -2, 1, 4, -1, -4
-        },
-        {
-            0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
-            -3, -3, -1, -2, -1, -4
-        },
-        {
-            -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,
-            -3, 0, 0, -1, -4
-        },
-        {
-            -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
-            -1, 3, -3, -3, -1, -4
-        },
-        {
-            -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
-            -1, 1, -4, -3, -1, -4
-        },
-        {
-            -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,
-            -2, 0, 1, -1, -4
-        },
-        {
-            -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
-            -1, 1, -3, -1, -1, -4
-        },
-        {
-            -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,
-            -1, -3, -3, -1, -4
-        },
-        {
-            -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
-            -4, -3, -2, -2, -1, -2, -4
-        },
-        {
-            1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
-            -2, 0, 0, 0, -4
-        },
-        {
-            0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
-            -2, 0, -1, -1, 0, -4
-        },
-        {
-            -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
-            11, 2, -3, -4, -3, -2, -4
-        },
-        {
-            -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,
-            7, -1, -3, -2, -1, -4
-        },
-        {
-            0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
-            -1, 4, -3, -2, -1, -4
-        },
-        {
-            -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,
-            -3, 4, 1, -1, -4
-        },
-        {
-            -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
-            -2, 1, 4, -1, -4
-        },
-        {
-            0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,
-            -1, -1, -1, -1, -1, -4
-        },
-        {
-            -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
-            -4, -4, -4, -4, -4, -4, 1
-        },
-    };
-    static final int[][] PAM250 = {
-        {
-            2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,
-            0, 0, 0, -8
-        },
-        {
-            -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
-            -2, -1, 0, -1, -8
-        },
-        {
-            0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
-            2, 1, 0, -8
-        },
-        {
-            0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,
-            3, 3, -1, -8
-        },
-        {
-            -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
-            -8, 0, -2, -4, -5, -3, -8
-        },
-        {
-            0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
-            -2, 1, 3, -1, -8
-        },
-        {
-            0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,
-            3, 3, -1, -8
-        },
-        {
-            1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
-            -1, 0, 0, -1, -8
-        },
-        {
-            -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
-            -2, 1, 2, -1, -8
-        },
-        {
-            -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
-            -1, 4, -2, -2, -1, -8
-        },
-        {
-            -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
-            -1, 2, -3, -3, -1, -8
-        },
-        {
-            -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,
-            1, 0, -1, -8
-        },
-        {
-            -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,
-            2, -2, -2, -1, -8
-        },
-        {
-            -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,
-            -1, -4, -5, -2, -8
-        },
-        {
-            1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
-            -1, -1, 0, -1, -8
-        },
-        {
-            1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,
-            0, 0, 0, -8
-        },
-        {
-            1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,
-            0, -1, 0, -8
-        },
-        {
-            -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,
-            0, -6, -5, -6, -4, -8
-        },
-        {
-            -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
-            10, -2, -3, -4, -2, -8
-        },
-        {
-            0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
-            -2, 4, -2, -2, -1, -8
-        },
-        {
-            0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,
-            3, 2, -1, -8
-        },
-        {
-            0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,
-            2, 3, -1, -8
-        },
-        {
-            0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
-            -2, -1, -1, -1, -1, -8
-        },
-        {
-            -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
-            -8, -8, -8, -8, -8, -8, 1
-        },
-    };
-    public static Hashtable ssHash = new Hashtable(); // stores the number value of the aa
-
-    static {
-        ssHash.put("H", Color.magenta);
-        ssHash.put("E", Color.yellow);
-        ssHash.put("-", Color.white);
-        ssHash.put(".", Color.white);
-        ssHash.put("S", Color.cyan);
-        ssHash.put("T", Color.blue);
-        ssHash.put("G", Color.pink);
-        ssHash.put("I", Color.pink);
-        ssHash.put("B", Color.yellow);
-    }
-
-    static final int[][] DNA = {
-        { 5, -4, -4, -4, 1 }, // C
-        { -4, 5, -4, -4, 1 }, // T
-        { -4, -4, 5, -4, 1 }, // A
-        { -4, -4, -4, 5, 1 }, // G
-        { 1, 1, 1, 1, 1 }, // -
-    };
-    public static Color[] pidColours = {
-        midBlue, new Color(153, 153, 255), 
-        //    Color.lightGray,
-        new Color(204, 204, 255),
-    };
-    public static float[] pidThresholds = { 80, 60, 40, };
-    public static Hashtable codonHash = new Hashtable();
-    public static Vector Lys = new Vector();
-    public static Vector Asn = new Vector();
-    public static Vector Gln = new Vector();
-    public static Vector His = new Vector();
-    public static Vector Glu = new Vector();
-    public static Vector Asp = new Vector();
-    public static Vector Tyr = new Vector();
-    public static Vector Thr = new Vector();
-    public static Vector Pro = new Vector();
-    public static Vector Ala = new Vector();
-    public static Vector Ser = new Vector();
-    public static Vector Arg = new Vector();
-    public static Vector Gly = new Vector();
-    public static Vector Trp = new Vector();
-    public static Vector Cys = new Vector();
-    public static Vector Ile = new Vector();
-    public static Vector Met = new Vector();
-    public static Vector Leu = new Vector();
-    public static Vector Val = new Vector();
-    public static Vector Phe = new Vector();
-    public static Vector STOP = new Vector();
-
-    static {
-        codonHash.put("K", Lys);
-        codonHash.put("N", Asn);
-        codonHash.put("Q", Gln);
-        codonHash.put("H", His);
-        codonHash.put("E", Glu);
-        codonHash.put("D", Asp);
-        codonHash.put("Y", Tyr);
-        codonHash.put("T", Thr);
-        codonHash.put("P", Pro);
-        codonHash.put("A", Ala);
-        codonHash.put("S", Ser);
-        codonHash.put("R", Arg);
-        codonHash.put("G", Gly);
-        codonHash.put("W", Trp);
-        codonHash.put("C", Cys);
-        codonHash.put("I", Ile);
-        codonHash.put("M", Met);
-        codonHash.put("L", Leu);
-        codonHash.put("V", Val);
-        codonHash.put("F", Phe);
-        codonHash.put("STOP", STOP);
+import java.awt.*;
+
+public class ResidueProperties
+{
+  //Stores residue codes/names and colours and other things
+  public static Hashtable aaHash = new Hashtable(); // stores the number value of the aa
+  public static Hashtable aa3Hash = new Hashtable();
+  public static Hashtable aa2Triplet = new Hashtable();
+  public static Hashtable nucleotideHash = new Hashtable();
+
+  static
+  {
+    aaHash.put("A", new Integer(0));
+    aaHash.put("R", new Integer(1));
+    aaHash.put("N", new Integer(2));
+    aaHash.put("D", new Integer(3));
+    aaHash.put("C", new Integer(4));
+    aaHash.put("Q", new Integer(5));
+    aaHash.put("E", new Integer(6));
+    aaHash.put("G", new Integer(7));
+    aaHash.put("H", new Integer(8));
+    aaHash.put("I", new Integer(9));
+    aaHash.put("L", new Integer(10));
+    aaHash.put("K", new Integer(11));
+    aaHash.put("M", new Integer(12));
+    aaHash.put("F", new Integer(13));
+    aaHash.put("P", new Integer(14));
+    aaHash.put("S", new Integer(15));
+    aaHash.put("T", new Integer(16));
+    aaHash.put("W", new Integer(17));
+    aaHash.put("Y", new Integer(18));
+    aaHash.put("V", new Integer(19));
+    aaHash.put("B", new Integer(20));
+    aaHash.put("Z", new Integer(21));
+    aaHash.put("X", new Integer(22));
+    aaHash.put("a", new Integer(0));
+    aaHash.put("r", new Integer(1));
+    aaHash.put("n", new Integer(2));
+    aaHash.put("d", new Integer(3));
+    aaHash.put("c", new Integer(4));
+    aaHash.put("q", new Integer(5));
+    aaHash.put("e", new Integer(6));
+    aaHash.put("g", new Integer(7));
+    aaHash.put("h", new Integer(8));
+    aaHash.put("i", new Integer(9));
+    aaHash.put("l", new Integer(10));
+    aaHash.put("k", new Integer(11));
+    aaHash.put("m", new Integer(12));
+    aaHash.put("f", new Integer(13));
+    aaHash.put("p", new Integer(14));
+    aaHash.put("s", new Integer(15));
+    aaHash.put("t", new Integer(16));
+    aaHash.put("w", new Integer(17));
+    aaHash.put("y", new Integer(18));
+    aaHash.put("v", new Integer(19));
+    aaHash.put("b", new Integer(20));
+    aaHash.put("z", new Integer(21));
+    aaHash.put("x", new Integer(22));
+    aaHash.put("-", new Integer(23));
+    aaHash.put("*", new Integer(23));
+    aaHash.put(".", new Integer(23));
+    aaHash.put(" ", new Integer(23));
+  }
+
+  static
+  {
+    nucleotideHash.put("A", new Integer(0));
+    nucleotideHash.put("C", new Integer(1));
+    nucleotideHash.put("G", new Integer(2));
+    nucleotideHash.put("T", new Integer(3));
+    nucleotideHash.put("U", new Integer(4));
+  }
+
+  // These numbers should correspond to the indices in the Color hashes
+  public static Hashtable aaSpecialsHash = new Hashtable();
+
+  static
+  {
+    aaSpecialsHash.put("-", new Integer(23));
+    aaSpecialsHash.put("*", new Integer(24));
+    aaSpecialsHash.put(".", new Integer(25));
+    aaSpecialsHash.put(" ", new Integer(26));
+  }
+
+  static
+  {
+    aa3Hash.put("ALA", new Integer(0));
+    aa3Hash.put("ARG", new Integer(1));
+    aa3Hash.put("ASN", new Integer(2));
+    aa3Hash.put("ASP", new Integer(3)); //D
+    aa3Hash.put("CYS", new Integer(4));
+    aa3Hash.put("GLN", new Integer(5)); //Q
+    aa3Hash.put("GLU", new Integer(6)); // E
+    aa3Hash.put("GLY", new Integer(7));
+    aa3Hash.put("HIS", new Integer(8));
+    aa3Hash.put("ILE", new Integer(9));
+    aa3Hash.put("LEU", new Integer(10));
+    aa3Hash.put("LYS", new Integer(11));
+    aa3Hash.put("MET", new Integer(12));
+    aa3Hash.put("PHE", new Integer(13));
+    aa3Hash.put("PRO", new Integer(14));
+    aa3Hash.put("SER", new Integer(15));
+    aa3Hash.put("THR", new Integer(16));
+    aa3Hash.put("TRP", new Integer(17));
+    aa3Hash.put("TYR", new Integer(18));
+    aa3Hash.put("VAL", new Integer(19));
+    aa3Hash.put("B", new Integer(20));
+    aa3Hash.put("Z", new Integer(21));
+    aa3Hash.put("X", new Integer(22));
+    aa3Hash.put("-", new Integer(23));
+    aa3Hash.put("*", new Integer(23));
+    aa3Hash.put(".", new Integer(23));
+    aa3Hash.put(" ", new Integer(23));
+  }
+
+  static
+  {
+    aa2Triplet.put("A", "ALA");
+    aa2Triplet.put("R", "ARG");
+    aa2Triplet.put("N", "ASN");
+    aa2Triplet.put("D", "ASP");
+    aa2Triplet.put("C", "CYS");
+    aa2Triplet.put("Q", "GLN");
+    aa2Triplet.put("E", "GLU");
+    aa2Triplet.put("G", "GLY");
+    aa2Triplet.put("H", "HIS");
+    aa2Triplet.put("I", "ILE");
+    aa2Triplet.put("L", "LEU");
+    aa2Triplet.put("K", "LYS");
+    aa2Triplet.put("M", "MET");
+    aa2Triplet.put("F", "PHE");
+    aa2Triplet.put("P", "PRO");
+    aa2Triplet.put("S", "SER");
+    aa2Triplet.put("T", "THR");
+    aa2Triplet.put("W", "TRP");
+    aa2Triplet.put("Y", "TYR");
+    aa2Triplet.put("V", "VAL");
+  }
+
+  public static String[] aa =
+      {
+      "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
+      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "
+  };
+  public static Color midBlue = new Color(100, 100, 255);
+  public static Vector scaleColours = new Vector();
+
+  static
+  {
+    scaleColours.addElement(new Color(114, 0, 147));
+    scaleColours.addElement(new Color(156, 0, 98));
+    scaleColours.addElement(new Color(190, 0, 0));
+    scaleColours.addElement(Color.red);
+    scaleColours.addElement(new Color(255, 125, 0));
+    scaleColours.addElement(Color.orange);
+    scaleColours.addElement(new Color(255, 194, 85));
+    scaleColours.addElement(Color.yellow);
+    scaleColours.addElement(new Color(255, 255, 181));
+    scaleColours.addElement(Color.white);
+  }
+
+  public static Color[] taylor =
+      {
+      new Color(204, 255, 0), // A  Greenish-yellowy-yellow
+      new Color(0, 0, 255), // R  Blueish-bluey-blue
+      new Color(204, 0, 255), // N  Blueish-reddy-blue
+      new Color(255, 0, 0), // D  Reddish-reddy-red
+      new Color(255, 255, 0), // C  Yellowish-yellowy-yellow
+      new Color(255, 0, 204), // Q  Reddish-bluey-red
+      new Color(255, 0, 102), // E  Blueish-reddy-red
+      new Color(255, 153, 0), // G  Yellowy-reddy-yellow
+      new Color(0, 102, 255), // H  Greenish-bluey-blue
+      new Color(102, 255, 0), // I  Greenish-yellowy-green
+      new Color(51, 255, 0), // L  Yellowish-greeny-green
+      new Color(102, 0, 255), // K  Reddish-bluey-blue
+      new Color(0, 255, 0), // M  Greenish-greeny-green
+      new Color(0, 255, 102), // F  Blueish-greeny-green
+      new Color(255, 204, 0), // P  Reddish-yellowy-yellow
+      new Color(255, 51, 0), // S  Yellowish-reddy-red
+      new Color(255, 102, 0), // T  Reddish-yellowy-red
+      new Color(0, 204, 255), // W  Blueish-greeny-green
+      new Color(0, 255, 204), // Y  Greenish-bluey-green
+      new Color(153, 255, 0), // V  Yellowish-greeny-yellow
+      Color.white, // B
+      Color.white, // Z
+      Color.white, // X
+      Color.white, // -
+      Color.white, // *
+      Color.white // .
+  };
+  public static Color[] nucleotide =
+      {
+      new Color(100, 247, 63), // A
+      new Color(255, 179, 64), // C
+      new Color(235, 65, 60), // G
+      new Color(60, 136, 238), // T
+      new Color(60, 136, 238) // U
+  };
+  public static Color[] color =
+      {
+      Color.pink, // A
+      midBlue, // R
+      Color.green, // N
+      Color.red, // D
+      Color.yellow, // C
+      Color.green, // Q
+      Color.red, // E
+      Color.magenta, // G
+      Color.red, // H
+      Color.pink, // I
+      Color.pink, // L
+      midBlue, // K
+      Color.pink, // M
+      Color.orange, // F
+      Color.magenta, // P
+      Color.green, // S
+      Color.green, // T
+      Color.orange, // W
+      Color.orange, // Y
+      Color.pink, // V
+      Color.white, // B
+      Color.white, // Z
+      Color.white, // X
+      Color.white, // -
+      Color.white, // *
+      Color.white, // .
+      Color.white // ' '
+  };
+
+  // Dunno where I got these numbers from
+  public static double[] hyd2 =
+      {
+      0.62, //A
+      0.29, //R
+      -0.90, //N
+      -0.74, //D
+      1.19, //C
+      0.48, //Q
+      -0.40, //E
+      1.38, //G
+      -1.50, //H
+      1.06, //I
+      0.64, //L
+      -0.78, //K
+      0.12, //M
+      -0.85, //F
+      -2.53, //P
+      -0.18, //S
+      -0.05, //T
+      1.08, //W
+      0.81, //Y
+      0.0, //V
+      0.26, //B
+      0.0, //Z
+      0.0 //X
+  };
+  public static double[] helix =
+      {
+      1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
+      1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0
+  };
+  public static double helixmin = 0.57;
+  public static double helixmax = 1.51;
+  public static double[] strand =
+      {
+      0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
+      1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0
+  };
+  public static double strandmin = 0.37;
+  public static double strandmax = 1.7;
+  public static double[] turn =
+      {
+      0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
+      0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0
+  };
+  public static double turnmin = 0.47;
+  public static double turnmax = 1.56;
+  public static double[] buried =
+      {
+      1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
+      0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00
+  };
+  public static double buriedmin = 0.05;
+  public static double buriedmax = 4.6;
+
+  // This is hydropathy index
+  // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
+  // 1157, 105-132, 1982
+  public static double[] hyd =
+      {
+      1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9,
+      2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0
+  };
+  public static final double hydmax = 4.5;
+  public static final double hydmin = -3.9;
+
+  //public static final double hydmax = 1.38;
+  //public static final double hydmin = -2.53;
+  static final int[][] BLOSUM62 =
+      {
+      {
+      4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
+      -2, 0, -2, -1, 0, -4
+  },
+      {
+      -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,
+      -3, -1, 0, -1, -4
+  },
+      {
+      -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,
+      3, 0, -1, -4
+  },
+      {
+      -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
+      -3, -3, 4, 1, -1, -4
+  },
+      {
+      0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,
+      -2, -1, -3, -3, -2, -4
+  },
+      {
+      -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
+      -2, 0, 3, -1, -4
+  },
+      {
+      -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
+      -2, 1, 4, -1, -4
+  },
+      {
+      0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
+      -3, -3, -1, -2, -1, -4
+  },
+      {
+      -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,
+      -3, 0, 0, -1, -4
+  },
+      {
+      -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
+      -1, 3, -3, -3, -1, -4
+  },
+      {
+      -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
+      -1, 1, -4, -3, -1, -4
+  },
+      {
+      -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,
+      -2, 0, 1, -1, -4
+  },
+      {
+      -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
+      -1, 1, -3, -1, -1, -4
+  },
+      {
+      -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,
+      -1, -3, -3, -1, -4
+  },
+      {
+      -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
+      -4, -3, -2, -2, -1, -2, -4
+  },
+      {
+      1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
+      -2, 0, 0, 0, -4
+  },
+      {
+      0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
+      -2, 0, -1, -1, 0, -4
+  },
+      {
+      -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
+      11, 2, -3, -4, -3, -2, -4
+  },
+      {
+      -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,
+      7, -1, -3, -2, -1, -4
+  },
+      {
+      0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
+      -1, 4, -3, -2, -1, -4
+  },
+      {
+      -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,
+      -3, 4, 1, -1, -4
+  },
+      {
+      -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
+      -2, 1, 4, -1, -4
+  },
+      {
+      0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,
+      -1, -1, -1, -1, -1, -4
+  },
+      {
+      -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
+      -4, -4, -4, -4, -4, -4, 1
+  },
+  };
+  static final int[][] PAM250 =
+      {
+      {
+      2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,
+      0, 0, 0, -8
+  },
+      {
+      -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
+      -2, -1, 0, -1, -8
+  },
+      {
+      0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
+      2, 1, 0, -8
+  },
+      {
+      0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,
+      3, 3, -1, -8
+  },
+      {
+      -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
+      -8, 0, -2, -4, -5, -3, -8
+  },
+      {
+      0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
+      -2, 1, 3, -1, -8
+  },
+      {
+      0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,
+      3, 3, -1, -8
+  },
+      {
+      1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
+      -1, 0, 0, -1, -8
+  },
+      {
+      -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
+      -2, 1, 2, -1, -8
+  },
+      {
+      -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
+      -1, 4, -2, -2, -1, -8
+  },
+      {
+      -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
+      -1, 2, -3, -3, -1, -8
+  },
+      {
+      -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,
+      1, 0, -1, -8
+  },
+      {
+      -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,
+      2, -2, -2, -1, -8
+  },
+      {
+      -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,
+      -1, -4, -5, -2, -8
+  },
+      {
+      1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
+      -1, -1, 0, -1, -8
+  },
+      {
+      1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,
+      0, 0, 0, -8
+  },
+      {
+      1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,
+      0, -1, 0, -8
+  },
+      {
+      -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,
+      0, -6, -5, -6, -4, -8
+  },
+      {
+      -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
+      10, -2, -3, -4, -2, -8
+  },
+      {
+      0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
+      -2, 4, -2, -2, -1, -8
+  },
+      {
+      0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,
+      3, 2, -1, -8
+  },
+      {
+      0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,
+      2, 3, -1, -8
+  },
+      {
+      0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
+      -2, -1, -1, -1, -1, -8
+  },
+      {
+      -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
+      -8, -8, -8, -8, -8, -8, 1
+  },
+  };
+  public static Hashtable ssHash = new Hashtable(); // stores the number value of the aa
+
+  static
+  {
+    ssHash.put("H", Color.magenta);
+    ssHash.put("E", Color.yellow);
+    ssHash.put("-", Color.white);
+    ssHash.put(".", Color.white);
+    ssHash.put("S", Color.cyan);
+    ssHash.put("T", Color.blue);
+    ssHash.put("G", Color.pink);
+    ssHash.put("I", Color.pink);
+    ssHash.put("B", Color.yellow);
+  }
+
+  static final int[][] DNA =
+      {
+      {
+      5, -4, -4, -4, 1}, // C
+      {
+      -4, 5, -4, -4, 1}, // T
+      {
+      -4, -4, 5, -4, 1}, // A
+      {
+      -4, -4, -4, 5, 1}, // G
+      {
+      1, 1, 1, 1, 1}, // -
+  };
+  public static Color[] pidColours =
+      {
+      midBlue, new Color(153, 153, 255),
+      //    Color.lightGray,
+      new Color(204, 204, 255),
+  };
+  public static float[] pidThresholds =
+      {
+      80, 60, 40, };
+  public static Hashtable codonHash = new Hashtable();
+  public static Vector Lys = new Vector();
+  public static Vector Asn = new Vector();
+  public static Vector Gln = new Vector();
+  public static Vector His = new Vector();
+  public static Vector Glu = new Vector();
+  public static Vector Asp = new Vector();
+  public static Vector Tyr = new Vector();
+  public static Vector Thr = new Vector();
+  public static Vector Pro = new Vector();
+  public static Vector Ala = new Vector();
+  public static Vector Ser = new Vector();
+  public static Vector Arg = new Vector();
+  public static Vector Gly = new Vector();
+  public static Vector Trp = new Vector();
+  public static Vector Cys = new Vector();
+  public static Vector Ile = new Vector();
+  public static Vector Met = new Vector();
+  public static Vector Leu = new Vector();
+  public static Vector Val = new Vector();
+  public static Vector Phe = new Vector();
+  public static Vector STOP = new Vector();
+
+  static
+  {
+    codonHash.put("K", Lys);
+    codonHash.put("N", Asn);
+    codonHash.put("Q", Gln);
+    codonHash.put("H", His);
+    codonHash.put("E", Glu);
+    codonHash.put("D", Asp);
+    codonHash.put("Y", Tyr);
+    codonHash.put("T", Thr);
+    codonHash.put("P", Pro);
+    codonHash.put("A", Ala);
+    codonHash.put("S", Ser);
+    codonHash.put("R", Arg);
+    codonHash.put("G", Gly);
+    codonHash.put("W", Trp);
+    codonHash.put("C", Cys);
+    codonHash.put("I", Ile);
+    codonHash.put("M", Met);
+    codonHash.put("L", Leu);
+    codonHash.put("V", Val);
+    codonHash.put("F", Phe);
+    codonHash.put("STOP", STOP);
+  }
+
+  public static Hashtable codonHash2 = new Hashtable();
+
+  static
+  {
+    codonHash2.put("AAA", "K");
+    codonHash2.put("AAG", "K");
+    codonHash2.put("AAC", "N");
+    codonHash2.put("AAT", "N");
+
+    codonHash2.put("CAA", "E");
+    codonHash2.put("CAG", "E");
+    codonHash2.put("CAC", "H");
+    codonHash2.put("CAT", "H");
+
+    codonHash2.put("GAA", "Q");
+    codonHash2.put("GAG", "Q");
+    codonHash2.put("GAC", "D");
+    codonHash2.put("GAT", "D");
+
+    codonHash2.put("TAC", "Y");
+    codonHash2.put("TAT", "Y");
+
+    codonHash2.put("ACA", "T");
+    codonHash2.put("AAG", "T");
+    codonHash2.put("ACC", "T");
+    codonHash2.put("ACT", "T");
+
+    codonHash2.put("CCA", "P");
+    codonHash2.put("CCG", "P");
+    codonHash2.put("CCC", "P");
+    codonHash2.put("CCT", "P");
+
+    codonHash2.put("GCA", "A");
+    codonHash2.put("GCG", "A");
+    codonHash2.put("GCC", "A");
+    codonHash2.put("GCT", "A");
+
+    codonHash2.put("TCA", "S");
+    codonHash2.put("TCG", "S");
+    codonHash2.put("TCC", "S");
+    codonHash2.put("TCT", "S");
+    codonHash2.put("AGC", "S");
+    codonHash2.put("AGT", "S");
+
+    codonHash2.put("AGA", "R");
+    codonHash2.put("AGG", "R");
+    codonHash2.put("CGA", "R");
+    codonHash2.put("CGG", "R");
+    codonHash2.put("CGC", "R");
+    codonHash2.put("CGT", "R");
+
+    codonHash2.put("GGA", "G");
+    codonHash2.put("GGG", "G");
+    codonHash2.put("GGC", "G");
+    codonHash2.put("GGT", "G");
+
+    codonHash2.put("TGA", "*");
+    codonHash2.put("TAA", "*");
+    codonHash2.put("TAG", "*");
+
+    codonHash2.put("TGG", "W");
+
+    codonHash2.put("TGC", "C");
+    codonHash2.put("TGT", "C");
+
+    codonHash2.put("ATA", "I");
+    codonHash2.put("ATC", "I");
+    codonHash2.put("ATT", "I");
+
+    codonHash2.put("ATG", "M");
+
+    codonHash2.put("CTA", "L");
+    codonHash2.put("CTG", "L");
+    codonHash2.put("CTC", "L");
+    codonHash2.put("CTT", "L");
+    codonHash2.put("TTA", "L");
+    codonHash2.put("TTG", "L");
+
+    codonHash2.put("GTA", "V");
+    codonHash2.put("GTG", "V");
+    codonHash2.put("GTC", "V");
+    codonHash2.put("GTT", "V");
+
+    codonHash2.put("TTC", "F");
+    codonHash2.put("TTT", "F");
+  }
+
+  static
+  {
+    Lys.addElement("AAA");
+    Lys.addElement("AAG");
+    Asn.addElement("AAC");
+    Asn.addElement("AAT");
+
+    Gln.addElement("CAA");
+    Gln.addElement("CAG");
+    His.addElement("CAC");
+    His.addElement("CAT");
+
+    Glu.addElement("GAA");
+    Glu.addElement("GAG");
+    Asp.addElement("GAC");
+    Asp.addElement("GAT");
+
+    Tyr.addElement("TAC");
+    Tyr.addElement("TAT");
+
+    Thr.addElement("ACA");
+    Thr.addElement("ACG");
+    Thr.addElement("ACC");
+    Thr.addElement("ACT");
+
+    Pro.addElement("CCA");
+    Pro.addElement("CCG");
+    Pro.addElement("CCC");
+    Pro.addElement("CCT");
+
+    Ala.addElement("GCA");
+    Ala.addElement("GCG");
+    Ala.addElement("GCC");
+    Ala.addElement("GCT");
+
+    Ser.addElement("TCA");
+    Ser.addElement("TCG");
+    Ser.addElement("TCC");
+    Ser.addElement("TCT");
+    Ser.addElement("AGC");
+    Ser.addElement("AGT");
+
+    Arg.addElement("AGA");
+    Arg.addElement("AGG");
+    Arg.addElement("CGA");
+    Arg.addElement("CGG");
+    Arg.addElement("CGC");
+    Arg.addElement("CGT");
+
+    Gly.addElement("GGA");
+    Gly.addElement("GGG");
+    Gly.addElement("GGC");
+    Gly.addElement("GGT");
+
+    STOP.addElement("TGA");
+    STOP.addElement("TAA");
+    STOP.addElement("TAG");
+
+    Trp.addElement("TGG");
+
+    Cys.addElement("TGC");
+    Cys.addElement("TGT");
+
+    Ile.addElement("ATA");
+    Ile.addElement("ATC");
+    Ile.addElement("ATT");
+
+    Met.addElement("ATG");
+
+    Leu.addElement("CTA");
+    Leu.addElement("CTG");
+    Leu.addElement("CTC");
+    Leu.addElement("CTT");
+    Leu.addElement("TTA");
+    Leu.addElement("TTG");
+
+    Val.addElement("GTA");
+    Val.addElement("GTG");
+    Val.addElement("GTC");
+    Val.addElement("GTT");
+
+    Phe.addElement("TTC");
+    Phe.addElement("TTT");
+  }
+
+  public static Color[][] groupColors =
+      {
+      {
+      Color.red, Color.red.brighter(), Color.red.brighter().brighter()},
+      {
+      Color.orange, Color.orange.brighter(),
+      Color.orange.brighter().brighter()
+  },
+      {
+      Color.green, Color.green.brighter(), Color.green.brighter().brighter()},
+      {
+      Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter()},
+      {
+      Color.magenta, Color.magenta.brighter(),
+      Color.magenta.brighter().brighter()
+  },
+      {
+      Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter()},
+      {
+      Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter()},
+  };
+
+  //Stores residue codes/names and colours and other things
+  public static Hashtable propHash = new Hashtable();
+  public static Hashtable hydrophobic = new Hashtable();
+  public static Hashtable polar = new Hashtable();
+  public static Hashtable small = new Hashtable();
+  public static Hashtable positive = new Hashtable();
+  public static Hashtable negative = new Hashtable();
+  public static Hashtable charged = new Hashtable();
+  public static Hashtable aromatic = new Hashtable();
+  public static Hashtable aliphatic = new Hashtable();
+  public static Hashtable tiny = new Hashtable();
+  public static Hashtable proline = new Hashtable();
+
+  static
+  {
+    hydrophobic.put("I", new Integer(1));
+    hydrophobic.put("L", new Integer(1));
+    hydrophobic.put("V", new Integer(1));
+    hydrophobic.put("C", new Integer(1));
+    hydrophobic.put("A", new Integer(1));
+    hydrophobic.put("G", new Integer(1));
+    hydrophobic.put("M", new Integer(1));
+    hydrophobic.put("F", new Integer(1));
+    hydrophobic.put("Y", new Integer(1));
+    hydrophobic.put("W", new Integer(1));
+    hydrophobic.put("H", new Integer(1));
+    hydrophobic.put("K", new Integer(1));
+    hydrophobic.put("X", new Integer(1));
+    hydrophobic.put("-", new Integer(1));
+    hydrophobic.put("*", new Integer(1));
+    hydrophobic.put("R", new Integer(0));
+    hydrophobic.put("E", new Integer(0));
+    hydrophobic.put("Q", new Integer(0));
+    hydrophobic.put("D", new Integer(0));
+    hydrophobic.put("N", new Integer(0));
+    hydrophobic.put("S", new Integer(0));
+    hydrophobic.put("T", new Integer(0));
+    hydrophobic.put("P", new Integer(0));
+  }
+
+  static
+  {
+    polar.put("Y", new Integer(1));
+    polar.put("W", new Integer(1));
+    polar.put("H", new Integer(1));
+    polar.put("K", new Integer(1));
+    polar.put("R", new Integer(1));
+    polar.put("E", new Integer(1));
+    polar.put("Q", new Integer(1));
+    polar.put("D", new Integer(1));
+    polar.put("N", new Integer(1));
+    polar.put("S", new Integer(1));
+    polar.put("T", new Integer(1));
+    polar.put("X", new Integer(1));
+    polar.put("-", new Integer(1));
+    polar.put("*", new Integer(1));
+    polar.put("I", new Integer(0));
+    polar.put("L", new Integer(0));
+    polar.put("V", new Integer(0));
+    polar.put("C", new Integer(0));
+    polar.put("A", new Integer(0));
+    polar.put("G", new Integer(0));
+    polar.put("M", new Integer(0));
+    polar.put("F", new Integer(0));
+    polar.put("P", new Integer(0));
+  }
+
+  static
+  {
+    small.put("I", new Integer(0));
+    small.put("L", new Integer(0));
+    small.put("V", new Integer(1));
+    small.put("C", new Integer(1));
+    small.put("A", new Integer(1));
+    small.put("G", new Integer(1));
+    small.put("M", new Integer(0));
+    small.put("F", new Integer(0));
+    small.put("Y", new Integer(0));
+    small.put("W", new Integer(0));
+    small.put("H", new Integer(0));
+    small.put("K", new Integer(0));
+    small.put("R", new Integer(0));
+    small.put("E", new Integer(0));
+    small.put("Q", new Integer(0));
+    small.put("D", new Integer(1));
+    small.put("N", new Integer(1));
+    small.put("S", new Integer(1));
+    small.put("T", new Integer(1));
+    small.put("P", new Integer(1));
+    small.put("-", new Integer(1));
+    small.put("*", new Integer(1));
+  }
+
+  static
+  {
+    positive.put("I", new Integer(0));
+    positive.put("L", new Integer(0));
+    positive.put("V", new Integer(0));
+    positive.put("C", new Integer(0));
+    positive.put("A", new Integer(0));
+    positive.put("G", new Integer(0));
+    positive.put("M", new Integer(0));
+    positive.put("F", new Integer(0));
+    positive.put("Y", new Integer(0));
+    positive.put("W", new Integer(0));
+    positive.put("H", new Integer(1));
+    positive.put("K", new Integer(1));
+    positive.put("R", new Integer(1));
+    positive.put("E", new Integer(0));
+    positive.put("Q", new Integer(0));
+    positive.put("D", new Integer(0));
+    positive.put("N", new Integer(0));
+    positive.put("S", new Integer(0));
+    positive.put("T", new Integer(0));
+    positive.put("P", new Integer(0));
+    positive.put("-", new Integer(1));
+    positive.put("*", new Integer(1));
+  }
+
+  static
+  {
+    negative.put("I", new Integer(0));
+    negative.put("L", new Integer(0));
+    negative.put("V", new Integer(0));
+    negative.put("C", new Integer(0));
+    negative.put("A", new Integer(0));
+    negative.put("G", new Integer(0));
+    negative.put("M", new Integer(0));
+    negative.put("F", new Integer(0));
+    negative.put("Y", new Integer(0));
+    negative.put("W", new Integer(0));
+    negative.put("H", new Integer(0));
+    negative.put("K", new Integer(0));
+    negative.put("R", new Integer(0));
+    negative.put("E", new Integer(1));
+    negative.put("Q", new Integer(0));
+    negative.put("D", new Integer(1));
+    negative.put("N", new Integer(0));
+    negative.put("S", new Integer(0));
+    negative.put("T", new Integer(0));
+    negative.put("P", new Integer(0));
+    negative.put("-", new Integer(1));
+    negative.put("*", new Integer(1));
+  }
+
+  static
+  {
+    charged.put("I", new Integer(0));
+    charged.put("L", new Integer(0));
+    charged.put("V", new Integer(0));
+    charged.put("C", new Integer(0));
+    charged.put("A", new Integer(0));
+    charged.put("G", new Integer(0));
+    charged.put("M", new Integer(0));
+    charged.put("F", new Integer(0));
+    charged.put("Y", new Integer(0));
+    charged.put("W", new Integer(0));
+    charged.put("H", new Integer(1));
+    charged.put("K", new Integer(1));
+    charged.put("R", new Integer(1));
+    charged.put("E", new Integer(1));
+    charged.put("Q", new Integer(0));
+    charged.put("D", new Integer(1));
+    charged.put("N", new Integer(1));
+    charged.put("S", new Integer(0));
+    charged.put("T", new Integer(0));
+    charged.put("P", new Integer(0));
+    charged.put("-", new Integer(1));
+    charged.put("*", new Integer(1));
+  }
+
+  static
+  {
+    aromatic.put("I", new Integer(0));
+    aromatic.put("L", new Integer(0));
+    aromatic.put("V", new Integer(0));
+    aromatic.put("C", new Integer(0));
+    aromatic.put("A", new Integer(0));
+    aromatic.put("G", new Integer(0));
+    aromatic.put("M", new Integer(0));
+    aromatic.put("F", new Integer(1));
+    aromatic.put("Y", new Integer(1));
+    aromatic.put("W", new Integer(1));
+    aromatic.put("H", new Integer(1));
+    aromatic.put("K", new Integer(0));
+    aromatic.put("R", new Integer(0));
+    aromatic.put("E", new Integer(0));
+    aromatic.put("Q", new Integer(0));
+    aromatic.put("D", new Integer(0));
+    aromatic.put("N", new Integer(0));
+    aromatic.put("S", new Integer(0));
+    aromatic.put("T", new Integer(0));
+    aromatic.put("P", new Integer(0));
+    aromatic.put("-", new Integer(1));
+    aromatic.put("*", new Integer(1));
+  }
+
+  static
+  {
+    aliphatic.put("I", new Integer(1));
+    aliphatic.put("L", new Integer(1));
+    aliphatic.put("V", new Integer(1));
+    aliphatic.put("C", new Integer(0));
+    aliphatic.put("A", new Integer(0));
+    aliphatic.put("G", new Integer(0));
+    aliphatic.put("M", new Integer(0));
+    aliphatic.put("F", new Integer(0));
+    aliphatic.put("Y", new Integer(0));
+    aliphatic.put("W", new Integer(0));
+    aliphatic.put("H", new Integer(0));
+    aliphatic.put("K", new Integer(0));
+    aliphatic.put("R", new Integer(0));
+    aliphatic.put("E", new Integer(0));
+    aliphatic.put("Q", new Integer(0));
+    aliphatic.put("D", new Integer(0));
+    aliphatic.put("N", new Integer(0));
+    aliphatic.put("S", new Integer(0));
+    aliphatic.put("T", new Integer(0));
+    aliphatic.put("P", new Integer(0));
+    aliphatic.put("-", new Integer(1));
+    aliphatic.put("*", new Integer(1));
+  }
+
+  static
+  {
+    tiny.put("I", new Integer(0));
+    tiny.put("L", new Integer(0));
+    tiny.put("V", new Integer(0));
+    tiny.put("C", new Integer(0));
+    tiny.put("A", new Integer(1));
+    tiny.put("G", new Integer(1));
+    tiny.put("M", new Integer(0));
+    tiny.put("F", new Integer(0));
+    tiny.put("Y", new Integer(0));
+    tiny.put("W", new Integer(0));
+    tiny.put("H", new Integer(0));
+    tiny.put("K", new Integer(0));
+    tiny.put("R", new Integer(0));
+    tiny.put("E", new Integer(0));
+    tiny.put("Q", new Integer(0));
+    tiny.put("D", new Integer(0));
+    tiny.put("N", new Integer(0));
+    tiny.put("S", new Integer(1));
+    tiny.put("T", new Integer(0));
+    tiny.put("P", new Integer(0));
+    tiny.put("-", new Integer(1));
+    tiny.put("*", new Integer(1));
+  }
+
+  static
+  {
+    proline.put("I", new Integer(0));
+    proline.put("L", new Integer(0));
+    proline.put("V", new Integer(0));
+    proline.put("C", new Integer(0));
+    proline.put("A", new Integer(0));
+    proline.put("G", new Integer(0));
+    proline.put("M", new Integer(0));
+    proline.put("F", new Integer(0));
+    proline.put("Y", new Integer(0));
+    proline.put("W", new Integer(0));
+    proline.put("H", new Integer(0));
+    proline.put("K", new Integer(0));
+    proline.put("R", new Integer(0));
+    proline.put("E", new Integer(0));
+    proline.put("Q", new Integer(0));
+    proline.put("D", new Integer(0));
+    proline.put("N", new Integer(0));
+    proline.put("S", new Integer(0));
+    proline.put("T", new Integer(0));
+    proline.put("P", new Integer(1));
+    proline.put("-", new Integer(1));
+    proline.put("*", new Integer(1));
+  }
+
+  static
+  {
+    propHash.put("hydrophobic", hydrophobic);
+    propHash.put("small", small);
+    propHash.put("positive", positive);
+    propHash.put("negative", negative);
+    propHash.put("charged", charged);
+    propHash.put("aromatic", aromatic);
+    propHash.put("aliphatic", aliphatic);
+    propHash.put("tiny", tiny);
+    propHash.put("proline", proline);
+    propHash.put("polar", polar);
+  }
+
+  public static Hashtable chainColours = new Hashtable();
+
+  static
+  {
+    chainColours.put("A", Color.red);
+    chainColours.put("B", Color.orange);
+    chainColours.put("C", Color.yellow);
+    chainColours.put("D", Color.green);
+    chainColours.put("E", Color.cyan);
+    chainColours.put("F", Color.blue);
+    chainColours.put("G", Color.magenta);
+    chainColours.put("H", Color.pink);
+  }
+
+  private ResidueProperties()
+  {
+  }
+
+  public static double getHydmax()
+  {
+    return hydmax;
+  }
+
+  public static double getHydmin()
+  {
+    return hydmin;
+  }
+
+  public static double[] getHyd()
+  {
+    return hyd;
+  }
+
+  public static Hashtable getAAHash()
+  {
+    return aaHash;
+  }
+
+  public static Hashtable getAA3Hash()
+  {
+    return aa3Hash;
+  }
+
+  public static int[][] getDNA()
+  {
+    return ResidueProperties.DNA;
+  }
+
+  public static int[][] getBLOSUM62()
+  {
+    return ResidueProperties.BLOSUM62;
+  }
+
+  public static int getPAM250(String A1, String A2)
+  {
+    Integer pog1 = (Integer) aaHash.get(A1);
+    Integer pog2 = (Integer) aaHash.get(A2);
+    int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];
+
+    return pog;
+  }
+
+  public static int getBLOSUM62(String A1, String A2)
+  {
+    int pog = 0;
+
+    try
+    {
+      Integer pog1 = (Integer) aaHash.get(A1);
+      Integer pog2 = (Integer) aaHash.get(A2);
+      pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];
     }
-
-    public static Hashtable codonHash2 = new Hashtable();
-
-    static {
-        codonHash2.put("AAA", "K");
-        codonHash2.put("AAG", "K");
-        codonHash2.put("AAC", "N");
-        codonHash2.put("AAT", "N");
-
-        codonHash2.put("CAA", "E");
-        codonHash2.put("CAG", "E");
-        codonHash2.put("CAC", "H");
-        codonHash2.put("CAT", "H");
-
-        codonHash2.put("GAA", "Q");
-        codonHash2.put("GAG", "Q");
-        codonHash2.put("GAC", "D");
-        codonHash2.put("GAT", "D");
-
-        codonHash2.put("TAC", "Y");
-        codonHash2.put("TAT", "Y");
-
-        codonHash2.put("ACA", "T");
-        codonHash2.put("AAG", "T");
-        codonHash2.put("ACC", "T");
-        codonHash2.put("ACT", "T");
-
-        codonHash2.put("CCA", "P");
-        codonHash2.put("CCG", "P");
-        codonHash2.put("CCC", "P");
-        codonHash2.put("CCT", "P");
-
-        codonHash2.put("GCA", "A");
-        codonHash2.put("GCG", "A");
-        codonHash2.put("GCC", "A");
-        codonHash2.put("GCT", "A");
-
-        codonHash2.put("TCA", "S");
-        codonHash2.put("TCG", "S");
-        codonHash2.put("TCC", "S");
-        codonHash2.put("TCT", "S");
-        codonHash2.put("AGC", "S");
-        codonHash2.put("AGT", "S");
-
-        codonHash2.put("AGA", "R");
-        codonHash2.put("AGG", "R");
-        codonHash2.put("CGA", "R");
-        codonHash2.put("CGG", "R");
-        codonHash2.put("CGC", "R");
-        codonHash2.put("CGT", "R");
-
-        codonHash2.put("GGA", "G");
-        codonHash2.put("GGG", "G");
-        codonHash2.put("GGC", "G");
-        codonHash2.put("GGT", "G");
-
-        codonHash2.put("TGA", "*");
-        codonHash2.put("TAA", "*");
-        codonHash2.put("TAG", "*");
-
-        codonHash2.put("TGG", "W");
-
-        codonHash2.put("TGC", "C");
-        codonHash2.put("TGT", "C");
-
-        codonHash2.put("ATA", "I");
-        codonHash2.put("ATC", "I");
-        codonHash2.put("ATT", "I");
-
-        codonHash2.put("ATG", "M");
-
-        codonHash2.put("CTA", "L");
-        codonHash2.put("CTG", "L");
-        codonHash2.put("CTC", "L");
-        codonHash2.put("CTT", "L");
-        codonHash2.put("TTA", "L");
-        codonHash2.put("TTG", "L");
-
-        codonHash2.put("GTA", "V");
-        codonHash2.put("GTG", "V");
-        codonHash2.put("GTC", "V");
-        codonHash2.put("GTT", "V");
-
-        codonHash2.put("TTC", "F");
-        codonHash2.put("TTT", "F");
+    catch (Exception e)
+    {
+      //System.out.println("Unknown residue in " + A1 + " " + A2);
     }
 
-    static {
-        Lys.addElement("AAA");
-        Lys.addElement("AAG");
-        Asn.addElement("AAC");
-        Asn.addElement("AAT");
-
-        Gln.addElement("CAA");
-        Gln.addElement("CAG");
-        His.addElement("CAC");
-        His.addElement("CAT");
-
-        Glu.addElement("GAA");
-        Glu.addElement("GAG");
-        Asp.addElement("GAC");
-        Asp.addElement("GAT");
-
-        Tyr.addElement("TAC");
-        Tyr.addElement("TAT");
-
-        Thr.addElement("ACA");
-        Thr.addElement("ACG");
-        Thr.addElement("ACC");
-        Thr.addElement("ACT");
-
-        Pro.addElement("CCA");
-        Pro.addElement("CCG");
-        Pro.addElement("CCC");
-        Pro.addElement("CCT");
-
-        Ala.addElement("GCA");
-        Ala.addElement("GCG");
-        Ala.addElement("GCC");
-        Ala.addElement("GCT");
-
-        Ser.addElement("TCA");
-        Ser.addElement("TCG");
-        Ser.addElement("TCC");
-        Ser.addElement("TCT");
-        Ser.addElement("AGC");
-        Ser.addElement("AGT");
-
-        Arg.addElement("AGA");
-        Arg.addElement("AGG");
-        Arg.addElement("CGA");
-        Arg.addElement("CGG");
-        Arg.addElement("CGC");
-        Arg.addElement("CGT");
-
-        Gly.addElement("GGA");
-        Gly.addElement("GGG");
-        Gly.addElement("GGC");
-        Gly.addElement("GGT");
-
-        STOP.addElement("TGA");
-        STOP.addElement("TAA");
-        STOP.addElement("TAG");
-
-        Trp.addElement("TGG");
-
-        Cys.addElement("TGC");
-        Cys.addElement("TGT");
-
-        Ile.addElement("ATA");
-        Ile.addElement("ATC");
-        Ile.addElement("ATT");
-
-        Met.addElement("ATG");
-
-        Leu.addElement("CTA");
-        Leu.addElement("CTG");
-        Leu.addElement("CTC");
-        Leu.addElement("CTT");
-        Leu.addElement("TTA");
-        Leu.addElement("TTG");
-
-        Val.addElement("GTA");
-        Val.addElement("GTG");
-        Val.addElement("GTC");
-        Val.addElement("GTT");
-
-        Phe.addElement("TTC");
-        Phe.addElement("TTT");
-    }
+    return pog;
+  }
 
-    public static Color[][] groupColors = {
-        { Color.red, Color.red.brighter(), Color.red.brighter().brighter() },
-        {
-            Color.orange, Color.orange.brighter(),
-            Color.orange.brighter().brighter()
-        },
-        { Color.green, Color.green.brighter(), Color.green.brighter().brighter() },
-        { Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter() },
-        {
-            Color.magenta, Color.magenta.brighter(),
-            Color.magenta.brighter().brighter()
-        },
-        { Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter() },
-        { Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter() },
-    };
-
-    //Stores residue codes/names and colours and other things
-    public static Hashtable propHash = new Hashtable();
-    public static Hashtable hydrophobic = new Hashtable();
-    public static Hashtable polar = new Hashtable();
-    public static Hashtable small = new Hashtable();
-    public static Hashtable positive = new Hashtable();
-    public static Hashtable negative = new Hashtable();
-    public static Hashtable charged = new Hashtable();
-    public static Hashtable aromatic = new Hashtable();
-    public static Hashtable aliphatic = new Hashtable();
-    public static Hashtable tiny = new Hashtable();
-    public static Hashtable proline = new Hashtable();
-
-    static {
-        hydrophobic.put("I", new Integer(1));
-        hydrophobic.put("L", new Integer(1));
-        hydrophobic.put("V", new Integer(1));
-        hydrophobic.put("C", new Integer(1));
-        hydrophobic.put("A", new Integer(1));
-        hydrophobic.put("G", new Integer(1));
-        hydrophobic.put("M", new Integer(1));
-        hydrophobic.put("F", new Integer(1));
-        hydrophobic.put("Y", new Integer(1));
-        hydrophobic.put("W", new Integer(1));
-        hydrophobic.put("H", new Integer(1));
-        hydrophobic.put("K", new Integer(1));
-        hydrophobic.put("X", new Integer(1));
-        hydrophobic.put("-", new Integer(1));
-        hydrophobic.put("*", new Integer(1));
-        hydrophobic.put("R", new Integer(0));
-        hydrophobic.put("E", new Integer(0));
-        hydrophobic.put("Q", new Integer(0));
-        hydrophobic.put("D", new Integer(0));
-        hydrophobic.put("N", new Integer(0));
-        hydrophobic.put("S", new Integer(0));
-        hydrophobic.put("T", new Integer(0));
-        hydrophobic.put("P", new Integer(0));
+  public static Vector getCodons(String res)
+  {
+    if (codonHash.containsKey(res))
+    {
+      return (Vector) codonHash.get(res);
     }
 
-    static {
-        polar.put("Y", new Integer(1));
-        polar.put("W", new Integer(1));
-        polar.put("H", new Integer(1));
-        polar.put("K", new Integer(1));
-        polar.put("R", new Integer(1));
-        polar.put("E", new Integer(1));
-        polar.put("Q", new Integer(1));
-        polar.put("D", new Integer(1));
-        polar.put("N", new Integer(1));
-        polar.put("S", new Integer(1));
-        polar.put("T", new Integer(1));
-        polar.put("X", new Integer(1));
-        polar.put("-", new Integer(1));
-        polar.put("*", new Integer(1));
-        polar.put("I", new Integer(0));
-        polar.put("L", new Integer(0));
-        polar.put("V", new Integer(0));
-        polar.put("C", new Integer(0));
-        polar.put("A", new Integer(0));
-        polar.put("G", new Integer(0));
-        polar.put("M", new Integer(0));
-        polar.put("F", new Integer(0));
-        polar.put("P", new Integer(0));
-    }
+    return null;
+  }
 
-    static {
-        small.put("I", new Integer(0));
-        small.put("L", new Integer(0));
-        small.put("V", new Integer(1));
-        small.put("C", new Integer(1));
-        small.put("A", new Integer(1));
-        small.put("G", new Integer(1));
-        small.put("M", new Integer(0));
-        small.put("F", new Integer(0));
-        small.put("Y", new Integer(0));
-        small.put("W", new Integer(0));
-        small.put("H", new Integer(0));
-        small.put("K", new Integer(0));
-        small.put("R", new Integer(0));
-        small.put("E", new Integer(0));
-        small.put("Q", new Integer(0));
-        small.put("D", new Integer(1));
-        small.put("N", new Integer(1));
-        small.put("S", new Integer(1));
-        small.put("T", new Integer(1));
-        small.put("P", new Integer(1));
-        small.put("-", new Integer(1));
-        small.put("*", new Integer(1));
-    }
+  public static String codonTranslate(String codon)
+  {
+    Enumeration e = codonHash.keys();
 
-    static {
-        positive.put("I", new Integer(0));
-        positive.put("L", new Integer(0));
-        positive.put("V", new Integer(0));
-        positive.put("C", new Integer(0));
-        positive.put("A", new Integer(0));
-        positive.put("G", new Integer(0));
-        positive.put("M", new Integer(0));
-        positive.put("F", new Integer(0));
-        positive.put("Y", new Integer(0));
-        positive.put("W", new Integer(0));
-        positive.put("H", new Integer(1));
-        positive.put("K", new Integer(1));
-        positive.put("R", new Integer(1));
-        positive.put("E", new Integer(0));
-        positive.put("Q", new Integer(0));
-        positive.put("D", new Integer(0));
-        positive.put("N", new Integer(0));
-        positive.put("S", new Integer(0));
-        positive.put("T", new Integer(0));
-        positive.put("P", new Integer(0));
-        positive.put("-", new Integer(1));
-        positive.put("*", new Integer(1));
-    }
+    while (e.hasMoreElements())
+    {
+      String key = (String) e.nextElement();
+      Vector tmp = (Vector) codonHash.get(key);
 
-    static {
-        negative.put("I", new Integer(0));
-        negative.put("L", new Integer(0));
-        negative.put("V", new Integer(0));
-        negative.put("C", new Integer(0));
-        negative.put("A", new Integer(0));
-        negative.put("G", new Integer(0));
-        negative.put("M", new Integer(0));
-        negative.put("F", new Integer(0));
-        negative.put("Y", new Integer(0));
-        negative.put("W", new Integer(0));
-        negative.put("H", new Integer(0));
-        negative.put("K", new Integer(0));
-        negative.put("R", new Integer(0));
-        negative.put("E", new Integer(1));
-        negative.put("Q", new Integer(0));
-        negative.put("D", new Integer(1));
-        negative.put("N", new Integer(0));
-        negative.put("S", new Integer(0));
-        negative.put("T", new Integer(0));
-        negative.put("P", new Integer(0));
-        negative.put("-", new Integer(1));
-        negative.put("*", new Integer(1));
+      if (tmp.contains(codon))
+      {
+        return key;
+      }
     }
 
-    static {
-        charged.put("I", new Integer(0));
-        charged.put("L", new Integer(0));
-        charged.put("V", new Integer(0));
-        charged.put("C", new Integer(0));
-        charged.put("A", new Integer(0));
-        charged.put("G", new Integer(0));
-        charged.put("M", new Integer(0));
-        charged.put("F", new Integer(0));
-        charged.put("Y", new Integer(0));
-        charged.put("W", new Integer(0));
-        charged.put("H", new Integer(1));
-        charged.put("K", new Integer(1));
-        charged.put("R", new Integer(1));
-        charged.put("E", new Integer(1));
-        charged.put("Q", new Integer(0));
-        charged.put("D", new Integer(1));
-        charged.put("N", new Integer(1));
-        charged.put("S", new Integer(0));
-        charged.put("T", new Integer(0));
-        charged.put("P", new Integer(0));
-        charged.put("-", new Integer(1));
-        charged.put("*", new Integer(1));
-    }
-
-    static {
-        aromatic.put("I", new Integer(0));
-        aromatic.put("L", new Integer(0));
-        aromatic.put("V", new Integer(0));
-        aromatic.put("C", new Integer(0));
-        aromatic.put("A", new Integer(0));
-        aromatic.put("G", new Integer(0));
-        aromatic.put("M", new Integer(0));
-        aromatic.put("F", new Integer(1));
-        aromatic.put("Y", new Integer(1));
-        aromatic.put("W", new Integer(1));
-        aromatic.put("H", new Integer(1));
-        aromatic.put("K", new Integer(0));
-        aromatic.put("R", new Integer(0));
-        aromatic.put("E", new Integer(0));
-        aromatic.put("Q", new Integer(0));
-        aromatic.put("D", new Integer(0));
-        aromatic.put("N", new Integer(0));
-        aromatic.put("S", new Integer(0));
-        aromatic.put("T", new Integer(0));
-        aromatic.put("P", new Integer(0));
-        aromatic.put("-", new Integer(1));
-        aromatic.put("*", new Integer(1));
-    }
+    return null;
+  }
 
-    static {
-        aliphatic.put("I", new Integer(1));
-        aliphatic.put("L", new Integer(1));
-        aliphatic.put("V", new Integer(1));
-        aliphatic.put("C", new Integer(0));
-        aliphatic.put("A", new Integer(0));
-        aliphatic.put("G", new Integer(0));
-        aliphatic.put("M", new Integer(0));
-        aliphatic.put("F", new Integer(0));
-        aliphatic.put("Y", new Integer(0));
-        aliphatic.put("W", new Integer(0));
-        aliphatic.put("H", new Integer(0));
-        aliphatic.put("K", new Integer(0));
-        aliphatic.put("R", new Integer(0));
-        aliphatic.put("E", new Integer(0));
-        aliphatic.put("Q", new Integer(0));
-        aliphatic.put("D", new Integer(0));
-        aliphatic.put("N", new Integer(0));
-        aliphatic.put("S", new Integer(0));
-        aliphatic.put("T", new Integer(0));
-        aliphatic.put("P", new Integer(0));
-        aliphatic.put("-", new Integer(1));
-        aliphatic.put("*", new Integer(1));
-    }
-
-    static {
-        tiny.put("I", new Integer(0));
-        tiny.put("L", new Integer(0));
-        tiny.put("V", new Integer(0));
-        tiny.put("C", new Integer(0));
-        tiny.put("A", new Integer(1));
-        tiny.put("G", new Integer(1));
-        tiny.put("M", new Integer(0));
-        tiny.put("F", new Integer(0));
-        tiny.put("Y", new Integer(0));
-        tiny.put("W", new Integer(0));
-        tiny.put("H", new Integer(0));
-        tiny.put("K", new Integer(0));
-        tiny.put("R", new Integer(0));
-        tiny.put("E", new Integer(0));
-        tiny.put("Q", new Integer(0));
-        tiny.put("D", new Integer(0));
-        tiny.put("N", new Integer(0));
-        tiny.put("S", new Integer(1));
-        tiny.put("T", new Integer(0));
-        tiny.put("P", new Integer(0));
-        tiny.put("-", new Integer(1));
-        tiny.put("*", new Integer(1));
-    }
-
-    static {
-        proline.put("I", new Integer(0));
-        proline.put("L", new Integer(0));
-        proline.put("V", new Integer(0));
-        proline.put("C", new Integer(0));
-        proline.put("A", new Integer(0));
-        proline.put("G", new Integer(0));
-        proline.put("M", new Integer(0));
-        proline.put("F", new Integer(0));
-        proline.put("Y", new Integer(0));
-        proline.put("W", new Integer(0));
-        proline.put("H", new Integer(0));
-        proline.put("K", new Integer(0));
-        proline.put("R", new Integer(0));
-        proline.put("E", new Integer(0));
-        proline.put("Q", new Integer(0));
-        proline.put("D", new Integer(0));
-        proline.put("N", new Integer(0));
-        proline.put("S", new Integer(0));
-        proline.put("T", new Integer(0));
-        proline.put("P", new Integer(1));
-        proline.put("-", new Integer(1));
-        proline.put("*", new Integer(1));
-    }
-
-    static {
-        propHash.put("hydrophobic", hydrophobic);
-        propHash.put("small", small);
-        propHash.put("positive", positive);
-        propHash.put("negative", negative);
-        propHash.put("charged", charged);
-        propHash.put("aromatic", aromatic);
-        propHash.put("aliphatic", aliphatic);
-        propHash.put("tiny", tiny);
-        propHash.put("proline", proline);
-        propHash.put("polar", polar);
-    }
-
-    public static Hashtable chainColours = new Hashtable();
-
-    static {
-        chainColours.put("A", Color.red);
-        chainColours.put("B", Color.orange);
-        chainColours.put("C", Color.yellow);
-        chainColours.put("D", Color.green);
-        chainColours.put("E", Color.cyan);
-        chainColours.put("F", Color.blue);
-        chainColours.put("G", Color.magenta);
-        chainColours.put("H", Color.pink);
-    }
-
-    private ResidueProperties() {
-    }
-
-    public static double getHydmax() {
-        return hydmax;
-    }
-
-    public static double getHydmin() {
-        return hydmin;
-    }
-
-    public static double[] getHyd() {
-        return hyd;
-    }
-
-    public static Hashtable getAAHash() {
-        return aaHash;
-    }
-
-    public static Hashtable getAA3Hash() {
-        return aa3Hash;
-    }
-
-    public static int[][] getDNA() {
-        return ResidueProperties.DNA;
-    }
-
-    public static int[][] getBLOSUM62() {
-        return ResidueProperties.BLOSUM62;
-    }
-
-    public static int getPAM250(String A1, String A2) {
-        Integer pog1 = (Integer) aaHash.get(A1);
-        Integer pog2 = (Integer) aaHash.get(A2);
-        int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];
-
-        return pog;
-    }
-
-    public static int getBLOSUM62(String A1, String A2) {
-        int pog = 0;
-
-        try {
-            Integer pog1 = (Integer) aaHash.get(A1);
-            Integer pog2 = (Integer) aaHash.get(A2);
-            pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];
-        } catch (Exception e) {
-            //System.out.println("Unknown residue in " + A1 + " " + A2);
-        }
-
-        return pog;
-    }
-
-    public static Vector getCodons(String res) {
-        if (codonHash.containsKey(res)) {
-            return (Vector) codonHash.get(res);
-        }
-
-        return null;
-    }
-
-    public static String codonTranslate(String codon) {
-        Enumeration e = codonHash.keys();
-
-        while (e.hasMoreElements()) {
-            String key = (String) e.nextElement();
-            Vector tmp = (Vector) codonHash.get(key);
-
-            if (tmp.contains(codon)) {
-                return key;
-            }
-        }
-
-        return null;
-    }
-
-    public static Hashtable getChainColours() {
-        return chainColours;
-    }
+  public static Hashtable getChainColours()
+  {
+    return chainColours;
+  }
 }
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 12f252d..b69e536 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -21,12 +21,32 @@ package jalview.schemes;
 import java.awt.*;
 
 
-public class ScoreColourScheme extends ResidueColourScheme {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+    /** DOCUMENT ME!! */
     public double min;
+
+    /** DOCUMENT ME!! */
     public double max;
+
+    /** DOCUMENT ME!! */
     public double[] scores;
 
-    public ScoreColourScheme(double[] scores, double min, double max) {
+    /**
+     * Creates a new ScoreColourScheme object.
+     *
+     * @param scores DOCUMENT ME!
+     * @param min DOCUMENT ME!
+     * @param max DOCUMENT ME!
+     */
+    public ScoreColourScheme(double[] scores, double min, double max)
+    {
         super();
 
         this.scores = scores;
@@ -34,9 +54,20 @@ public class ScoreColourScheme extends ResidueColourScheme {
         this.max = max;
     }
 
-    public Color findColour(String s, int j) {
-        if (threshold > 0) {
-            if (!aboveThreshold(s, j)) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String s, int j)
+    {
+        if (threshold > 0)
+        {
+            if (!aboveThreshold(s, j))
+            {
                 return Color.white;
             }
         }
@@ -44,17 +75,20 @@ public class ScoreColourScheme extends ResidueColourScheme {
         float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -
             (float) min) / (float) (max - min);
 
-        if (red > 1.0f) {
+        if (red > 1.0f)
+        {
             red = 1.0f;
         }
 
-        if (red < 0.0f) {
+        if (red < 0.0f)
+        {
             red = 0.0f;
         }
 
         char c = s.charAt(0);
 
-        if (jalview.util.Comparison.isGap((c))) {
+        if (jalview.util.Comparison.isGap((c)))
+        {
             return Color.white;
         }
 
@@ -62,7 +96,15 @@ public class ScoreColourScheme extends ResidueColourScheme {
         return makeColour(red);
     }
 
-    public Color makeColour(float c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color makeColour(float c)
+    {
         return new Color(c, (float) 0.0, (float) 1.0 - c);
     }
 }
diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index 717e6dc..9944155 100755
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -21,13 +21,32 @@ package jalview.schemes;
 import java.awt.*;
 
 
-public class StrandColourScheme extends ScoreColourScheme {
-    public StrandColourScheme() {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class StrandColourScheme extends ScoreColourScheme
+{
+    /**
+     * Creates a new StrandColourScheme object.
+     */
+    public StrandColourScheme()
+    {
         super(ResidueProperties.strand, ResidueProperties.strandmin,
             ResidueProperties.strandmax);
     }
 
-    public Color makeColour(float c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color makeColour(float c)
+    {
         return new Color(c, c, (float) 1.0 - c);
     }
 }
diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java
index 10277e9..6220eaa 100755
--- a/src/jalview/schemes/TaylorColourScheme.java
+++ b/src/jalview/schemes/TaylorColourScheme.java
@@ -1,25 +1,28 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
-public class TaylorColourScheme extends ResidueColourScheme {
-    public TaylorColourScheme() {
-        super(ResidueProperties.taylor, 0);
-    }
+public class TaylorColourScheme
+    extends ResidueColourScheme
+{
+  public TaylorColourScheme()
+  {
+    super(ResidueProperties.taylor, 0);
+  }
 }
diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index e86c44c..dbf36e3 100755
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -21,13 +21,32 @@ package jalview.schemes;
 import java.awt.*;
 
 
-public class TurnColourScheme extends ScoreColourScheme {
-    public TurnColourScheme() {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TurnColourScheme extends ScoreColourScheme
+{
+    /**
+     * Creates a new TurnColourScheme object.
+     */
+    public TurnColourScheme()
+    {
         super(ResidueProperties.turn, ResidueProperties.turnmin,
             ResidueProperties.turnmax);
     }
 
-    public Color makeColour(float c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color makeColour(float c)
+    {
         return new Color(c, 1 - c, 1 - c);
     }
 }
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 38a1291..7bd61c1 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,32 +1,57 @@
 /*
-* 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
-*/
+ * 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.schemes;
 
 import java.awt.*;
 
-
-public class UserColourScheme extends ResidueColourScheme {
-    public UserColourScheme(Color[] newColors) {
-        colors = newColors;
+public class UserColourScheme
+    extends ResidueColourScheme
+{
+  public UserColourScheme(String colour)
+  {
+    Color col = null;
+    try{
+      int value = Integer.parseInt(colour, 16);
+      col = new Color(value);
     }
+    catch(NumberFormatException ex){}
+
+    if(col==null)
+      col = ColourSchemeProperty.getAWTColorFromName(colour);
 
-    public Color[] getColours() {
-        return colors;
+    if(col==null)
+    {
+      System.out.println("Unknown colour!! "+colour);
     }
+
+    colors = new Color[24];
+    for(int i=0; i<24; i++)
+      colors[i] = col;
+  }
+
+  public UserColourScheme(Color[] newColors)
+  {
+    colors = newColors;
+  }
+
+  public Color[] getColours()
+  {
+    return colors;
+  }
 }
diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index 2a439c0..4f5c42a 100755
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -18,8 +18,20 @@
 */
 package jalview.schemes;
 
-public class ZappoColourScheme extends ResidueColourScheme {
-    public ZappoColourScheme() {
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ZappoColourScheme extends ResidueColourScheme
+{
+    /**
+     * Creates a new ZappoColourScheme object.
+     */
+    public ZappoColourScheme()
+    {
         super(ResidueProperties.color, 0);
     }
 }
diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index 12d6f02..6bac25b 100755
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -1,767 +1,930 @@
-/*
-* 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
-*/
+/*
+ * 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.util;
 
-import java.io.File;
-import java.io.IOException;
-
-import java.lang.reflect.Constructor;
-import java.lang.reflect.Field;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-
-
-/**
- * BrowserLauncher is a class that provides one static method, openURL, which opens the default
- * web browser for the current user of the system to the given URL.  It may support other
- * protocols depending on the system -- mailto, ftp, etc. -- but that has not been rigorously
- * tested and is not guaranteed to work.
- * <p>
- * Yes, this is platform-specific code, and yes, it may rely on classes on certain platforms
- * that are not part of the standard JDK.  What we're trying to do, though, is to take something
- * that's frequently desirable but inherently platform-specific -- opening a default browser --
- * and allow programmers (you, for example) to do so without worrying about dropping into native
- * code or doing anything else similarly evil.
- * <p>
- * Anyway, this code is completely in Java and will run on all JDK 1.1-compliant systems without
- * modification or a need for additional libraries.  All classes that are required on certain
- * platforms to allow this to run are dynamically loaded at runtime via reflection and, if not
- * found, will not cause this to do anything other than returning an error when opening the
- * browser.
- * <p>
- * There are certain system requirements for this class, as it's running through Runtime.exec(),
- * which is Java's way of making a native system call.  Currently, this requires that a Macintosh
- * have a Finder which supports the GURL event, which is true for Mac OS 8.0 and 8.1 systems that
- * have the Internet Scripting AppleScript dictionary installed in the Scripting Additions folder
- * in the Extensions folder (which is installed by default as far as I know under Mac OS 8.0 and
- * 8.1), and for all Mac OS 8.5 and later systems.  On Windows, it only runs under Win32 systems
- * (Windows 95, 98, and NT 4.0, as well as later versions of all).  On other systems, this drops
- * back from the inherently platform-sensitive concept of a default browser and simply attempts
- * to launch Netscape via a shell command.
- * <p>
- * This code is Copyright 1999-2001 by Eric Albert (ejalbert\@cs.stanford.edu) and may be
- * redistributed or modified in any form without restrictions as long as the portion of this
- * comment from this paragraph through the end of the comment is not removed.  The author
- * requests that he be notified of any application, applet, or other binary that makes use of
- * this code, but that's more out of curiosity than anything and is not required.  This software
- * includes no warranty.  The author is not repsonsible for any loss of data or functionality
- * or any adverse or unexpected effects of using this software.
- * <p>
- * Credits:
- * <br>Steven Spencer, JavaWorld magazine (<a href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java Tip 66</a>)
- * <br>Thanks also to Ron B. Yeh, Eric Shapiro, Ben Engber, Paul Teitlebaum, Andrea Cantatore,
- * Larry Barowski, Trevor Bedzek, Frank Miedrich, and Ron Rabakukk
- *
- * @author Eric Albert (<a href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
- * @version 1.4b1 (Released June 20, 2001)
- */
-public class BrowserLauncher {
-    /**
- * The Java virtual machine that we are running on.  Actually, in most cases we only care
- * about the operating system, but some operating systems require us to switch on the VM. */
-    private static int jvm;
-
-    /** The browser for the system */
-    private static Object browser;
-
-    /**
- * Caches whether any classes, methods, and fields that are not part of the JDK and need to
- * be dynamically loaded at runtime loaded successfully.
- * <p>
- * Note that if this is <code>false</code>, <code>openURL()</code> will always return an
- * IOException.
+import java.io.*;
+import java.lang.reflect.*;
+
+/**
+ * BrowserLauncher is a class that provides one static method, openURL, which opens the default
+ * web browser for the current user of the system to the given URL.  It may support other
+ * protocols depending on the system -- mailto, ftp, etc. -- but that has not been rigorously
+ * tested and is not guaranteed to work.
+ * <p>
+ * Yes, this is platform-specific code, and yes, it may rely on classes on certain platforms
+ * that are not part of the standard JDK.  What we're trying to do, though, is to take something
+ * that's frequently desirable but inherently platform-specific -- opening a default browser --
+ * and allow programmers (you, for example) to do so without worrying about dropping into native
+ * code or doing anything else similarly evil.
+ * <p>
+ * Anyway, this code is completely in Java and will run on all JDK 1.1-compliant systems without
+ * modification or a need for additional libraries.  All classes that are required on certain
+ * platforms to allow this to run are dynamically loaded at runtime via reflection and, if not
+ * found, will not cause this to do anything other than returning an error when opening the
+ * browser.
+ * <p>
+ * There are certain system requirements for this class, as it's running through Runtime.exec(),
+ * which is Java's way of making a native system call.  Currently, this requires that a Macintosh
+ * have a Finder which supports the GURL event, which is true for Mac OS 8.0 and 8.1 systems that
+ * have the Internet Scripting AppleScript dictionary installed in the Scripting Additions folder
+ * in the Extensions folder (which is installed by default as far as I know under Mac OS 8.0 and
+ * 8.1), and for all Mac OS 8.5 and later systems.  On Windows, it only runs under Win32 systems
+ * (Windows 95, 98, and NT 4.0, as well as later versions of all).  On other systems, this drops
+ * back from the inherently platform-sensitive concept of a default browser and simply attempts
+ * to launch Netscape via a shell command.
+ * <p>
+ * This code is Copyright 1999-2001 by Eric Albert (ejalbert\@cs.stanford.edu) and may be
+ * redistributed or modified in any form without restrictions as long as the portion of this
+ * comment from this paragraph through the end of the comment is not removed.  The author
+ * requests that he be notified of any application, applet, or other binary that makes use of
+ * this code, but that's more out of curiosity than anything and is not required.  This software
+ * includes no warranty.  The author is not repsonsible for any loss of data or functionality
+ * or any adverse or unexpected effects of using this software.
+ * <p>
+ * Credits:
+ * <br>Steven Spencer, JavaWorld magazine (<a href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java Tip 66</a>)
+ * <br>Thanks also to Ron B. Yeh, Eric Shapiro, Ben Engber, Paul Teitlebaum, Andrea Cantatore,
+ * Larry Barowski, Trevor Bedzek, Frank Miedrich, and Ron Rabakukk
+ *
+ * @author Eric Albert (<a href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
+ * @version 1.4b1 (Released June 20, 2001)
  */
-    private static boolean loadedWithoutErrors;
+public class BrowserLauncher
+{
+  /**
+   * The Java virtual machine that we are running on.  Actually, in most cases we only care
+   * about the operating system, but some operating systems require us to switch on the VM. */
+  private static int jvm;
 
-    /** The com.apple.mrj.MRJFileUtils class */
-    private static Class mrjFileUtilsClass;
+  /** The browser for the system */
+  private static Object browser;
 
-    /** The com.apple.mrj.MRJOSType class */
-    private static Class mrjOSTypeClass;
+  /**
+   * Caches whether any classes, methods, and fields that are not part of the JDK and need to
+   * be dynamically loaded at runtime loaded successfully.
+   * <p>
+   * Note that if this is <code>false</code>, <code>openURL()</code> will always return an
+   * IOException.
+   */
+  private static boolean loadedWithoutErrors;
 
-    /** The com.apple.MacOS.AEDesc class */
-    private static Class aeDescClass;
+  /** The com.apple.mrj.MRJFileUtils class */
+  private static Class mrjFileUtilsClass;
 
-    /** The &lt;init&gt;(int) method of com.apple.MacOS.AETarget */
-    private static Constructor aeTargetConstructor;
+  /** The com.apple.mrj.MRJOSType class */
+  private static Class mrjOSTypeClass;
 
-    /** The &lt;init&gt;(int, int, int) method of com.apple.MacOS.AppleEvent */
-    private static Constructor appleEventConstructor;
+  /** The com.apple.MacOS.AEDesc class */
+  private static Class aeDescClass;
 
-    /** The &lt;init&gt;(String) method of com.apple.MacOS.AEDesc */
-    private static Constructor aeDescConstructor;
+  /** The &lt;init&gt;(int) method of com.apple.MacOS.AETarget */
+  private static Constructor aeTargetConstructor;
 
-    /** The findFolder method of com.apple.mrj.MRJFileUtils */
-    private static Method findFolder;
+  /** The &lt;init&gt;(int, int, int) method of com.apple.MacOS.AppleEvent */
+  private static Constructor appleEventConstructor;
 
-    /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
-    private static Method getFileCreator;
+  /** The &lt;init&gt;(String) method of com.apple.MacOS.AEDesc */
+  private static Constructor aeDescConstructor;
 
-    /** The getFileType method of com.apple.mrj.MRJFileUtils */
-    private static Method getFileType;
+  /** The findFolder method of com.apple.mrj.MRJFileUtils */
+  private static Method findFolder;
 
-    /** The openURL method of com.apple.mrj.MRJFileUtils */
-    private static Method openURL;
+  /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
+  private static Method getFileCreator;
 
-    /** The makeOSType method of com.apple.MacOS.OSUtils */
-    private static Method makeOSType;
+  /** The getFileType method of com.apple.mrj.MRJFileUtils */
+  private static Method getFileType;
 
-    /** The putParameter method of com.apple.MacOS.AppleEvent */
-    private static Method putParameter;
+  /** The openURL method of com.apple.mrj.MRJFileUtils */
+  private static Method openURL;
 
-    /** The sendNoReply method of com.apple.MacOS.AppleEvent */
-    private static Method sendNoReply;
+  /** The makeOSType method of com.apple.MacOS.OSUtils */
+  private static Method makeOSType;
 
-    /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
-    private static Object kSystemFolderType;
+  /** The putParameter method of com.apple.MacOS.AppleEvent */
+  private static Method putParameter;
 
-    /** The keyDirectObject AppleEvent parameter type */
-    private static Integer keyDirectObject;
+  /** The sendNoReply method of com.apple.MacOS.AppleEvent */
+  private static Method sendNoReply;
 
-    /** The kAutoGenerateReturnID AppleEvent code */
-    private static Integer kAutoGenerateReturnID;
+  /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
+  private static Object kSystemFolderType;
 
-    /** The kAnyTransactionID AppleEvent code */
-    private static Integer kAnyTransactionID;
+  /** The keyDirectObject AppleEvent parameter type */
+  private static Integer keyDirectObject;
 
-    /** The linkage object required for JDirect 3 on Mac OS X. */
-    private static Object linkage;
+  /** The kAutoGenerateReturnID AppleEvent code */
+  private static Integer kAutoGenerateReturnID;
 
-    /** The framework to reference on Mac OS X */
-    private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";
+  /** The kAnyTransactionID AppleEvent code */
+  private static Integer kAnyTransactionID;
 
-    /** JVM constant for MRJ 2.0 */
-    private static final int MRJ_2_0 = 0;
+  /** The linkage object required for JDirect 3 on Mac OS X. */
+  private static Object linkage;
 
-    /** JVM constant for MRJ 2.1 or later */
-    private static final int MRJ_2_1 = 1;
+  /** The framework to reference on Mac OS X */
+  private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";
 
-    /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */
-    private static final int MRJ_3_0 = 3;
+  /** JVM constant for MRJ 2.0 */
+  private static final int MRJ_2_0 = 0;
 
-    /** JVM constant for MRJ 3.1 */
-    private static final int MRJ_3_1 = 4;
+  /** JVM constant for MRJ 2.1 or later */
+  private static final int MRJ_2_1 = 1;
 
-    /** JVM constant for any Windows NT JVM */
-    private static final int WINDOWS_NT = 5;
+  /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */
+  private static final int MRJ_3_0 = 3;
 
-    /** JVM constant for any Windows 9x JVM */
-    private static final int WINDOWS_9x = 6;
+  /** JVM constant for MRJ 3.1 */
+  private static final int MRJ_3_1 = 4;
 
-    /** JVM constant for any other platform */
-    private static final int OTHER = -1;
+  /** JVM constant for any Windows NT JVM */
+  private static final int WINDOWS_NT = 5;
 
-    /**
- * The file type of the Finder on a Macintosh.  Hardcoding "Finder" would keep non-U.S. English
- * systems from working properly.
- */
-    private static final String FINDER_TYPE = "FNDR";
+  /** JVM constant for any Windows 9x JVM */
+  private static final int WINDOWS_9x = 6;
 
-    /**
- * The creator code of the Finder on a Macintosh, which is needed to send AppleEvents to the
- * application.
- */
-    private static final String FINDER_CREATOR = "MACS";
+  /** JVM constant for any other platform */
+  private static final int OTHER = -1;
 
-    /** The name for the AppleEvent type corresponding to a GetURL event. */
-    private static final String GURL_EVENT = "GURL";
+  /**
+   * The file type of the Finder on a Macintosh.  Hardcoding "Finder" would keep non-U.S. English
+   * systems from working properly.
+   */
+  private static final String FINDER_TYPE = "FNDR";
 
-    /**
- * The first parameter that needs to be passed into Runtime.exec() to open the default web
- * browser on Windows.
- */
-    private static final String FIRST_WINDOWS_PARAMETER = "/c";
+  /**
+   * The creator code of the Finder on a Macintosh, which is needed to send AppleEvents to the
+   * application.
+   */
+  private static final String FINDER_CREATOR = "MACS";
 
-    /** The second parameter for Runtime.exec() on Windows. */
-    private static final String SECOND_WINDOWS_PARAMETER = "start";
+  /** The name for the AppleEvent type corresponding to a GetURL event. */
+  private static final String GURL_EVENT = "GURL";
 
-    /**
- * The third parameter for Runtime.exec() on Windows.  This is a "title"
- * parameter that the command line expects.  Setting this parameter allows
- * URLs containing spaces to work.
- */
-    private static final String THIRD_WINDOWS_PARAMETER = "\"\"";
+  /**
+   * The first parameter that needs to be passed into Runtime.exec() to open the default web
+   * browser on Windows.
+   */
+  private static final String FIRST_WINDOWS_PARAMETER = "/c";
 
-    /**
- * The shell parameters for Netscape that opens a given URL in an already-open copy of Netscape
- * on many command-line systems.
- */
-    private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";
-    private static final String NETSCAPE_OPEN_PARAMETER_START = "openURL(";
-    private static final String NETSCAPE_OPEN_NEW_WINDOW = ", new-window";
-    private static final String NETSCAPE_OPEN_PARAMETER_END = ")";
+  /** The second parameter for Runtime.exec() on Windows. */
+  private static final String SECOND_WINDOWS_PARAMETER = "start";
 
-    /**
- * The message from any exception thrown throughout the initialization process.
- */
-    private static String errorMessage;
+  /**
+   * The third parameter for Runtime.exec() on Windows.  This is a "title"
+   * parameter that the command line expects.  Setting this parameter allows
+   * URLs containing spaces to work.
+   */
+  private static final String THIRD_WINDOWS_PARAMETER = "\"\"";
 
-    /**
- * An initialization block that determines the operating system and loads the necessary
- * runtime data.
- */
-    static {
-        loadedWithoutErrors = true;
-
-        String osName = System.getProperty("os.name");
-
-        if (osName.startsWith("Mac OS")) {
-            String mrjVersion = System.getProperty("mrj.version");
-            String majorMRJVersion = mrjVersion.substring(0, 3);
-
-            try {
-                double version = Double.valueOf(majorMRJVersion).doubleValue();
-
-                if (version == 2) {
-                    jvm = MRJ_2_0;
-                } else if ((version >= 2.1) && (version < 3)) {
-                    // Assume that all 2.x versions of MRJ work the same.  MRJ 2.1 actually
-                    // works via Runtime.exec() and 2.2 supports that but has an openURL() method
-                    // as well that we currently ignore.
-                    jvm = MRJ_2_1;
-                } else if (version == 3.0) {
-                    jvm = MRJ_3_0;
-                } else if (version >= 3.1) {
-                    // Assume that all 3.1 and later versions of MRJ work the same.
-                    jvm = MRJ_3_1;
-                } else {
-                    loadedWithoutErrors = false;
-                    errorMessage = "Unsupported MRJ version: " + version;
-                }
-            } catch (NumberFormatException nfe) {
-                loadedWithoutErrors = false;
-                errorMessage = "Invalid MRJ version: " + mrjVersion;
-            }
-        } else if (osName.startsWith("Windows")) {
-            if (osName.indexOf("9") != -1) {
-                jvm = WINDOWS_9x;
-            } else {
-                jvm = WINDOWS_NT;
-            }
-        } else {
-            jvm = OTHER;
-        }
+  /**
+   * The shell parameters for Netscape that opens a given URL in an already-open copy of Netscape
+   * on many command-line systems.
+   */
+  private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";
+  private static final String NETSCAPE_OPEN_PARAMETER_START = "openURL(";
+  private static final String NETSCAPE_OPEN_NEW_WINDOW = ", new-window";
+  private static final String NETSCAPE_OPEN_PARAMETER_END = ")";
+
+  /**
+   * The message from any exception thrown throughout the initialization process.
+   */
+  private static String errorMessage;
 
-        if (loadedWithoutErrors) { // if we haven't hit any errors yet
-            loadedWithoutErrors = loadClasses();
+  /**
+   * An initialization block that determines the operating system and loads the necessary
+   * runtime data.
+   */
+  static
+  {
+    loadedWithoutErrors = true;
+
+    String osName = System.getProperty("os.name");
+
+    if (osName.startsWith("Mac OS"))
+    {
+      String mrjVersion = System.getProperty("mrj.version");
+      String majorMRJVersion = mrjVersion.substring(0, 3);
+
+      try
+      {
+        double version = Double.valueOf(majorMRJVersion).doubleValue();
+
+        if (version == 2)
+        {
+          jvm = MRJ_2_0;
+        }
+        else if ( (version >= 2.1) && (version < 3))
+        {
+          // Assume that all 2.x versions of MRJ work the same.  MRJ 2.1 actually
+          // works via Runtime.exec() and 2.2 supports that but has an openURL() method
+          // as well that we currently ignore.
+          jvm = MRJ_2_1;
+        }
+        else if (version == 3.0)
+        {
+          jvm = MRJ_3_0;
         }
+        else if (version >= 3.1)
+        {
+          // Assume that all 3.1 and later versions of MRJ work the same.
+          jvm = MRJ_3_1;
+        }
+        else
+        {
+          loadedWithoutErrors = false;
+          errorMessage = "Unsupported MRJ version: " + version;
+        }
+      }
+      catch (NumberFormatException nfe)
+      {
+        loadedWithoutErrors = false;
+        errorMessage = "Invalid MRJ version: " + mrjVersion;
+      }
+    }
+    else if (osName.startsWith("Windows"))
+    {
+      if (osName.indexOf("9") != -1)
+      {
+        jvm = WINDOWS_9x;
+      }
+      else
+      {
+        jvm = WINDOWS_NT;
+      }
+    }
+    else
+    {
+      jvm = OTHER;
     }
 
-    /**
- * This class should be never be instantiated; this just ensures so.
- */
-    private BrowserLauncher() {
+    if (loadedWithoutErrors)
+    { // if we haven't hit any errors yet
+      loadedWithoutErrors = loadClasses();
     }
+  }
+
+  /**
+   * This class should be never be instantiated; this just ensures so.
+   */
+  private BrowserLauncher()
+  {
+  }
+
+  /**
+   * Called by a static initializer to load any classes, fields, and methods required at runtime
+   * to locate the user's web browser.
+   * @return <code>true</code> if all intialization succeeded
+   *                        <code>false</code> if any portion of the initialization failed
+   */
+  private static boolean loadClasses()
+  {
+    switch (jvm)
+    {
+      case MRJ_2_0:
+
+        try
+        {
+          Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");
+          Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");
+          Class appleEventClass = Class.forName(
+              "com.apple.MacOS.AppleEvent");
+          Class aeClass = Class.forName("com.apple.MacOS.ae");
+          aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
+
+          aeTargetConstructor = aeTargetClass.getDeclaredConstructor(new Class[]
+              {
+              int.class
+          });
+          appleEventConstructor = appleEventClass.getDeclaredConstructor(new
+              Class[]
+              {
+              int.class, int.class, aeTargetClass, int.class,
+              int.class
+          });
+          aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[]
+              {
+              String.class
+          });
+
+          makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",
+              new Class[]
+              {String.class});
+          putParameter = appleEventClass.getDeclaredMethod("putParameter",
+              new Class[]
+              {int.class, aeDescClass});
+          sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",
+              new Class[]
+              {});
+
+          Field keyDirectObjectField = aeClass.getDeclaredField(
+              "keyDirectObject");
+          keyDirectObject = (Integer) keyDirectObjectField.get(null);
+
+          Field autoGenerateReturnIDField = appleEventClass.getDeclaredField(
+              "kAutoGenerateReturnID");
+          kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField.get(null);
+
+          Field anyTransactionIDField = appleEventClass.getDeclaredField(
+              "kAnyTransactionID");
+          kAnyTransactionID = (Integer) anyTransactionIDField.get(null);
+        }
+        catch (ClassNotFoundException cnfe)
+        {
+          errorMessage = cnfe.getMessage();
 
-    /**
- * Called by a static initializer to load any classes, fields, and methods required at runtime
- * to locate the user's web browser.
- * @return <code>true</code> if all intialization succeeded
- *                        <code>false</code> if any portion of the initialization failed
- */
-    private static boolean loadClasses() {
-        switch (jvm) {
-        case MRJ_2_0:
-
-            try {
-                Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");
-                Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");
-                Class appleEventClass = Class.forName(
-                        "com.apple.MacOS.AppleEvent");
-                Class aeClass = Class.forName("com.apple.MacOS.ae");
-                aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
-
-                aeTargetConstructor = aeTargetClass.getDeclaredConstructor(new Class[] {
-                            int.class
-                        });
-                appleEventConstructor = appleEventClass.getDeclaredConstructor(new Class[] {
-                            int.class, int.class, aeTargetClass, int.class,
-                            int.class
-                        });
-                aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[] {
-                            String.class
-                        });
-
-                makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",
-                        new Class[] { String.class });
-                putParameter = appleEventClass.getDeclaredMethod("putParameter",
-                        new Class[] { int.class, aeDescClass });
-                sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",
-                        new Class[] {  });
-
-                Field keyDirectObjectField = aeClass.getDeclaredField(
-                        "keyDirectObject");
-                keyDirectObject = (Integer) keyDirectObjectField.get(null);
-
-                Field autoGenerateReturnIDField = appleEventClass.getDeclaredField(
-                        "kAutoGenerateReturnID");
-                kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField.get(null);
-
-                Field anyTransactionIDField = appleEventClass.getDeclaredField(
-                        "kAnyTransactionID");
-                kAnyTransactionID = (Integer) anyTransactionIDField.get(null);
-            } catch (ClassNotFoundException cnfe) {
-                errorMessage = cnfe.getMessage();
-
-                return false;
-            } catch (NoSuchMethodException nsme) {
-                errorMessage = nsme.getMessage();
-
-                return false;
-            } catch (NoSuchFieldException nsfe) {
-                errorMessage = nsfe.getMessage();
-
-                return false;
-            } catch (IllegalAccessException iae) {
-                errorMessage = iae.getMessage();
-
-                return false;
-            }
+          return false;
+        }
+        catch (NoSuchMethodException nsme)
+        {
+          errorMessage = nsme.getMessage();
 
-            break;
+          return false;
+        }
+        catch (NoSuchFieldException nsfe)
+        {
+          errorMessage = nsfe.getMessage();
 
-        case MRJ_2_1:
+          return false;
+        }
+        catch (IllegalAccessException iae)
+        {
+          errorMessage = iae.getMessage();
 
-            try {
-                mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
-                mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");
-
-                Field systemFolderField = mrjFileUtilsClass.getDeclaredField(
-                        "kSystemFolderType");
-                kSystemFolderType = systemFolderField.get(null);
-                findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",
-                        new Class[] { mrjOSTypeClass });
-                getFileCreator = mrjFileUtilsClass.getDeclaredMethod("getFileCreator",
-                        new Class[] { File.class });
-                getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",
-                        new Class[] { File.class });
-            } catch (ClassNotFoundException cnfe) {
-                errorMessage = cnfe.getMessage();
-
-                return false;
-            } catch (NoSuchFieldException nsfe) {
-                errorMessage = nsfe.getMessage();
-
-                return false;
-            } catch (NoSuchMethodException nsme) {
-                errorMessage = nsme.getMessage();
-
-                return false;
-            } catch (SecurityException se) {
-                errorMessage = se.getMessage();
-
-                return false;
-            } catch (IllegalAccessException iae) {
-                errorMessage = iae.getMessage();
-
-                return false;
-            }
+          return false;
+        }
 
-            break;
+        break
+            ;
+
+      case MRJ_2_1:
+
+        try
+        {
+          mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
+          mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");
+
+          Field systemFolderField = mrjFileUtilsClass.getDeclaredField(
+              "kSystemFolderType");
+          kSystemFolderType = systemFolderField.get(null);
+          findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",
+              new Class[]
+              {mrjOSTypeClass});
+          getFileCreator = mrjFileUtilsClass.getDeclaredMethod("getFileCreator",
+              new Class[]
+              {File.class});
+          getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",
+              new Class[]
+              {File.class});
+        }
+        catch (ClassNotFoundException cnfe)
+        {
+          errorMessage = cnfe.getMessage();
 
-        case MRJ_3_0:
+          return false;
+        }
+        catch (NoSuchFieldException nsfe)
+        {
+          errorMessage = nsfe.getMessage();
 
-            try {
-                Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
-                Constructor constructor = linker.getConstructor(new Class[] {
-                            Class.class
-                        });
-                linkage = constructor.newInstance(new Object[] {
-                            BrowserLauncher.class
-                        });
-            } catch (ClassNotFoundException cnfe) {
-                errorMessage = cnfe.getMessage();
+          return false;
+        }
+        catch (NoSuchMethodException nsme)
+        {
+          errorMessage = nsme.getMessage();
 
-                return false;
-            } catch (NoSuchMethodException nsme) {
-                errorMessage = nsme.getMessage();
+          return false;
+        }
+        catch (SecurityException se)
+        {
+          errorMessage = se.getMessage();
 
-                return false;
-            } catch (InvocationTargetException ite) {
-                errorMessage = ite.getMessage();
+          return false;
+        }
+        catch (IllegalAccessException iae)
+        {
+          errorMessage = iae.getMessage();
 
-                return false;
-            } catch (InstantiationException ie) {
-                errorMessage = ie.getMessage();
+          return false;
+        }
 
-                return false;
-            } catch (IllegalAccessException iae) {
-                errorMessage = iae.getMessage();
+        break
+            ;
+
+      case MRJ_3_0:
+
+        try
+        {
+          Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
+          Constructor constructor = linker.getConstructor(new Class[]
+              {
+              Class.class
+          });
+          linkage = constructor.newInstance(new Object[]
+                                            {
+                                            BrowserLauncher.class
+          });
+        }
+        catch (ClassNotFoundException cnfe)
+        {
+          errorMessage = cnfe.getMessage();
 
-                return false;
-            }
+          return false;
+        }
+        catch (NoSuchMethodException nsme)
+        {
+          errorMessage = nsme.getMessage();
 
-            break;
+          return false;
+        }
+        catch (InvocationTargetException ite)
+        {
+          errorMessage = ite.getMessage();
 
-        case MRJ_3_1:
+          return false;
+        }
+        catch (InstantiationException ie)
+        {
+          errorMessage = ie.getMessage();
 
-            try {
-                mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
-                openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",
-                        new Class[] { String.class });
-            } catch (ClassNotFoundException cnfe) {
-                errorMessage = cnfe.getMessage();
+          return false;
+        }
+        catch (IllegalAccessException iae)
+        {
+          errorMessage = iae.getMessage();
 
-                return false;
-            } catch (NoSuchMethodException nsme) {
-                errorMessage = nsme.getMessage();
+          return false;
+        }
 
-                return false;
-            }
+        break
+            ;
 
-            break;
+      case MRJ_3_1:
 
-        default:
-            break;
+        try
+        {
+          mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
+          openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",
+              new Class[]
+              {String.class});
         }
+        catch (ClassNotFoundException cnfe)
+        {
+          errorMessage = cnfe.getMessage();
 
-        return true;
-    }
+          return false;
+        }
+        catch (NoSuchMethodException nsme)
+        {
+          errorMessage = nsme.getMessage();
 
-    /**
- * Attempts to locate the default web browser on the local system.  Caches results so it
- * only locates the browser once for each use of this class per JVM instance.
- * @return The browser for the system.  Note that this may not be what you would consider
- *                        to be a standard web browser; instead, it's the application that gets called to
- *                        open the default web browser.  In some cases, this will be a non-String object
- *                        that provides the means of calling the default browser.
- */
-    private static Object locateBrowser() {
-        if (browser != null) {
-            return browser;
+          return false;
         }
 
-        switch (jvm) {
-        case MRJ_2_0:
-
-            try {
-                Integer finderCreatorCode = (Integer) makeOSType.invoke(null,
-                        new Object[] { FINDER_CREATOR });
-                Object aeTarget = aeTargetConstructor.newInstance(new Object[] {
-                            finderCreatorCode
-                        });
-                Integer gurlType = (Integer) makeOSType.invoke(null,
-                        new Object[] { GURL_EVENT });
-                Object appleEvent = appleEventConstructor.newInstance(new Object[] {
-                            gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
-                            kAnyTransactionID
-                        });
-
-                // Don't set browser = appleEvent because then the next time we call
-                // locateBrowser(), we'll get the same AppleEvent, to which we'll already have
-                // added the relevant parameter. Instead, regenerate the AppleEvent every time.
-                // There's probably a way to do this better; if any has any ideas, please let
-                // me know.
-                return appleEvent;
-            } catch (IllegalAccessException iae) {
-                browser = null;
-                errorMessage = iae.getMessage();
-
-                return browser;
-            } catch (InstantiationException ie) {
-                browser = null;
-                errorMessage = ie.getMessage();
-
-                return browser;
-            } catch (InvocationTargetException ite) {
-                browser = null;
-                errorMessage = ite.getMessage();
-
-                return browser;
-            }
+        break
+            ;
 
-        case MRJ_2_1:
+      default:
+        break;
+    }
 
-            File systemFolder;
+    return true;
+  }
+
+  /**
+   * Attempts to locate the default web browser on the local system.  Caches results so it
+   * only locates the browser once for each use of this class per JVM instance.
+   * @return The browser for the system.  Note that this may not be what you would consider
+   *                        to be a standard web browser; instead, it's the application that gets called to
+   *                        open the default web browser.  In some cases, this will be a non-String object
+   *                        that provides the means of calling the default browser.
+   */
+  private static Object locateBrowser()
+  {
+    if (browser != null)
+    {
+      return browser;
+    }
 
-            try {
-                systemFolder = (File) findFolder.invoke(null,
-                        new Object[] { kSystemFolderType });
-            } catch (IllegalArgumentException iare) {
-                browser = null;
-                errorMessage = iare.getMessage();
+    switch (jvm)
+    {
+      case MRJ_2_0:
+
+        try
+        {
+          Integer finderCreatorCode = (Integer) makeOSType.invoke(null,
+              new Object[]
+              {FINDER_CREATOR});
+          Object aeTarget = aeTargetConstructor.newInstance(new Object[]
+              {
+              finderCreatorCode
+          });
+          Integer gurlType = (Integer) makeOSType.invoke(null,
+              new Object[]
+              {GURL_EVENT});
+          Object appleEvent = appleEventConstructor.newInstance(new Object[]
+              {
+              gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
+              kAnyTransactionID
+          });
+
+          // Don't set browser = appleEvent because then the next time we call
+          // locateBrowser(), we'll get the same AppleEvent, to which we'll already have
+          // added the relevant parameter. Instead, regenerate the AppleEvent every time.
+          // There's probably a way to do this better; if any has any ideas, please let
+          // me know.
+          return appleEvent;
+        }
+        catch (IllegalAccessException iae)
+        {
+          browser = null;
+          errorMessage = iae.getMessage();
 
-                return browser;
-            } catch (IllegalAccessException iae) {
-                browser = null;
-                errorMessage = iae.getMessage();
+          return browser;
+        }
+        catch (InstantiationException ie)
+        {
+          browser = null;
+          errorMessage = ie.getMessage();
 
-                return browser;
-            } catch (InvocationTargetException ite) {
-                browser = null;
-                errorMessage = ite.getTargetException().getClass() + ": " +
-                    ite.getTargetException().getMessage();
+          return browser;
+        }
+        catch (InvocationTargetException ite)
+        {
+          browser = null;
+          errorMessage = ite.getMessage();
 
-                return browser;
-            }
+          return browser;
+        }
 
-            String[] systemFolderFiles = systemFolder.list();
-
-            // Avoid a FilenameFilter because that can't be stopped mid-list
-            for (int i = 0; i < systemFolderFiles.length; i++) {
-                try {
-                    File file = new File(systemFolder, systemFolderFiles[i]);
-
-                    if (!file.isFile()) {
-                        continue;
-                    }
-
-                    // We're looking for a file with a creator code of 'MACS' and
-                    // a type of 'FNDR'.  Only requiring the type results in non-Finder
-                    // applications being picked up on certain Mac OS 9 systems,
-                    // especially German ones, and sending a GURL event to those
-                    // applications results in a logout under Multiple Users.
-                    Object fileType = getFileType.invoke(null,
-                            new Object[] { file });
-
-                    if (FINDER_TYPE.equals(fileType.toString())) {
-                        Object fileCreator = getFileCreator.invoke(null,
-                                new Object[] { file });
-
-                        if (FINDER_CREATOR.equals(fileCreator.toString())) {
-                            browser = file.toString(); // Actually the Finder, but that's OK
-
-                            return browser;
-                        }
-                    }
-                } catch (IllegalArgumentException iare) {
-                    browser = browser;
-                    errorMessage = iare.getMessage();
-
-                    return null;
-                } catch (IllegalAccessException iae) {
-                    browser = null;
-                    errorMessage = iae.getMessage();
-
-                    return browser;
-                } catch (InvocationTargetException ite) {
-                    browser = null;
-                    errorMessage = ite.getTargetException().getClass() + ": " +
-                        ite.getTargetException().getMessage();
-
-                    return browser;
-                }
-            }
+        case MRJ_2_1:
 
+          File systemFolder;
+
+          try
+          {
+            systemFolder = (File) findFolder.invoke(null,
+                new Object[]
+                {kSystemFolderType});
+          }
+          catch (IllegalArgumentException iare)
+          {
             browser = null;
+            errorMessage = iare.getMessage();
 
-            break;
+            return browser;
+          }
+          catch (IllegalAccessException iae)
+          {
+            browser = null;
+            errorMessage = iae.getMessage();
 
-        case MRJ_3_0:
-        case MRJ_3_1:
-            browser = ""; // Return something non-null
+            return browser;
+          }
+          catch (InvocationTargetException ite)
+          {
+            browser = null;
+            errorMessage = ite.getTargetException().getClass() + ": " +
+                ite.getTargetException().getMessage();
 
-            break;
+            return browser;
+          }
+
+          String[] systemFolderFiles = systemFolder.list();
+
+          // Avoid a FilenameFilter because that can't be stopped mid-list
+          for (int i = 0; i < systemFolderFiles.length; i++)
+          {
+            try
+            {
+              File file = new File(systemFolder, systemFolderFiles[i]);
+
+              if (!file.isFile())
+              {
+                continue;
+              }
+
+              // We're looking for a file with a creator code of 'MACS' and
+              // a type of 'FNDR'.  Only requiring the type results in non-Finder
+              // applications being picked up on certain Mac OS 9 systems,
+              // especially German ones, and sending a GURL event to those
+              // applications results in a logout under Multiple Users.
+              Object fileType = getFileType.invoke(null,
+                  new Object[]
+                  {file});
+
+              if (FINDER_TYPE.equals(fileType.toString()))
+              {
+                Object fileCreator = getFileCreator.invoke(null,
+                    new Object[]
+                    {file});
+
+                if (FINDER_CREATOR.equals(fileCreator.toString()))
+                {
+                  browser = file.toString(); // Actually the Finder, but that's OK
+
+                  return browser;
+                }
+              }
+            }
+            catch (IllegalArgumentException iare)
+            {
+              browser = browser;
+              errorMessage = iare.getMessage();
 
-        case WINDOWS_NT:
-            browser = "cmd.exe";
+              return null;
+            }
+            catch (IllegalAccessException iae)
+            {
+              browser = null;
+              errorMessage = iae.getMessage();
 
-            break;
+              return browser;
+            }
+            catch (InvocationTargetException ite)
+            {
+              browser = null;
+              errorMessage = ite.getTargetException().getClass() + ": " +
+                  ite.getTargetException().getMessage();
 
-        case WINDOWS_9x:
-            browser = "command.com";
+              return browser;
+            }
+          }
 
-            break;
+          browser = null;
 
-        case OTHER:default:
-            browser = jalview.bin.Cache.applicationProperties.getProperty(
-                    "jalview.browser");
+          break;
 
-            if (browser == null) {
-                // hope firefox exists :-/
-                browser = "firefox";
-            }
+      case MRJ_3_0:
+      case MRJ_3_1:
+        browser = ""; // Return something non-null
 
-            break;
-        }
+        break;
 
-        return browser;
-    }
+      case WINDOWS_NT:
+        browser = "cmd.exe";
 
-    /**
- * Attempts to open the default web browser to the given URL.
- * @param url The URL to open
- * @throws IOException If the web browser could not be located or does not run
- */
-    public static void openURL(String url) throws IOException {
-        if (!loadedWithoutErrors) {
-            throw new IOException("Exception in finding browser: " +
-                errorMessage);
-        }
-
-        Object browser = locateBrowser();
-
-        if (browser == null) {
-            throw new IOException("Unable to locate browser: " + errorMessage);
-        }
-
-        switch (jvm) {
-        case MRJ_2_0:
-
-            Object aeDesc = null;
-
-            try {
-                aeDesc = aeDescConstructor.newInstance(new Object[] { url });
-                putParameter.invoke(browser,
-                    new Object[] { keyDirectObject, aeDesc });
-                sendNoReply.invoke(browser, new Object[] {  });
-            } catch (InvocationTargetException ite) {
-                throw new IOException(
-                    "InvocationTargetException while creating AEDesc: " +
-                    ite.getMessage());
-            } catch (IllegalAccessException iae) {
-                throw new IOException(
-                    "IllegalAccessException while building AppleEvent: " +
-                    iae.getMessage());
-            } catch (InstantiationException ie) {
-                throw new IOException(
-                    "InstantiationException while creating AEDesc: " +
-                    ie.getMessage());
-            } finally {
-                aeDesc = null; // Encourage it to get disposed if it was created
-                browser = null; // Ditto
-            }
+        break;
 
-            break;
+      case WINDOWS_9x:
+        browser = "command.com";
 
-        case MRJ_2_1:
-            Runtime.getRuntime().exec(new String[] { (String) browser, url });
+        break;
 
-            break;
+      case OTHER:
+      default:
+        browser = jalview.bin.Cache.applicationProperties.getProperty(
+            "jalview.browser");
 
-        case MRJ_3_0:
+        if (browser == null)
+        {
+          // hope firefox exists :-/
+          browser = "firefox";
+        }
 
-            int[] instance = new int[1];
-            int result = ICStart(instance, 0);
+        break;
+    }
 
-            if (result == 0) {
-                int[] selectionStart = new int[] { 0 };
-                byte[] urlBytes = url.getBytes();
-                int[] selectionEnd = new int[] { urlBytes.length };
-                result = ICLaunchURL(instance[0], new byte[] { 0 }, urlBytes,
-                        urlBytes.length, selectionStart, selectionEnd);
+    return browser;
+  }
+
+  /**
+   * Attempts to open the default web browser to the given URL.
+   * @param url The URL to open
+   * @throws IOException If the web browser could not be located or does not run
+   */
+  public static void openURL(String url)
+      throws IOException
+  {
+    if (!loadedWithoutErrors)
+    {
+      throw new IOException("Exception in finding browser: " +
+                            errorMessage);
+    }
 
-                if (result == 0) {
-                    // Ignore the return value; the URL was launched successfully
-                    // regardless of what happens here.
-                    ICStop(instance);
-                } else {
-                    throw new IOException("Unable to launch URL: " + result);
-                }
-            } else {
-                throw new IOException(
-                    "Unable to create an Internet Config instance: " + result);
-            }
+    Object browser = locateBrowser();
 
-            break;
+    if (browser == null)
+    {
+      throw new IOException("Unable to locate browser: " + errorMessage);
+    }
 
-        case MRJ_3_1:
+    switch (jvm)
+    {
+      case MRJ_2_0:
+
+        Object aeDesc = null;
+
+        try
+        {
+          aeDesc = aeDescConstructor.newInstance(new Object[]
+                                                 {url});
+          putParameter.invoke(browser,
+                              new Object[]
+                              {keyDirectObject, aeDesc});
+          sendNoReply.invoke(browser, new Object[]
+                             {});
+        }
+        catch (InvocationTargetException ite)
+        {
+          throw new IOException(
+              "InvocationTargetException while creating AEDesc: " +
+              ite.getMessage());
+        }
+        catch (IllegalAccessException iae)
+        {
+          throw new IOException(
+              "IllegalAccessException while building AppleEvent: " +
+              iae.getMessage());
+        }
+        catch (InstantiationException ie)
+        {
+          throw new IOException(
+              "InstantiationException while creating AEDesc: " +
+              ie.getMessage());
+        }
+        finally
+        {
+          aeDesc = null; // Encourage it to get disposed if it was created
+          browser = null; // Ditto
+        }
 
-            try {
-                openURL.invoke(null, new Object[] { url });
-            } catch (InvocationTargetException ite) {
-                throw new IOException(
-                    "InvocationTargetException while calling openURL: " +
-                    ite.getMessage());
-            } catch (IllegalAccessException iae) {
-                throw new IOException(
-                    "IllegalAccessException while calling openURL: " +
-                    iae.getMessage());
-            }
+        break;
+
+      case MRJ_2_1:
+        Runtime.getRuntime().exec(new String[]
+                                  { (String) browser, url});
+
+        break;
+
+      case MRJ_3_0:
+
+        int[] instance = new int[1];
+        int result = ICStart(instance, 0);
+
+        if (result == 0)
+        {
+          int[] selectionStart = new int[]
+              {
+              0};
+          byte[] urlBytes = url.getBytes();
+          int[] selectionEnd = new int[]
+              {
+              urlBytes.length};
+          result = ICLaunchURL(instance[0], new byte[]
+                               {0}, urlBytes,
+                               urlBytes.length, selectionStart, selectionEnd);
+
+          if (result == 0)
+          {
+            // Ignore the return value; the URL was launched successfully
+            // regardless of what happens here.
+            ICStop(instance);
+          }
+          else
+          {
+            throw new IOException("Unable to launch URL: " + result);
+          }
+        }
+        else
+        {
+          throw new IOException(
+              "Unable to create an Internet Config instance: " + result);
+        }
 
-            break;
-
-        case WINDOWS_NT:
-        case WINDOWS_9x:
-
-            // Add quotes around the URL to allow ampersands and other special
-            // characters to work.
-            Process process = Runtime.getRuntime().exec(new String[] {
-                        (String) browser, FIRST_WINDOWS_PARAMETER,
-                        SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,
-                        '"' + url + '"'
-                    });
-
-            // This avoids a memory leak on some versions of Java on Windows.
-            // That's hinted at in <http://developer.java.sun.com/developer/qow/archive/68/>.
-            try {
-                process.waitFor();
-                process.exitValue();
-            } catch (InterruptedException ie) {
-                throw new IOException(
-                    "InterruptedException while launching browser: " +
-                    ie.getMessage());
-            }
+        break;
 
-            break;
+      case MRJ_3_1:
 
-        case OTHER:
+        try
+        {
+          openURL.invoke(null, new Object[]
+                         {url});
+        }
+        catch (InvocationTargetException ite)
+        {
+          throw new IOException(
+              "InvocationTargetException while calling openURL: " +
+              ite.getMessage());
+        }
+        catch (IllegalAccessException iae)
+        {
+          throw new IOException(
+              "IllegalAccessException while calling openURL: " +
+              iae.getMessage());
+        }
 
-            // Assume that we're on Unix and that Netscape (actually Firefox) is installed
-            // First, attempt to open the URL in a currently running session of Netscape
-            // JBPNote log debug
+        break
+            ;
+
+      case WINDOWS_NT:
+      case WINDOWS_9x:
+
+        // Add quotes around the URL to allow ampersands and other special
+        // characters to work.
+        Process process = Runtime.getRuntime().exec(new String[]
+            {
+            (String) browser, FIRST_WINDOWS_PARAMETER,
+            SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,
+            '"' + url + '"'
+        });
+
+        // This avoids a memory leak on some versions of Java on Windows.
+        // That's hinted at in <http://developer.java.sun.com/developer/qow/archive/68/>.
+        try
+        {
+          process.waitFor();
+          process.exitValue();
+        }
+        catch (InterruptedException ie)
+        {
+          throw new IOException(
+              "InterruptedException while launching browser: " +
+              ie.getMessage());
+        }
 
-            /* System.out.println("Executing : "+browser+" "+
-                                                                                                    NETSCAPE_REMOTE_PARAMETER+" "+
-                                                                                                    NETSCAPE_OPEN_PARAMETER_START +
-                                                                                                    url +
-                                                                                                    NETSCAPE_OPEN_NEW_WINDOW +
-                                                                                                    NETSCAPE_OPEN_PARAMETER_END);
- */
-            process = Runtime.getRuntime().exec(new String[] {
-                        (String) browser, NETSCAPE_REMOTE_PARAMETER,
-                        
-                    NETSCAPE_OPEN_PARAMETER_START + url +
-                        NETSCAPE_OPEN_NEW_WINDOW + NETSCAPE_OPEN_PARAMETER_END
-                    });
-
-            try {
-                int exitCode = process.waitFor();
-
-                if (exitCode != 0) { // if Netscape was not open
-                    Runtime.getRuntime().exec(new String[] { (String) browser, url });
-                }
-            } catch (InterruptedException ie) {
-                throw new IOException(
-                    "InterruptedException while launching browser: " +
-                    ie.getMessage());
-            }
+        break
+            ;
+
+      case OTHER:
+
+        // Assume that we're on Unix and that Netscape (actually Firefox) is installed
+        // First, attempt to open the URL in a currently running session of Netscape
+        // JBPNote log debug
+
+        /* System.out.println("Executing : "+browser+" "+
+         NETSCAPE_REMOTE_PARAMETER+" "+
+         NETSCAPE_OPEN_PARAMETER_START +
+         url +
+         NETSCAPE_OPEN_NEW_WINDOW +
+         NETSCAPE_OPEN_PARAMETER_END);
+         */
+        process = Runtime.getRuntime().exec(new String[]
+                                            {
+                                            (String) browser,
+                                            NETSCAPE_REMOTE_PARAMETER,
+
+                                            NETSCAPE_OPEN_PARAMETER_START + url +
+                                            NETSCAPE_OPEN_NEW_WINDOW +
+                                            NETSCAPE_OPEN_PARAMETER_END
+        });
+
+        try
+        {
+          int exitCode = process.waitFor();
+
+          if (exitCode != 0)
+          { // if Netscape was not open
+            Runtime.getRuntime().exec(new String[]
+                                      { (String) browser, url});
+          }
+        }
+        catch (InterruptedException ie)
+        {
+          throw new IOException(
+              "InterruptedException while launching browser: " +
+              ie.getMessage());
+        }
 
-            break;
+        break
+            ;
 
-        default:
+      default:
 
-            // This should never occur, but if it does, we'll try the simplest thing possible
-            Runtime.getRuntime().exec(new String[] { (String) browser, url });
+        // This should never occur, but if it does, we'll try the simplest thing possible
+        Runtime.getRuntime().exec(new String[]
+                                  { (String) browser, url});
 
-            break;
-        }
+        break;
     }
+  }
 
-    /**
- * Methods required for Mac OS X.  The presence of native methods does not cause
- * any problems on other platforms.
- */
-    private native static int ICStart(int[] instance, int signature);
+  /**
+   * Methods required for Mac OS X.  The presence of native methods does not cause
+   * any problems on other platforms.
+   */
+  private native static int ICStart(int[] instance, int signature);
 
-    private native static int ICStop(int[] instance);
+  private native static int ICStop(int[] instance);
 
-    private native static int ICLaunchURL(int instance, byte[] hint,
-        byte[] data, int len, int[] selectionStart, int[] selectionEnd);
+  private native static int ICLaunchURL(int instance, byte[] hint,
+                                        byte[] data, int len,
+                                        int[] selectionStart,
+                                        int[] selectionEnd);
 }
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 8041d80..c779bb1 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -21,10 +21,27 @@ package jalview.util;
 import jalview.datamodel.*;
 
 
-public class Comparison {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Comparison
+{
+    /** DOCUMENT ME!! */
     public static String GapChars = " .-";
 
-    public static float compare(SequenceI ii, SequenceI jj) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ii DOCUMENT ME!
+     * @param jj DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static float compare(SequenceI ii, SequenceI jj)
+    {
         return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
     }
 
@@ -36,18 +53,21 @@ public class Comparison {
      * @param end int
      * @return float
      */
-    public static float compare(SequenceI ii, SequenceI jj, int start, int end) {
+    public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+    {
         String si = ii.getSequence();
         String sj = jj.getSequence();
 
         int ilen = si.length() - 1;
         int jlen = sj.length() - 1;
 
-        while (jalview.util.Comparison.isGap(si.charAt(start + ilen))) {
+        while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+        {
             ilen--;
         }
 
-        while (jalview.util.Comparison.isGap(sj.charAt(start + jlen))) {
+        while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+        {
             jlen--;
         }
 
@@ -55,10 +75,13 @@ public class Comparison {
         int match = 0;
         float pid = -1;
 
-        if (ilen > jlen) {
-            for (int j = 0; j < jlen; j++) {
+        if (ilen > jlen)
+        {
+            for (int j = 0; j < jlen; j++)
+            {
                 if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
-                                j, start + j + 1))) {
+                                j, start + j + 1)))
+                {
                     match++;
                 }
 
@@ -66,10 +89,14 @@ public class Comparison {
             }
 
             pid = (float) match / (float) ilen * 100;
-        } else {
-            for (int j = 0; j < jlen; j++) {
+        }
+        else
+        {
+            for (int j = 0; j < jlen; j++)
+            {
                 if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
-                                j, start + j + 1))) {
+                                j, start + j + 1)))
+                {
                     match++;
                 }
 
@@ -89,36 +116,49 @@ public class Comparison {
      * @param s2 SequenceI
      * @return float
      */
-    public static float PID(SequenceI s1, SequenceI s2) {
+    public static float PID(SequenceI s1, SequenceI s2)
+    {
         int len;
 
-        if (s1.getSequence().length() > s2.getSequence().length()) {
+        if (s1.getSequence().length() > s2.getSequence().length())
+        {
             len = s1.getSequence().length();
-        } else {
+        }
+        else
+        {
             len = s2.getSequence().length();
         }
 
         int bad = 0;
 
-        for (int i = 0; i < len; i++) {
+        for (int i = 0; i < len; i++)
+        {
             char chr1;
             char chr2;
 
-            if (i < s1.getSequence().length()) {
+            if (i < s1.getSequence().length())
+            {
                 chr1 = s1.getSequence().charAt(i);
-            } else {
+            }
+            else
+            {
                 chr1 = '.';
             }
 
-            if (i < s2.getSequence().length()) {
+            if (i < s2.getSequence().length())
+            {
                 chr2 = s2.getSequence().charAt(i);
-            } else {
+            }
+            else
+            {
                 chr2 = '.';
             }
 
             if (!(jalview.util.Comparison.isGap(chr1)) &&
-                    !(jalview.util.Comparison.isGap(chr2))) {
-                if (chr1 != chr2) {
+                    !(jalview.util.Comparison.isGap(chr2)))
+            {
+                if (chr1 != chr2)
+                {
                     bad++;
                 }
             }
@@ -128,44 +168,59 @@ public class Comparison {
     }
 
     // Another pid with region specification
-    public static float PID(SequenceI s1, SequenceI s2, int start, int end) {
+    public static float PID(SequenceI s1, SequenceI s2, int start, int end)
+    {
         int len;
 
-        if (s1.getSequence().length() > s2.getSequence().length()) {
+        if (s1.getSequence().length() > s2.getSequence().length())
+        {
             len = s1.getSequence().length();
-        } else {
+        }
+        else
+        {
             len = s2.getSequence().length();
         }
 
-        if (end < len) {
+        if (end < len)
+        {
             len = end;
         }
 
-        if (len < start) {
+        if (len < start)
+        {
             start = len - 1; // we just use a single residue for the difference
         }
 
         int bad = 0;
 
-        for (int i = start; i < len; i++) {
+        for (int i = start; i < len; i++)
+        {
             char chr1;
             char chr2;
 
-            if (i < s1.getSequence().length()) {
+            if (i < s1.getSequence().length())
+            {
                 chr1 = s1.getSequence().charAt(i);
-            } else {
+            }
+            else
+            {
                 chr1 = '.';
             }
 
-            if (i < s2.getSequence().length()) {
+            if (i < s2.getSequence().length())
+            {
                 chr2 = s2.getSequence().charAt(i);
-            } else {
+            }
+            else
+            {
                 chr2 = '.';
             }
 
             if (!(jalview.util.Comparison.isGap(chr1)) &&
-                    !(jalview.util.Comparison.isGap(chr2))) {
-                if (chr1 != chr2) {
+                    !(jalview.util.Comparison.isGap(chr2)))
+            {
+                if (chr1 != chr2)
+                {
                     bad++;
                 }
             }
@@ -174,7 +229,15 @@ public class Comparison {
         return ((float) 100 * (len - bad)) / len;
     }
 
-    public static boolean isGap(char c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static boolean isGap(char c)
+    {
         return ((c != '.') && (c != '-') && (c != ' ')) ? false : true;
     }
 }
diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index 4c47f65..629fbcf 100755
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -30,7 +30,14 @@ package jalview.util;
 import java.io.*;
 
 
-public class Format {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Format
+{
     private int width;
     private int precision;
     private String pre;
@@ -42,7 +49,13 @@ public class Format {
     private boolean left_align;
     private char fmt; // one of cdeEfgGiosxXos
 
-    public Format(String s) {
+    /**
+     * Creates a new Format object.
+     *
+     * @param s DOCUMENT ME!
+     */
+    public Format(String s)
+    {
         width = 0;
         precision = -1;
         pre = "";
@@ -62,41 +75,67 @@ public class Format {
         // 4 = format, 5 = end
         int i = 0;
 
-        while (parse_state == 0) {
-            if (i >= length) {
+        while (parse_state == 0)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else if (s.charAt(i) == '%') {
-                if (i < (length - 1)) {
-                    if (s.charAt(i + 1) == '%') {
+            }
+            else if (s.charAt(i) == '%')
+            {
+                if (i < (length - 1))
+                {
+                    if (s.charAt(i + 1) == '%')
+                    {
                         pre = pre + '%';
                         i++;
-                    } else {
+                    }
+                    else
+                    {
                         parse_state = 1;
                     }
-                } else {
+                }
+                else
+                {
                     throw new java.lang.IllegalArgumentException();
                 }
-            } else {
+            }
+            else
+            {
                 pre = pre + s.charAt(i);
             }
 
             i++;
         }
 
-        while (parse_state == 1) {
-            if (i >= length) {
+        while (parse_state == 1)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else if (s.charAt(i) == ' ') {
+            }
+            else if (s.charAt(i) == ' ')
+            {
                 show_space = true;
-            } else if (s.charAt(i) == '-') {
+            }
+            else if (s.charAt(i) == '-')
+            {
                 left_align = true;
-            } else if (s.charAt(i) == '+') {
+            }
+            else if (s.charAt(i) == '+')
+            {
                 show_plus = true;
-            } else if (s.charAt(i) == '0') {
+            }
+            else if (s.charAt(i) == '0')
+            {
                 leading_zeroes = true;
-            } else if (s.charAt(i) == '#') {
+            }
+            else if (s.charAt(i) == '#')
+            {
                 alternate = true;
-            } else {
+            }
+            else
+            {
                 parse_state = 2;
                 i--;
             }
@@ -104,43 +143,62 @@ public class Format {
             i++;
         }
 
-        while (parse_state == 2) {
-            if (i >= length) {
+        while (parse_state == 2)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9')) {
+            }
+            else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
+            {
                 width = ((width * 10) + s.charAt(i)) - '0';
                 i++;
-            } else if (s.charAt(i) == '.') {
+            }
+            else if (s.charAt(i) == '.')
+            {
                 parse_state = 3;
                 precision = 0;
                 i++;
-            } else {
+            }
+            else
+            {
                 parse_state = 4;
             }
         }
 
-        while (parse_state == 3) {
-            if (i >= length) {
+        while (parse_state == 3)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9')) {
+            }
+            else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
+            {
                 precision = ((precision * 10) + s.charAt(i)) - '0';
                 i++;
-            } else {
+            }
+            else
+            {
                 parse_state = 4;
             }
         }
 
-        if (parse_state == 4) {
-            if (i >= length) {
+        if (parse_state == 4)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else {
+            }
+            else
+            {
                 fmt = s.charAt(i);
             }
 
             i++;
         }
 
-        if (i < length) {
+        if (i < length)
+        {
             post = s.substring(i, length);
         }
     }
@@ -181,25 +239,29 @@ public class Format {
      * @exception IllegalArgumentException if bad format
      *
      */
-    public static String getHexString(java.awt.Color color) {
+    public static String getHexString(java.awt.Color color)
+    {
         String r;
         String g;
         String b;
         r = Integer.toHexString(color.getRed());
 
-        if (r.length() < 2) {
+        if (r.length() < 2)
+        {
             r = "0" + r;
         }
 
         g = Integer.toHexString(color.getGreen());
 
-        if (g.length() < 2) {
+        if (g.length() < 2)
+        {
             g = "0" + g;
         }
 
         b = Integer.toHexString(color.getBlue());
 
-        if (b.length() < 2) {
+        if (b.length() < 2)
+        {
             b = "0" + b;
         }
 
@@ -212,7 +274,8 @@ public class Format {
     * @param fmt the format string
     * @param x the double to print
     */
-    public static void print(java.io.PrintStream s, String fmt, double x) {
+    public static void print(java.io.PrintStream s, String fmt, double x)
+    {
         s.print(new Format(fmt).form(x));
     }
 
@@ -222,7 +285,8 @@ public class Format {
     * @param fmt the format string
     * @param x the long to print
     */
-    public static void print(java.io.PrintStream s, String fmt, long x) {
+    public static void print(java.io.PrintStream s, String fmt, long x)
+    {
         s.print(new Format(fmt).form(x));
     }
 
@@ -232,7 +296,8 @@ public class Format {
     * @param fmt the format string
     * @param x the character to
     */
-    public static void print(java.io.PrintStream s, String fmt, char x) {
+    public static void print(java.io.PrintStream s, String fmt, char x)
+    {
         s.print(new Format(fmt).form(x));
     }
 
@@ -241,7 +306,8 @@ public class Format {
     * @param s a PrintStream, fmt the format string
     * @param x a string that represents the digits to print
     */
-    public static void print(java.io.PrintStream s, String fmt, String x) {
+    public static void print(java.io.PrintStream s, String fmt, String x)
+    {
         s.print(new Format(fmt).form(x));
     }
 
@@ -250,7 +316,8 @@ public class Format {
     * @param s a string
     * @return the numeric value of the prefix of s representing a base 10 integer
     */
-    public static int atoi(String s) {
+    public static int atoi(String s)
+    {
         return (int) atol(s);
     }
 
@@ -259,25 +326,41 @@ public class Format {
     * @param s a string
     * @return the numeric value of the prefix of s representing a base 10 integer
     */
-    public static long atol(String s) {
+    public static long atol(String s)
+    {
         int i = 0;
 
         while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
             i++;
 
-        if ((i < s.length()) && (s.charAt(i) == '0')) {
+        if ((i < s.length()) && (s.charAt(i) == '0'))
+        {
             if (((i + 1) < s.length()) &&
-                    ((s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X'))) {
+                    ((s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X')))
+            {
                 return parseLong(s.substring(i + 2), 16);
-            } else {
+            }
+            else
+            {
                 return parseLong(s, 8);
             }
-        } else {
+        }
+        else
+        {
             return parseLong(s, 10);
         }
     }
 
-    private static long parseLong(String s, int base) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param base DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static long parseLong(String s, int base)
+    {
         int i = 0;
         int sign = 1;
         long r = 0;
@@ -285,23 +368,34 @@ public class Format {
         while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
             i++;
 
-        if ((i < s.length()) && (s.charAt(i) == '-')) {
+        if ((i < s.length()) && (s.charAt(i) == '-'))
+        {
             sign = -1;
             i++;
-        } else if ((i < s.length()) && (s.charAt(i) == '+')) {
+        }
+        else if ((i < s.length()) && (s.charAt(i) == '+'))
+        {
             i++;
         }
 
-        while (i < s.length()) {
+        while (i < s.length())
+        {
             char ch = s.charAt(i);
 
-            if (('0' <= ch) && (ch < ('0' + base))) {
+            if (('0' <= ch) && (ch < ('0' + base)))
+            {
                 r = ((r * base) + ch) - '0';
-            } else if (('A' <= ch) && (ch < (('A' + base) - 10))) {
+            }
+            else if (('A' <= ch) && (ch < (('A' + base) - 10)))
+            {
                 r = ((r * base) + ch) - 'A' + 10;
-            } else if (('a' <= ch) && (ch < (('a' + base) - 10))) {
+            }
+            else if (('a' <= ch) && (ch < (('a' + base) - 10)))
+            {
                 r = ((r * base) + ch) - 'a' + 10;
-            } else {
+            }
+            else
+            {
                 return r * sign;
             }
 
@@ -315,7 +409,8 @@ public class Format {
     * Converts a string of digits to an double
     * @param s a string
     */
-    public static double atof(String s) {
+    public static double atof(String s)
+    {
         int i = 0;
         int sign = 1;
         double r = 0; // integer part
@@ -326,34 +421,51 @@ public class Format {
         while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
             i++;
 
-        if ((i < s.length()) && (s.charAt(i) == '-')) {
+        if ((i < s.length()) && (s.charAt(i) == '-'))
+        {
             sign = -1;
             i++;
-        } else if ((i < s.length()) && (s.charAt(i) == '+')) {
+        }
+        else if ((i < s.length()) && (s.charAt(i) == '+'))
+        {
             i++;
         }
 
-        while (i < s.length()) {
+        while (i < s.length())
+        {
             char ch = s.charAt(i);
 
-            if (('0' <= ch) && (ch <= '9')) {
-                if (state == 0) {
+            if (('0' <= ch) && (ch <= '9'))
+            {
+                if (state == 0)
+                {
                     r = ((r * 10) + ch) - '0';
-                } else if (state == 1) {
+                }
+                else if (state == 1)
+                {
                     p = p / 10;
                     r = r + (p * (ch - '0'));
                 }
-            } else if (ch == '.') {
-                if (state == 0) {
+            }
+            else if (ch == '.')
+            {
+                if (state == 0)
+                {
                     state = 1;
-                } else {
+                }
+                else
+                {
                     return sign * r;
                 }
-            } else if ((ch == 'e') || (ch == 'E')) {
+            }
+            else if ((ch == 'e') || (ch == 'E'))
+            {
                 long e = (int) parseLong(s.substring(i + 1), 10);
 
                 return sign * r * Math.pow(10, e);
-            } else {
+            }
+            else
+            {
                 return sign * r;
             }
 
@@ -369,26 +481,33 @@ public class Format {
     * @return the formatted string
     * @exception IllegalArgumentException if bad argument
     */
-    public String form(double x) {
+    public String form(double x)
+    {
         String r;
 
-        if (precision < 0) {
+        if (precision < 0)
+        {
             precision = 6;
         }
 
         int s = 1;
 
-        if (x < 0) {
+        if (x < 0)
+        {
             x = -x;
             s = -1;
         }
 
-        if (fmt == 'f') {
+        if (fmt == 'f')
+        {
             r = fixed_format(x);
-        } else if ((fmt == 'e') || (fmt == 'E') || (fmt == 'g') ||
-                (fmt == 'G')) {
+        }
+        else if ((fmt == 'e') || (fmt == 'E') || (fmt == 'g') || (fmt == 'G'))
+        {
             r = exp_format(x);
-        } else {
+        }
+        else
+        {
             throw new java.lang.IllegalArgumentException();
         }
 
@@ -400,25 +519,38 @@ public class Format {
     * @param x the number to format
     * @return the formatted string
     */
-    public String form(long x) {
+    public String form(long x)
+    {
         String r;
         int s = 0;
 
-        if ((fmt == 'd') || (fmt == 'i')) {
-            if (x < 0) {
+        if ((fmt == 'd') || (fmt == 'i'))
+        {
+            if (x < 0)
+            {
                 r = ("" + x).substring(1);
                 s = -1;
-            } else {
+            }
+            else
+            {
                 r = "" + x;
                 s = 1;
             }
-        } else if (fmt == 'o') {
+        }
+        else if (fmt == 'o')
+        {
             r = convert(x, 3, 7, "01234567");
-        } else if (fmt == 'x') {
+        }
+        else if (fmt == 'x')
+        {
             r = convert(x, 4, 15, "0123456789abcdef");
-        } else if (fmt == 'X') {
+        }
+        else if (fmt == 'X')
+        {
             r = convert(x, 4, 15, "0123456789ABCDEF");
-        } else {
+        }
+        else
+        {
             throw new java.lang.IllegalArgumentException();
         }
 
@@ -430,8 +562,10 @@ public class Format {
     * @param x the value to format
     * @return the formatted string
     */
-    public String form(char c) {
-        if (fmt != 'c') {
+    public String form(char c)
+    {
+        if (fmt != 'c')
+        {
             throw new java.lang.IllegalArgumentException();
         }
 
@@ -445,12 +579,15 @@ public class Format {
     * @param x the value to format
     * @return the formatted string
     */
-    public String form(String s) {
-        if (fmt != 's') {
+    public String form(String s)
+    {
+        if (fmt != 's')
+        {
             throw new java.lang.IllegalArgumentException();
         }
 
-        if (precision >= 0) {
+        if (precision >= 0)
+        {
             s = s.substring(0, precision);
         }
 
@@ -460,7 +597,8 @@ public class Format {
     /**
     * a test stub for the format class
     */
-    public static void main(String[] a) {
+    public static void main(String[] a)
+    {
         double x = 1.23456789012;
         double y = 123;
         double z = 1.2345e30;
@@ -530,8 +668,18 @@ public class Format {
         Format.print(System.out, "|%6.0f|\n", 9.999);
     }
 
-    private static String repeat(char c, int n) {
-        if (n <= 0) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static String repeat(char c, int n)
+    {
+        if (n <= 0)
+        {
             return "";
         }
 
@@ -543,14 +691,27 @@ public class Format {
         return s.toString();
     }
 
-    private static String convert(long x, int n, int m, String d) {
-        if (x == 0) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param x DOCUMENT ME!
+     * @param n DOCUMENT ME!
+     * @param m DOCUMENT ME!
+     * @param d DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static String convert(long x, int n, int m, String d)
+    {
+        if (x == 0)
+        {
             return "0";
         }
 
         String r = "";
 
-        while (x != 0) {
+        while (x != 0)
+        {
             r = d.charAt((int) (x & m)) + r;
             x = x >>> n;
         }
@@ -558,66 +719,113 @@ public class Format {
         return r;
     }
 
-    private String pad(String r) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param r DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String pad(String r)
+    {
         String p = repeat(' ', width - r.length());
 
-        if (left_align) {
+        if (left_align)
+        {
             return pre + r + p + post;
-        } else {
+        }
+        else
+        {
             return pre + p + r + post;
         }
     }
 
-    private String sign(int s, String r) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param r DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String sign(int s, String r)
+    {
         String p = "";
 
-        if (s < 0) {
+        if (s < 0)
+        {
             p = "-";
-        } else if (s > 0) {
-            if (show_plus) {
+        }
+        else if (s > 0)
+        {
+            if (show_plus)
+            {
                 p = "+";
-            } else if (show_space) {
+            }
+            else if (show_space)
+            {
                 p = " ";
             }
-        } else {
+        }
+        else
+        {
             if ((fmt == 'o') && alternate && (r.length() > 0) &&
-                    (r.charAt(0) != '0')) {
+                    (r.charAt(0) != '0'))
+            {
                 p = "0";
-            } else if ((fmt == 'x') && alternate) {
+            }
+            else if ((fmt == 'x') && alternate)
+            {
                 p = "0x";
-            } else if ((fmt == 'X') && alternate) {
+            }
+            else if ((fmt == 'X') && alternate)
+            {
                 p = "0X";
             }
         }
 
         int w = 0;
 
-        if (leading_zeroes) {
+        if (leading_zeroes)
+        {
             w = width;
-        } else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') ||
-                (fmt == 'X') || (fmt == 'o')) && (precision > 0)) {
+        }
+        else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X') ||
+                (fmt == 'o')) && (precision > 0))
+        {
             w = precision;
         }
 
         return p + repeat('0', w - p.length() - r.length()) + r;
     }
 
-    private String fixed_format(double d) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param d DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String fixed_format(double d)
+    {
         boolean removeTrailing = ((fmt == 'G') || (fmt == 'g')) && !alternate;
 
         // remove trailing zeroes and decimal point
-        if (d > 0x7FFFFFFFFFFFFFFFL) {
+        if (d > 0x7FFFFFFFFFFFFFFFL)
+        {
             return exp_format(d);
         }
 
-        if (precision == 0) {
+        if (precision == 0)
+        {
             return (long) (d + 0.5) + (removeTrailing ? "" : ".");
         }
 
         long whole = (long) d;
         double fr = d - whole; // fractional part
 
-        if ((fr >= 1) || (fr < 0)) {
+        if ((fr >= 1) || (fr < 0))
+        {
             return exp_format(d);
         }
 
@@ -625,29 +833,33 @@ public class Format {
         String leading_zeroes = "";
 
         for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL);
-                i++) {
+                i++)
+        {
             factor *= 10;
             leading_zeroes = leading_zeroes + "0";
         }
 
         long l = (long) ((factor * fr) + 0.5);
 
-        if (l >= factor) {
+        if (l >= factor)
+        {
             l = 0;
             whole++;
         }
-         // CSH 10-25-97
 
+        // CSH 10-25-97
         String z = leading_zeroes + l;
         z = "." + z.substring(z.length() - precision, z.length());
 
-        if (removeTrailing) {
+        if (removeTrailing)
+        {
             int t = z.length() - 1;
 
             while ((t >= 0) && (z.charAt(t) == '0'))
                 t--;
 
-            if ((t >= 0) && (z.charAt(t) == '.')) {
+            if ((t >= 0) && (z.charAt(t) == '.'))
+            {
                 t--;
             }
 
@@ -657,45 +869,63 @@ public class Format {
         return whole + z;
     }
 
-    private String exp_format(double d) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param d DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String exp_format(double d)
+    {
         String f = "";
         int e = 0;
         double dd = d;
         double factor = 1;
 
-        if (d != 0) {
-            while (dd > 10) {
+        if (d != 0)
+        {
+            while (dd > 10)
+            {
                 e++;
                 factor /= 10;
                 dd = dd / 10;
             }
 
-            while (dd < 1) {
+            while (dd < 1)
+            {
                 e--;
                 factor *= 10;
                 dd = dd * 10;
             }
         }
 
-        if (((fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision)) {
+        if (((fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision))
+        {
             return fixed_format(d);
         }
 
         d = d * factor;
         f = f + fixed_format(d);
 
-        if ((fmt == 'e') || (fmt == 'g')) {
+        if ((fmt == 'e') || (fmt == 'g'))
+        {
             f = f + "e";
-        } else {
+        }
+        else
+        {
             f = f + "E";
         }
 
         String p = "000";
 
-        if (e >= 0) {
+        if (e >= 0)
+        {
             f = f + "+";
             p = p + e;
-        } else {
+        }
+        else
+        {
             f = f + "-";
             p = p + (-e);
         }
diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 127b419..80734f7 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,105 +1,130 @@
 /*
-* 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
-*/
+ * 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.util;
 
-public class QuickSort {
-    public static void sort(float[] arr, Object[] s) {
-        sort(arr, 0, arr.length - 1, s);
+public class QuickSort
+{
+  public static void sort(float[] arr, Object[] s)
+  {
+    sort(arr, 0, arr.length - 1, s);
+  }
+
+  public static void sort(String[] arr, Object[] s)
+  {
+    stringSort(arr, 0, arr.length - 1, s);
+  }
+
+  public static void stringSort(String[] arr, int p, int r, Object[] s)
+  {
+    int q;
+
+    if (p < r)
+    {
+      q = stringPartition(arr, p, r, s);
+      stringSort(arr, p, q, s);
+      stringSort(arr, q + 1, r, s);
     }
+  }
 
-    public static void sort(String[] arr, Object[] s) {
-        stringSort(arr, 0, arr.length - 1, s);
-    }
-
-    public static void stringSort(String[] arr, int p, int r, Object[] s) {
-        int q;
+  public static void sort(float[] arr, int p, int r, Object[] s)
+  {
+    int q;
 
-        if (p < r) {
-            q = stringPartition(arr, p, r, s);
-            stringSort(arr, p, q, s);
-            stringSort(arr, q + 1, r, s);
-        }
+    if (p < r)
+    {
+      q = partition(arr, p, r, s);
+      sort(arr, p, q, s);
+      sort(arr, q + 1, r, s);
     }
-
-    public static void sort(float[] arr, int p, int r, Object[] s) {
-        int q;
-
-        if (p < r) {
-            q = partition(arr, p, r, s);
-            sort(arr, p, q, s);
-            sort(arr, q + 1, r, s);
-        }
+  }
+
+  private static int partition(float[] arr, int p, int r, Object[] s)
+  {
+    float x = arr[p];
+    int i = p - 1;
+    int j = r + 1;
+
+    while (true)
+    {
+      do
+      {
+        j = j - 1;
+      }
+      while (arr[j] > x);
+
+      do
+      {
+        i = i + 1;
+      }
+      while (arr[i] < x);
+
+      if (i < j)
+      {
+        float tmp = arr[i];
+        arr[i] = arr[j];
+        arr[j] = tmp;
+
+        Object tmp2 = s[i];
+        s[i] = s[j];
+        s[j] = tmp2;
+      }
+      else
+      {
+        return j;
+      }
     }
-
-    private static int partition(float[] arr, int p, int r, Object[] s) {
-        float x = arr[p];
-        int i = p - 1;
-        int j = r + 1;
-
-        while (true) {
-            do {
-                j = j - 1;
-            } while (arr[j] > x);
-
-            do {
-                i = i + 1;
-            } while (arr[i] < x);
-
-            if (i < j) {
-                float tmp = arr[i];
-                arr[i] = arr[j];
-                arr[j] = tmp;
-
-                Object tmp2 = s[i];
-                s[i] = s[j];
-                s[j] = tmp2;
-            } else {
-                return j;
-            }
-        }
-    }
-
-    private static int stringPartition(String[] arr, int p, int r, Object[] s) {
-        String x = arr[p];
-        int i = p - 1;
-        int j = r + 1;
-
-        while (true) {
-            do {
-                j = j - 1;
-            } while (arr[j].compareTo(x) < 0);
-
-            do {
-                i = i + 1;
-            } while (arr[i].compareTo(x) > 0);
-
-            if (i < j) {
-                String tmp = arr[i];
-                arr[i] = arr[j];
-                arr[j] = tmp;
-
-                Object tmp2 = s[i];
-                s[i] = s[j];
-                s[j] = tmp2;
-            } else {
-                return j;
-            }
-        }
+  }
+
+  private static int stringPartition(String[] arr, int p, int r, Object[] s)
+  {
+    String x = arr[p];
+    int i = p - 1;
+    int j = r + 1;
+
+    while (true)
+    {
+      do
+      {
+        j = j - 1;
+      }
+      while (arr[j].compareTo(x) < 0);
+
+      do
+      {
+        i = i + 1;
+      }
+      while (arr[i].compareTo(x) > 0);
+
+      if (i < j)
+      {
+        String tmp = arr[i];
+        arr[i] = arr[j];
+        arr[j] = tmp;
+
+        Object tmp2 = s[i];
+        s[i] = s[j];
+        s[j] = tmp2;
+      }
+      else
+      {
+        return j;
+      }
     }
+  }
 }
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index fefb74c..e6f3899 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -1,396 +1,481 @@
 /*
-* 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
-*/
+ * 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.ws;
 
-import ext.vamsas.*;
+import java.util.*;
 
-import jalview.analysis.AlignSeq;
+import javax.swing.*;
 
+import ext.vamsas.*;
+import jalview.analysis.*;
 import jalview.datamodel.*;
-
 import jalview.gui.*;
 
-import org.apache.axis.client.*;
+public class JPredClient
+    extends WSClient
+{
+  ext.vamsas.JPredWS server;
+  String altitle = "";
+  java.util.Hashtable SequenceInfo = null;
 
-import java.awt.*;
+  public JPredClient(String title, SequenceI[] msf)
+  {
+    wsInfo = setWebService();
 
-import java.util.*;
+    SequenceI seq = msf[0];
+    altitle = "JNet prediction on " + seq.getName() +
+        " using alignment from " + title;
 
-import javax.swing.*;
-
-import javax.xml.namespace.QName;
+    wsInfo.setProgressText("Job details for MSA based prediction (" +
+                           title + ") on sequence :\n>" + seq.getName() + "\n" +
+                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           "\n");
 
+    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
 
-public class JPredClient extends WSClient {
-    ext.vamsas.JPredWS server;
-    String altitle = "";
-    java.util.Hashtable SequenceInfo = null;
+    if (!locateWebService())
+    {
+      return;
+    }
 
-    public JPredClient(String title, SequenceI[] msf) {
-        wsInfo = setWebService();
+    JPredThread jthread = new JPredThread(msf);
+    jthread.start();
+  }
+
+  public JPredClient(String title, SequenceI seq)
+  {
+    wsInfo = setWebService();
+    wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
+                           seq.getName() + "\n" +
+                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           "\n");
+    altitle = "JNet prediction for sequence " + seq.getName() + " from " +
+        title;
+
+    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+
+    if (!locateWebService())
+    {
+      return;
+    }
 
-        SequenceI seq = msf[0];
-        altitle = "JNet prediction on " + seq.getName() +
-            " using alignment from " + title;
+    JPredThread jthread = new JPredThread(seq);
+    jthread.start();
+  }
+
+  private WebserviceInfo setWebService()
+  {
+    WebServiceName = "JNetWS";
+    WebServiceJobTitle = "JNet secondary structure prediction";
+    WebServiceReference =
+        "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +
+        "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
+        "Proteins 40:502-511\".";
+    WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
+
+    WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
+                                               WebServiceReference);
+
+    return wsInfo;
+  }
+
+  private boolean locateWebService()
+  {
+    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
+
+    try
+    {
+      this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
+      ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub
+    }
+    catch (Exception ex)
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Secondary Structure Prediction Service named " +
+                                    WebServiceName + " at " + WsURL +
+                                    " couldn't be located.",
+                                    "Internal Jalview Error",
+                                    JOptionPane.WARNING_MESSAGE);
+      wsInfo.setProgressText("Serious! " + WebServiceName +
+                             " Service location failed\nfor URL :" + WsURL +
+                             "\n" +
+                             ex.getMessage());
+      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+
+      return false;
+    }
 
-        wsInfo.setProgressText("Job details for MSA based prediction (" +
-            title + ") on sequence :\n>" + seq.getName() + "\n" +
-            AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");
+    return true;
+  }
+
+  class JPredThread
+      extends Thread
+  {
+    String OutputHeader;
+    ext.vamsas.JpredResult result;
+    ext.vamsas.Sequence sequence;
+    ext.vamsas.Msfalignment msa;
+    String jobId;
+    boolean jobComplete = false;
+    int allowedServerExceptions = 3; // thread dies if too many exceptions.
+
+    JPredThread(SequenceI seq)
+    {
+      OutputHeader = wsInfo.getProgressText();
+      this.sequence = new ext.vamsas.Sequence();
+      this.sequence.setId(seq.getName());
+      this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));
+    }
 
-        SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+    JPredThread(SequenceI[] msf)
+    {
+      OutputHeader = wsInfo.getProgressText();
+      this.sequence = new ext.vamsas.Sequence();
+      this.sequence.setId(msf[0].getName());
+      this.sequence.setSeq(AlignSeq.extractGaps("-. ",
+                                                msf[0].getSequence()));
+
+      jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();
+      this.msa = new ext.vamsas.Msfalignment();
+      msa.setMsf(mwrite.print(msf));
+    }
 
-        if (!locateWebService()) {
-            return;
+    public void run()
+    {
+      StartJob();
+
+      while (!jobComplete && (allowedServerExceptions > 0))
+      {
+        try
+        {
+          if ( (result = server.getresult(jobId)) == null)
+          {
+            throw (new Exception(
+                "Timed out when communicating with server\nTry again later.\n"));
+          }
+
+          if (result.isRunning())
+          {
+            wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+          }
+          else if (result.isQueued())
+          {
+            wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+          }
+
+          if (result.isFinished())
+          {
+            parseResult();
+            jobComplete = true;
+            jobsRunning--;
+          }
+          else
+          {
+            wsInfo.setProgressText(OutputHeader + "\n" +
+                                   result.getStatus());
+
+            if (! (result.isJobFailed() || result.isServerError()))
+            {
+              try
+              {
+                Thread.sleep(5000);
+              }
+              catch (InterruptedException ex1)
+              {
+              }
+
+              //  System.out.println("I'm alive "+seqid+" "+jobid);
+            }
+            else
+            {
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+            }
+          }
         }
-
-        JPredThread jthread = new JPredThread(msf);
-        jthread.start();
+        catch (Exception ex)
+        {
+          allowedServerExceptions--;
+          wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
+                                    ex.getMessage());
+
+          try
+          {
+            if (allowedServerExceptions > 0)
+            {
+              Thread.sleep(5000);
+            }
+          }
+          catch (InterruptedException ex1)
+          {
+          }
+        }
+      }
+
+      if (! (result.isJobFailed() || result.isServerError()))
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+      }
+      else
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+      }
     }
 
-    public JPredClient(String title, SequenceI seq) {
-        wsInfo = setWebService();
-        wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
-            seq.getName() + "\n" +
-            AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");
-        altitle = "JNet prediction for sequence " + seq.getName() + " from " +
-            title;
-
-        SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
-
-        if (!locateWebService()) {
-            return;
+    void StartJob()
+    {
+      try
+      {
+        if (msa != null)
+        {
+          jobId = server.predictOnMsa(msa);
+        }
+        else
+        {
+          jobId = server.predict(sequence);
         }
 
-        JPredThread jthread = new JPredThread(seq);
-        jthread.start();
+        if (jobId != null)
+        {
+          if (jobId.startsWith("Broken"))
+          {
+            throw new Exception("Submission " + jobId);
+          }
+          else
+          {
+            System.out.println(WsURL + " Job Id '" + jobId + "'");
+          }
+        }
+        else
+        {
+          throw new Exception("Server timed out - try again later\n");
+        }
+      }
+      catch (Exception e)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        allowedServerExceptions = 0;
+        jobComplete = false;
+
+        wsInfo.appendProgressText("Failed to submit the prediction.\n"
+                                  +
+                                  "It is most likely that there is a problem with the server.\n"
+                                  + "Just close the window\n");
+        System.err.println(
+            "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" +
+            e.toString() + "\n");
+
+        // e.printStackTrace(); TODO: JBPNote DEBUG
+      }
     }
 
-    private WebserviceInfo setWebService() {
-        WebServiceName = "JNetWS";
-        WebServiceJobTitle = "JNet secondary structure prediction";
-        WebServiceReference = "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +
-            "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
-            "Proteins 40:502-511\".";
-        WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
-
-        WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
-                WebServiceReference);
-
-        return wsInfo;
+    private void addFloatAnnotations(Alignment al, int[] gapmap,
+                                     Vector values, String Symname,
+                                     String Visname, float min,
+                                     float max, int winLength)
+    {
+      Annotation[] annotations = new Annotation[al.getWidth()];
+
+      for (int j = 0; j < values.size(); j++)
+      {
+        float value = Float.parseFloat(values.get(j).toString());
+        annotations[gapmap[j]] = new Annotation("", value + "", ' ',
+                                                value);
+      }
+
+      al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
+                                               annotations, min, max, winLength));
     }
 
-    private boolean locateWebService() {
-        JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
-
-        try {
-            this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
-            ((JpredSoapBindingStub) this.server).setTimeout(60000); // one minute stub
-        } catch (Exception ex) {
-            JOptionPane.showMessageDialog(Desktop.desktop,
-                "The Secondary Structure Prediction Service named " +
-                WebServiceName + " at " + WsURL + " couldn't be located.",
-                "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
-            wsInfo.setProgressText("Serious! " + WebServiceName +
-                " Service location failed\nfor URL :" + WsURL + "\n" +
-                ex.getMessage());
-            wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
-
-            return false;
+    void parseResult()
+    {
+      // OutputHeader = output.getText();
+      if (result.isFailed())
+      {
+        OutputHeader += "Job failed.\n";
+      }
+
+      if (result.getStatus() != null)
+      {
+        OutputHeader += ("\n" + result.getStatus());
+      }
+
+      if (result.getPredfile() != null)
+      {
+        OutputHeader += ("\n" + result.getPredfile());
+
+        // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
+      }
+
+      if (result.getAligfile() != null)
+      {
+        OutputHeader += ("\n" + result.getAligfile());
+      }
+
+      wsInfo.setProgressText(OutputHeader);
+
+      try
+      {
+        // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
+        jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
+            getPredfile(),
+            "Paste");
+        SequenceI[] preds = prediction.getSeqsAsArray();
+        Alignment al;
+        int FirstSeq; // the position of the query sequence in Alignment al
+        boolean noMsa = true; // set if no MSA has been returned by JPred
+
+        if ( (this.msa != null) && (result.getAligfile() != null))
+        {
+          // we ignore the returned alignment if we only predicted on a single sequence
+          String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),
+              "Paste");
+
+          if (jalview.io.FormatAdapter.formats.contains(format))
+          {
+            al = new Alignment(jalview.io.FormatAdapter.readFile(
+                result.getAligfile(), "Paste", format));
+            noMsa = false;
+            FirstSeq = 0;
+          }
+          else
+          {
+            throw (new Exception(
+                "Unknown format 'format' for file : \n" +
+                result.getAligfile()));
+          }
         }
-
-        return true;
-    }
-
-    class JPredThread extends Thread {
-        String OutputHeader;
-        ext.vamsas.JpredResult result;
-        ext.vamsas.Sequence sequence;
-        ext.vamsas.Msfalignment msa;
-        String jobId;
-        boolean jobComplete = false;
-        int allowedServerExceptions = 3; // thread dies if too many exceptions.
-
-        JPredThread(SequenceI seq) {
-            OutputHeader = wsInfo.getProgressText();
-            this.sequence = new ext.vamsas.Sequence();
-            this.sequence.setId(seq.getName());
-            this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));
+        else
+        {
+          al = new Alignment(preds);
+          FirstSeq = prediction.getQuerySeqPosition();
         }
 
-        JPredThread(SequenceI[] msf) {
-            OutputHeader = wsInfo.getProgressText();
-            this.sequence = new ext.vamsas.Sequence();
-            this.sequence.setId(msf[0].getName());
-            this.sequence.setSeq(AlignSeq.extractGaps("-. ",
-                    msf[0].getSequence()));
+        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+            al.getSequenceAt(FirstSeq), SequenceInfo))
+        {
+          throw (new Exception(
+              "Couldn't recover sequence properties for JNet Query sequence!"));
+        }
 
-            jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();
-            this.msa = new ext.vamsas.Msfalignment();
-            msa.setMsf(mwrite.print(msf));
+        AlignmentAnnotation annot;
+        Annotation[] annotations = null;
+        int i = 0;
+        int width = preds[0].getSequence().length();
+
+        int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
+
+        if (gapmap.length != width)
+        {
+          throw (new Exception(
+              "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +
+              al.getSequenceAt(FirstSeq).getName() + "\n" +
+              al.getSequenceAt(FirstSeq).getSequence() +
+              "\nDiffer from number of prediction sites in \n" +
+              result.getPredfile() + "\n"));
         }
 
-        public void run() {
-            StartJob();
-
-            while (!jobComplete && (allowedServerExceptions > 0)) {
-                try {
-                    if ((result = server.getresult(jobId)) == null) {
-                        throw (new Exception(
-                            "Timed out when communicating with server\nTry again later.\n"));
-                    }
-
-                    if (result.isRunning()) {
-                        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-                    } else if (result.isQueued()) {
-                        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-                    }
-
-                    if (result.isFinished()) {
-                        parseResult();
-                        jobComplete = true;
-                        jobsRunning--;
-                    } else {
-                        wsInfo.setProgressText(OutputHeader + "\n" +
-                            result.getStatus());
-
-                        if (!(result.isJobFailed() || result.isServerError())) {
-                            try {
-                                Thread.sleep(5000);
-                            } catch (InterruptedException ex1) {
-                            }
-
-                            //  System.out.println("I'm alive "+seqid+" "+jobid);
-                        } else {
-                            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-                        }
-                    }
-                } catch (Exception ex) {
-                    allowedServerExceptions--;
-                    wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
-                        ex.getMessage());
-
-                    try {
-                        if (allowedServerExceptions > 0) {
-                            Thread.sleep(5000);
-                        }
-                    } catch (InterruptedException ex1) {
-                    }
-                }
+        // JBPNote Should also rename the query sequence sometime...
+        i = 0;
+
+        while (i < preds.length)
+        {
+          String id = preds[i].getName().toUpperCase();
+
+          if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
+              id.startsWith("JPRED"))
+          {
+            annotations = new Annotation[al.getWidth()];
+
+            if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
+                id.equals("JNETFREQ") || id.equals("JNETHMM") ||
+                id.equals("JNETALIGN") || id.equals("JPRED"))
+            {
+              for (int j = 0; j < width; j++)
+              {
+                annotations[gapmap[j]] = new Annotation("", "",
+                    preds[i].getCharAt(j), 0);
+              }
             }
-
-            if (!(result.isJobFailed() || result.isServerError())) {
-                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-            } else {
-                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+            else if (id.equals("JNETCONF"))
+            {
+              for (int j = 0; j < width; j++)
+              {
+                float value = Float.parseFloat(preds[i].getCharAt(
+                    j) + "");
+                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                    j) + "", "", preds[i].getCharAt(j),
+                    value);
+              }
+            }
+            else
+            {
+              for (int j = 0; j < width; j++)
+              {
+                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                    j) + "", "", ' ', 0);
+              }
             }
-        }
 
-        void StartJob() {
-            try {
-                if (msa != null) {
-                    jobId = server.predictOnMsa(msa);
-                } else {
-                    jobId = server.predict(sequence);
-                }
-
-                if (jobId != null) {
-                    if (jobId.startsWith("Broken")) {
-                        throw new Exception("Submission " + jobId);
-                    } else {
-                        System.out.println(WsURL + " Job Id '" + jobId + "'");
-                    }
-                } else {
-                    throw new Exception("Server timed out - try again later\n");
-                }
-            } catch (Exception e) {
-                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-                allowedServerExceptions = 0;
-                jobComplete = false;
-
-                wsInfo.appendProgressText("Failed to submit the prediction.\n"
-                                          +"It is most likely that there is a problem with the server.\n"
-                                          +"Just close the window\n");
-                System.err.println(
-                    "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" +
-                    e.toString() + "\n");
-
-                // e.printStackTrace(); TODO: JBPNote DEBUG
+            if (id.equals("JNETCONF"))
+            {
+              annot = new AlignmentAnnotation(preds[i].getName(),
+                                              "JNet Output", annotations, 0f,
+                                              10f, 1);
+            }
+            else
+            {
+              annot = new AlignmentAnnotation(preds[i].getName(),
+                                              "JNet Output", annotations);
             }
-        }
 
-        private void addFloatAnnotations(Alignment al, int[] gapmap,
-            Vector values, String Symname, String Visname, float min,
-            float max, int winLength) {
-            Annotation[] annotations = new Annotation[al.getWidth()];
+            al.addAnnotation(annot);
 
-            for (int j = 0; j < values.size(); j++) {
-                float value = Float.parseFloat(values.get(j).toString());
-                annotations[gapmap[j]] = new Annotation("", value + "", ' ',
-                        value);
+            if (noMsa)
+            {
+              al.deleteSequence(preds[i]);
             }
+          }
 
-            al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
-                    annotations, min, max, winLength));
+          i++;
         }
 
-        void parseResult() {
-            // OutputHeader = output.getText();
-            if (result.isFailed()) {
-                OutputHeader += "Job failed.\n";
-            }
-
-            if (result.getStatus() != null) {
-                OutputHeader += ("\n" + result.getStatus());
-            }
+        Hashtable scores = prediction.getScores();
 
-            if (result.getPredfile() != null) {
-                OutputHeader += ("\n" + result.getPredfile());
+        /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
+                              "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
 
-                // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
-            }
+          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
+         "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
 
-            if (result.getAligfile() != null) {
-                OutputHeader += ("\n" + result.getAligfile());
-            }
+          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
+                              "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
+         */
+        AlignFrame af = new AlignFrame(al);
 
-            wsInfo.setProgressText(OutputHeader);
-
-            try {
-                // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
-                jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(),
-                        "Paste");
-                SequenceI[] preds = prediction.getSeqsAsArray();
-                Alignment al;
-                int FirstSeq; // the position of the query sequence in Alignment al
-                boolean noMsa = true; // set if no MSA has been returned by JPred
-
-                if ((this.msa != null) && (result.getAligfile() != null)) {
-                    // we ignore the returned alignment if we only predicted on a single sequence
-                    String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),
-                            "Paste");
-
-                    if (jalview.io.FormatAdapter.formats.contains(format)) {
-                        al = new Alignment(jalview.io.FormatAdapter.readFile(
-                                    result.getAligfile(), "Paste", format));
-                        noMsa = false;
-                        FirstSeq = 0;
-                    } else {
-                        throw (new Exception(
-                            "Unknown format 'format' for file : \n" +
-                            result.getAligfile()));
-                    }
-                } else {
-                    al = new Alignment(preds);
-                    FirstSeq = prediction.getQuerySeqPosition();
-                }
-
-                if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-                            al.getSequenceAt(FirstSeq), SequenceInfo)) {
-                    throw (new Exception(
-                        "Couldn't recover sequence properties for JNet Query sequence!"));
-                }
-
-                AlignmentAnnotation annot;
-                Annotation[] annotations = null;
-                int i = 0;
-                int width = preds[0].getSequence().length();
-
-                int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
-
-                if (gapmap.length != width) {
-                    throw (new Exception(
-                        "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +
-                        al.getSequenceAt(FirstSeq).getName() + "\n" +
-                        al.getSequenceAt(FirstSeq).getSequence() +
-                        "\nDiffer from number of prediction sites in \n" +
-                        result.getPredfile() + "\n"));
-                }
-
-                // JBPNote Should also rename the query sequence sometime...
-                i = 0;
-
-                while (i < preds.length) {
-                    String id = preds[i].getName().toUpperCase();
-
-                    if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
-                            id.startsWith("JPRED")) {
-                        annotations = new Annotation[al.getWidth()];
-
-                        if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
-                                id.equals("JNETFREQ") || id.equals("JNETHMM") ||
-                                id.equals("JNETALIGN") || id.equals("JPRED")) {
-                            for (int j = 0; j < width; j++) {
-                                annotations[gapmap[j]] = new Annotation("", "",
-                                        preds[i].getCharAt(j), 0);
-                            }
-                        } else if (id.equals("JNETCONF")) {
-                            for (int j = 0; j < width; j++) {
-                                float value = Float.parseFloat(preds[i].getCharAt(
-                                            j) + "");
-                                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
-                                            j) + "", "", preds[i].getCharAt(j),
-                                        value);
-                            }
-                        } else {
-                            for (int j = 0; j < width; j++) {
-                                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
-                                            j) + "", "", ' ', 0);
-                            }
-                        }
-
-                        if (id.equals("JNETCONF")) {
-                            annot = new AlignmentAnnotation(preds[i].getName(),
-                                    "JNet Output", annotations, 0f, 10f, 1);
-                        }
-                        else {
-                            annot = new AlignmentAnnotation(preds[i].getName(),
-                                    "JNet Output", annotations);
-                        }
-
-                        al.addAnnotation(annot);
-
-                        if (noMsa) {
-                            al.deleteSequence(preds[i]);
-                        }
-                    }
-
-                    i++;
-                }
-
-                Hashtable scores = prediction.getScores();
-
-                /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
-                                      "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
-
-                  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-                 "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
-
-                  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
-                                      "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
-                 */
-                AlignFrame af = new AlignFrame(al);
-
-                Desktop.addInternalFrame(af, altitle,
-                    AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
-            } catch (Exception ex) {
-                ex.printStackTrace();
-            }
-        }
+        Desktop.addInternalFrame(af, altitle,
+                                 AlignFrame.NEW_WINDOW_WIDTH,
+                                 AlignFrame.NEW_WINDOW_HEIGHT);
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
     }
+  }
 }
diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 94e19e7..0d5c22e 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -26,28 +26,38 @@ import jalview.datamodel.*;
 
 import jalview.gui.*;
 
-import org.apache.axis.client.*;
-
-import vamsas.objects.*;
-
-import java.awt.*;
-
 import java.util.*;
 
 import javax.swing.*;
 
-import javax.xml.namespace.QName;
 
-
-public class MsaWSClient extends WSClient {
-    /**
- * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
  */
+public class MsaWSClient extends WSClient
+{
+    /**
+    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+    */
     ext.vamsas.MuscleWS server;
 
+    /**
+     * Creates a new MsaWSClient object.
+     *
+     * @param MsaWSName DOCUMENT ME!
+     * @param altitle DOCUMENT ME!
+     * @param msa DOCUMENT ME!
+     * @param submitGaps DOCUMENT ME!
+     * @param preserveOrder DOCUMENT ME!
+     */
     public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,
-        boolean submitGaps, boolean preserveOrder) {
-        if (setWebService(MsaWSName) == false) {
+        boolean submitGaps, boolean preserveOrder)
+    {
+        if (setWebService(MsaWSName) == false)
+        {
             JOptionPane.showMessageDialog(Desktop.desktop,
                 "The Multiple Sequence Alignment Service named " + MsaWSName +
                 " is unknown", "Internal Jalview Error",
@@ -59,7 +69,8 @@ public class MsaWSClient extends WSClient {
         wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,
                 WebServiceReference);
 
-        if (!locateWebService()) {
+        if (!locateWebService())
+        {
             return;
         }
 
@@ -73,8 +84,10 @@ public class MsaWSClient extends WSClient {
     }
 
     // JBPNote Nasty object-global state setting methods shouldn't be allowed
-    private boolean setWebService(String MsaWSName) {
-        if (MsaWServices.info.containsKey(MsaWSName)) {
+    private boolean setWebService(String MsaWSName)
+    {
+        if (MsaWServices.info.containsKey(MsaWSName))
+        {
             WebServiceName = MsaWSName;
 
             String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
@@ -83,19 +96,30 @@ public class MsaWSClient extends WSClient {
             WebServiceReference = wsinfo[2];
 
             return true;
-        } else {
+        }
+        else
+        {
             return false;
         }
     }
 
-    private boolean locateWebService() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private boolean locateWebService()
+    {
         // TODO: MuscleWS transmuted to generic MsaWS client
         MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
 
-        try {
+        try
+        {
             this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
             ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             wsInfo.setProgressText("Serious! " + WebServiceName +
                 " Service location failed\nfor URL :" + WsURL + "\n" +
                 ex.getMessage());
@@ -110,7 +134,8 @@ public class MsaWSClient extends WSClient {
         return true;
     }
 
-    protected class MsaWSThread extends Thread implements WSClientI {
+    protected class MsaWSThread extends Thread implements WSClientI
+    {
         String ServiceName = WebServiceName;
         String OutputHeader;
         vamsas.objects.simple.MsaResult result = null;
@@ -124,7 +149,8 @@ public class MsaWSClient extends WSClient {
         boolean jobComplete = false;
 
         MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
-            boolean presorder) {
+            boolean presorder)
+        {
             alTitle = title;
             submitGaps = subgaps;
             preserveOrder = presorder;
@@ -134,7 +160,8 @@ public class MsaWSClient extends WSClient {
 
             vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.Sequence[msa.length];
 
-            for (int i = 0; i < msa.length; i++) {
+            for (int i = 0; i < msa.length; i++)
+            {
                 String newname = jalview.analysis.SeqsetUtils.unique_name(i);
 
                 // uniquify as we go
@@ -152,85 +179,114 @@ public class MsaWSClient extends WSClient {
             this.seqs.setSeqs(seqarray);
         }
 
-        public boolean isCancellable() {
+        public boolean isCancellable()
+        {
             return true;
         }
 
-        public void cancelJob() {
-            if ((jobId != null) && !jobId.equals("") && !jobComplete) {
+        public void cancelJob()
+        {
+            if ((jobId != null) && !jobId.equals("") && !jobComplete)
+            {
                 String cancelledMessage = "";
 
-                try {
+                try
+                {
                     vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
 
-                    if (cancelledJob.getStatus() == 2) {
+                    if (cancelledJob.getStatus() == 2)
+                    {
                         // CANCELLED_JOB
                         cancelledMessage = "Job cancelled.";
                         wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
                         jobComplete = true;
                         jobsRunning--;
                         result = null;
-                    } else if (cancelledJob.getStatus() == 3) {
+                    }
+                    else if (cancelledJob.getStatus() == 3)
+                    {
                         // VALID UNSTOPPABLE JOB
                         cancelledMessage += "Server cannot cancel this job. just close the window.\n";
                     }
 
-                    if (cancelledJob.getJobId() != null) {
+                    if (cancelledJob.getJobId() != null)
+                    {
                         cancelledMessage += ("[" + cancelledJob.getJobId() +
                         "]");
                     }
 
                     cancelledMessage += "\n";
-                } catch (Exception exc) {
+                }
+                catch (Exception exc)
+                {
                     cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" +
                     exc + "\n");
                     exc.printStackTrace();
                 }
 
                 wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");
-            } else {
-                if (!jobComplete) {
+            }
+            else
+            {
+                if (!jobComplete)
+                {
                     wsInfo.setProgressText(OutputHeader +
                         "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
                 }
             }
         }
 
-        public void run() {
+        public void run()
+        {
             StartJob();
 
-            while (!jobComplete && (allowedServerExceptions > 0)) {
-                try {
-                    if ((result = server.getResult(jobId)) == null) {
+            while (!jobComplete && (allowedServerExceptions > 0))
+            {
+                try
+                {
+                    if ((result = server.getResult(jobId)) == null)
+                    {
                         throw (new Exception(
                             "Timed out when communicating with server\nTry again later.\n"));
                     }
 
-                    if (result.isRunning()) {
+                    if (result.isRunning())
+                    {
                         wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-                    } else if (result.isQueued()) {
+                    }
+                    else if (result.isQueued())
+                    {
                         wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
                     }
 
-                    if (result.isFinished()) {
+                    if (result.isFinished())
+                    {
                         parseResult();
                         jobComplete = true;
                         jobsRunning--;
-                    } else {
-                        if (result.getStatus() != null) {
+                    }
+                    else
+                    {
+                        if (result.getStatus() != null)
+                        {
                             wsInfo.setProgressText(OutputHeader + "\n" +
                                 result.getStatus());
                         }
 
-                        if (!(result.isJobFailed() || result.isServerError())) {
+                        if (!(result.isJobFailed() || result.isServerError()))
+                        {
                             Thread.sleep(5000);
 
                             //  System.out.println("I'm alive "+seqid+" "+jobid);
-                        } else {
+                        }
+                        else
+                        {
                             break;
                         }
                     }
-                } catch (Exception ex) {
+                }
+                catch (Exception ex)
+                {
                     allowedServerExceptions--;
                     wsInfo.appendProgressText("\n" + ServiceName +
                         " Server exception!\n" + ex.getMessage());
@@ -238,59 +294,81 @@ public class MsaWSClient extends WSClient {
                         ex.getMessage());
 
                     //          ex.printStackTrace(); JBPNote Debug
-                    try {
-                        if (allowedServerExceptions > 0) {
+                    try
+                    {
+                        if (allowedServerExceptions > 0)
+                        {
                             Thread.sleep(5000);
                         }
-                    } catch (InterruptedException ex1) {
+                    }
+                    catch (InterruptedException ex1)
+                    {
                     }
                 }
             }
 
-            if (allowedServerExceptions == 0) {
+            if (allowedServerExceptions == 0)
+            {
                 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-            } else {
+            }
+            else
+            {
                 if (!((result != null) &&
-                        (result.isJobFailed() || result.isServerError()))) {
+                        (result.isJobFailed() || result.isServerError())))
+                {
                     wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-                } else {
-                    if (result.isFailed()) {
+                }
+                else
+                {
+                    if (result.isFailed())
+                    {
                         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
                     }
 
-                    if (result.isServerError()) {
+                    if (result.isServerError())
+                    {
                         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
                     }
                 }
             }
         }
 
-        void StartJob() {
-            try {
+        void StartJob()
+        {
+            try
+            {
                 vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
 
-                if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {
+                if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
+                {
                     jobId = jobsubmit.getJobId();
                     System.out.println(WsURL + " Job Id '" + jobId + "'");
-                } else {
-                    if (jobsubmit == null) {
+                }
+                else
+                {
+                    if (jobsubmit == null)
+                    {
                         throw new Exception("Server at " + WsURL +
                             " returned null object, it probably cannot be contacted. Try again later ?");
                     }
 
                     throw new Exception(jobsubmit.getJobId());
                 }
-            } catch (Exception e) {
+            }
+            catch (Exception e)
+            {
                 // TODO: JBPNote catch timeout or other fault types explicitly
                 // For unexpected errors
                 System.err.println(WebServiceName +
-                    "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
-                    + "When contacting Server:"+WsURL + "\n" + e.toString() + "\n");
+                    "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" +
+                    "When contacting Server:" + WsURL + "\n" + e.toString() +
+                    "\n");
                 this.allowedServerExceptions = 0;
                 wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
-                wsInfo.appendProgressText("Failed to submit sequences for alignment.\n"
-                    + "It is most likely that there is a problem with the server.\n"
-                    + "Just close the window\n");
+                wsInfo.appendProgressText(
+                    "Failed to submit sequences for alignment.\n" +
+                    "It is most likely that there is a problem with the server.\n" +
+                    "Just close the window\n");
 
                 // e.printStackTrace(); // TODO: JBPNote DEBUG
             }
@@ -298,10 +376,12 @@ public class MsaWSClient extends WSClient {
 
         private void addFloatAnnotations(Alignment al, int[] gapmap,
             Vector values, String Symname, String Visname, float min,
-            float max, int winLength) {
+            float max, int winLength)
+        {
             Annotation[] annotations = new Annotation[al.getWidth()];
 
-            for (int j = 0; j < values.size(); j++) {
+            for (int j = 0; j < values.size(); j++)
+            {
                 float value = Float.parseFloat(values.get(j).toString());
                 annotations[gapmap[j]] = new Annotation("", value + "", ' ',
                         value);
@@ -312,7 +392,8 @@ public class MsaWSClient extends WSClient {
         }
 
         private jalview.datamodel.Sequence[] getVamsasAlignment(
-            vamsas.objects.simple.Alignment valign) {
+            vamsas.objects.simple.Alignment valign)
+        {
             vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
             jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
 
@@ -323,20 +404,25 @@ public class MsaWSClient extends WSClient {
             return msa;
         }
 
-        void parseResult() {
+        void parseResult()
+        {
             SequenceI[] seqs = null;
 
-            try {
+            try
+            {
                 // OutputHeader = output.getText();
-                if (result.isFailed()) {
+                if (result.isFailed())
+                {
                     OutputHeader += "Job failed.\n";
                 }
 
-                if (result.getStatus() != null) {
+                if (result.getStatus() != null)
+                {
                     OutputHeader += ("\n" + result.getStatus());
                 }
 
-                if (result.getMsa() != null) {
+                if (result.getMsa() != null)
+                {
                     OutputHeader += "\nAlignment Object Method Notes\n";
 
                     String[] lines = result.getMsa().getMethod();
@@ -350,10 +436,12 @@ public class MsaWSClient extends WSClient {
 
                 wsInfo.setProgressText(OutputHeader);
 
-                if (seqs != null) {
+                if (seqs != null)
+                {
                     AlignmentOrder msaorder = new AlignmentOrder(seqs);
 
-                    if (preserveOrder) {
+                    if (preserveOrder)
+                    {
                         jalview.analysis.AlignmentSorter.recoverOrder(seqs);
                     }
 
@@ -370,7 +458,9 @@ public class MsaWSClient extends WSClient {
                         AlignFrame.NEW_WINDOW_WIDTH,
                         AlignFrame.NEW_WINDOW_HEIGHT);
                 }
-            } catch (Exception ex) {
+            }
+            catch (Exception ex)
+            {
                 ex.printStackTrace();
             }
         }
diff --git a/src/jalview/ws/MsaWServices.java b/src/jalview/ws/MsaWServices.java
index 84c07a2..75ddf16 100755
--- a/src/jalview/ws/MsaWServices.java
+++ b/src/jalview/ws/MsaWServices.java
@@ -36,25 +36,30 @@ import java.util.Hashtable;
 /**
  * TODO: MsaWServices will be set from properties and be dynamically discovered.
  */
-public class MsaWServices {
+public class MsaWServices
+{
+    /** DOCUMENT ME!! */
     public static Hashtable info;
 
-    static {
+    static
+    {
         info = new Hashtable();
         info.put("ClustalWS",
-            new String[] {
+            new String[]
+            {
                 "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
                 "ClustalW Alignment job",
-
+                
             "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +
                 " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." +
                 " Nucleic Acids Research, 22 4673-4680"
             });
         info.put("MuscleWS",
-            new String[] {
+            new String[]
+            {
                 "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
                 "Muscle Alignment job",
-
+                
             "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " +
                 "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97."
             });
diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java
index 506bd9b..0ffb060 100755
--- a/src/jalview/ws/WSClient.java
+++ b/src/jalview/ws/WSClient.java
@@ -1,40 +1,40 @@
 /*
-* 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.ws;
-
-import jalview.gui.WebserviceInfo;
-
-
-public class WSClient {
-    /**
+ * 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.ws;
 
-* MsaWSClient
-*
-* @param msa SequenceI[]
-*/
-    protected String WebServiceName;
-    protected String WebServiceJobTitle;
-    protected String WebServiceReference;
-    protected String WsURL;
-    protected WebserviceInfo wsInfo;
-    int jobsRunning = 0;
-
-    public WSClient() {
-    }
-}
+import jalview.gui.*;
+
+public class WSClient
+{
+  /**
+   * MsaWSClient
+   *
+   * @param msa SequenceI[]
+   */
+  protected String WebServiceName;
+  protected String WebServiceJobTitle;
+  protected String WebServiceReference;
+  protected String WsURL;
+  protected WebserviceInfo wsInfo;
+  int jobsRunning = 0;
+
+  public WSClient()
+  {
+  }
+}
diff --git a/src/jalview/ws/WSClientI.java b/src/jalview/ws/WSClientI.java
index c2db8c1..97eaa7f 100755
--- a/src/jalview/ws/WSClientI.java
+++ b/src/jalview/ws/WSClientI.java
@@ -1,25 +1,26 @@
 /*
-* 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.ws;
-
-public interface WSClientI {
-    boolean isCancellable();
-
-    void cancelJob();
-}
+ * 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.ws;
+
+public interface WSClientI
+{
+  boolean isCancellable();
+
+  void cancelJob();
+}
-- 
1.7.10.2